Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/molmodel-3.0~svn842/OpenMMPlugin/OpenMMPlugin.cpp
Examining data/molmodel-3.0~svn842/src/DuMMForceFieldSubsystem.cpp
Examining data/molmodel-3.0~svn842/src/CompoundAtom.h
Examining data/molmodel-3.0~svn842/src/MolecularMechanicsSystem.cpp
Examining data/molmodel-3.0~svn842/src/vmdsock.c
Examining data/molmodel-3.0~svn842/src/ElementRep.h
Examining data/molmodel-3.0~svn842/src/PeriodicVmdReporter.cpp
Examining data/molmodel-3.0~svn842/src/BiotypeRep.h
Examining data/molmodel-3.0~svn842/src/Biotype.cpp
Examining data/molmodel-3.0~svn842/src/CompoundRep.h
Examining data/molmodel-3.0~svn842/src/mol.h
Examining data/molmodel-3.0~svn842/src/mol.cpp
Examining data/molmodel-3.0~svn842/src/OpenMMPlugin.h
Examining data/molmodel-3.0~svn842/src/TinkerAmber99.h
Examining data/molmodel-3.0~svn842/src/CompoundSystem.cpp
Examining data/molmodel-3.0~svn842/src/Element.cpp
Examining data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp
Examining data/molmodel-3.0~svn842/src/RiboseMobilizer.cpp
Examining data/molmodel-3.0~svn842/src/AtomSubsystem.cpp
Examining data/molmodel-3.0~svn842/src/MolecularMechanicsSystemRep.h
Examining data/molmodel-3.0~svn842/src/TinkerAmber99.cpp
Examining data/molmodel-3.0~svn842/src/DuMMForceFieldSubsystemRep.h
Examining data/molmodel-3.0~svn842/src/About.cpp
Examining data/molmodel-3.0~svn842/src/imd.cpp
Examining data/molmodel-3.0~svn842/src/DuMMForceFieldSubsystemRep.cpp
Examining data/molmodel-3.0~svn842/src/PDBReader.cpp
Examining data/molmodel-3.0~svn842/src/Compound.cpp
Examining data/molmodel-3.0~svn842/src/VanderWallSphere.cpp
Examining data/molmodel-3.0~svn842/src/VmdConnection.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/cpuObcInterface.h
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMCommon.h
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMLog.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMCommon.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/CpuObc.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/ImplicitSolventParameters.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMRealType.h
Examining data/molmodel-3.0~svn842/src/gbsa/ObcParameters.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/ObcParameters.h
Examining data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.h
Examining data/molmodel-3.0~svn842/src/gbsa/cpuObcInterface.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMLog.h
Examining data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMWindowLinux.h
Examining data/molmodel-3.0~svn842/src/gbsa/CpuObc.h
Examining data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.h
Examining data/molmodel-3.0~svn842/src/gbsa/ImplicitSolventParameters.h
Examining data/molmodel-3.0~svn842/src/imd.h
Examining data/molmodel-3.0~svn842/src/BondGeometry.cpp
Examining data/molmodel-3.0~svn842/src/vmdsock.h
Examining data/molmodel-3.0~svn842/src/Pdb.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp
Examining data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp
Examining data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp
Examining data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp
Examining data/molmodel-3.0~svn842/MolmodelMainpage.h
Examining data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp
Examining data/molmodel-3.0~svn842/examplesNotReadyYet/ExamplePuckerRibose.cpp
Examining data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp
Examining data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Superpose.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Ions.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Ligands.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/VelocityRescalingThermostat.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/RNA.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/CompoundSystem.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/DNA.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/GrinPointer.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Clonable.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/AtomSubsystem.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/VanDerWaalsForce.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Pdb.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Biotype.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Water.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/VanderWallSphere.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/common.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/NA.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Protein.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/CompoundModeler.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/NoseHooverThermostat.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/PDBReader.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/bondGeometry.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/units.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/VmdConnection.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Compound.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/MolecularMechanicsSystem.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/VoxelHash.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/Element.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicVmdReporter.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/DuMMForceFieldSubsystem.h
Examining data/molmodel-3.0~svn842/include/molmodel/internal/RiboseMobilizer.h
Examining data/molmodel-3.0~svn842/include/SimTKmolmodel.h
Examining data/molmodel-3.0~svn842/include/Molmodel.h
Examining data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp
Examining data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp
Examining data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp
Examining data/molmodel-3.0~svn842/tests/TestGetAtomName.cpp
Examining data/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp
Examining data/molmodel-3.0~svn842/tests/TestPositiveControl.cpp
Examining data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp
Examining data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp
Examining data/molmodel-3.0~svn842/tests/TestSanityDuMM.cpp
Examining data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp
Examining data/molmodel-3.0~svn842/tests/TestBiotypeSelfCode.cpp
Examining data/molmodel-3.0~svn842/tests/TestEthane.cpp
Examining data/molmodel-3.0~svn842/tests/TestShortPdbLines.cpp
Examining data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp
Examining data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp
Examining data/molmodel-3.0~svn842/tests/TestPartitioner.cpp
Examining data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp
Examining data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp
Examining data/molmodel-3.0~svn842/tests/TestProtein.cpp
Examining data/molmodel-3.0~svn842/tests/TestMethanol.cpp
Examining data/molmodel-3.0~svn842/tests/TestTinkerAmber.cpp
Examining data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp
Examining data/molmodel-3.0~svn842/tests/TestProteinDihedrals.cpp
Examining data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp
Examining data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp
Examining data/molmodel-3.0~svn842/tests/TestSerine.cpp
Examining data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp
Examining data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/TestEthaneFromSimbody.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp
Examining data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp
Examining data/molmodel-3.0~svn842/tests/TestBodyIds.cpp
Examining data/molmodel-3.0~svn842/tests/TestAtomTargetLocations.cpp
Examining data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp
Examining data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp
Examining data/molmodel-3.0~svn842/tests/TestBiopolymer.cpp
Examining data/molmodel-3.0~svn842/tests/TestGbsa.cpp
Examining data/molmodel-3.0~svn842/tests/TestRna.cpp
Examining data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp
Examining data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp
FINAL RESULTS:
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1437:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem system;
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1438:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1440:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1503:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(new VTKEventReporter(system, 0.5));
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1503:69: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(new VTKEventReporter(system, 0.5));
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1505:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1506:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1510:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator integ(system);
data/molmodel-3.0~svn842/CoarseDNA/TestCoarseDNA.cpp:1511:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:12:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:13:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:14:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decoration(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:15:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forces(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:39:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:40:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:47:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:48:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:51:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicVmdReporter(system, 0.015, 3000, true));
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:51:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicVmdReporter(system, 0.015, 3000, true));
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:60:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:61:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:64:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:66:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integrator(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp:67:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper timeStepper(system, integrator);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:11:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:12:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:13:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decoration(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:14:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forces(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:39:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:40:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:43:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:44:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:47:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:48:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.015) );
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:50:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:51:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:54:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:57:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integrator(system);
data/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp:59:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper timeStepper(system, integrator);
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:103:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:104:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:105:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:106:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:118:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(propane1, Transform(Vec3(-0.5, 0, 0))
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:122:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(propane2, Vec3( 0.5, 0, 0));
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:125:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:126:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.100) );
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:128:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:130:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:132:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp:133:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:54:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SaySomething(const CompoundSystem& system,
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:57:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system), thermo(thermo) {}
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:57:59: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system), thermo(thermo) {}
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:60:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:61:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Dynamics);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:62:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const Real pe = system.calcPotentialEnergy(state);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:77:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system;
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:85:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ChangeTemperature(const CompoundSystem& system,
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:90:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventHandler(interval), system(system), thermo(thermo),
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:90:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventHandler(interval), system(system), thermo(thermo),
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:97:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:116:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system;
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:126:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:127:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:128:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:129:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:132:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:168:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:171:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:180:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PeriodicPdbWriter* pdbWriter = new PeriodicPdbWriter(system, pdbFile, 0.1);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:181:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(pdbWriter); // System takes ownership
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:185:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:186:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(viz, 0.1) );
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:195:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:196:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
new ChangeTemperature(system, thermo,
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:203:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new MassCenterMotionRemover(system, 10));
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:203:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new MassCenterMotionRemover(system, 10));
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:207:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new SaySomething(system, thermo, 1));
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:207:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new SaySomething(system, thermo, 1));
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:211:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:212:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:217:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:222:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 10);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:224:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:234:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:236:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:246:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(finalState, Stage::Dynamics);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:247:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::cout << "Best PE=" << system.calcPotentialEnergy(finalState) << std::endl;
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:251:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, finalState, 5);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:253:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(finalState, Stage::Dynamics);
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:254:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::cout << "Final PE=" << system.calcPotentialEnergy(finalState) << std::endl;
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:11:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:12:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:13:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:14:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:18:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
pdb.createCompounds(system,"");
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:19:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:21:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:22:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:25:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:26:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.025) );
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:28:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:32:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:33:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
pdb.createState(system, state);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:34:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:38:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp:40:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:12:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:13:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:14:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:15:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:22:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:23:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:25:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:26:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:29:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:30:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.025) );
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:32:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:36:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:37:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:41:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp:43:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:10:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:11:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:12:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:13:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:19:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:32:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:33:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.020) );
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:36:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:39:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:40:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:43:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:44:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:47:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:51:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp:52:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:19:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:20:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:21:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:24:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:33:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:36:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:39:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(system, 0.020));
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:39:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(system, 0.020));
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:43:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:44:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:47:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:50:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:53:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp:54:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:25:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:26:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:27:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system); // for Nose-Hoover
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:28:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:31:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:37:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:45:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(system, 0.020) );
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:45:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(system, 0.020) );
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:49:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, pdbFile, 0.100));
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:49:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, pdbFile, 0.100));
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:52:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:55:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:56:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:59:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:62:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:63:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:11:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:12:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:13:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:16:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:46:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(argonAtom1, Vec3(-0.3, 0, 0));
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:49:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(argonAtom2, Vec3( 0.3, 0, 0));
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:52:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:53:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.50) );
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:55:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:57:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:61:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp:62:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:11:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:12:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:13:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:14:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:50:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(ethane1, Transform(Vec3(-0.5, 0, 0))
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:54:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(ethane2, Vec3( 0.5, 0, 0));
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:57:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:58:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.050) );
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:60:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:62:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:66:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp:67:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:22:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:23:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:24:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:27:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:36:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:39:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:42:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(system, 0.020));
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:42:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new Visualizer::Reporter(system, 0.020));
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:46:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:47:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:50:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:53:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:56:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp:57:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:24:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:25:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:26:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:29:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:38:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:41:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:44:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, std::cout, 0.100));
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:44:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, std::cout, 0.100));
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:48:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:49:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system, 293.15, 0.1));
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:52:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:55:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:58:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp:59:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:14:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system; // molecule-specialized simbody System
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:15:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:16:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:17:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TinkerDuMMForceFieldSubsystem dumm(system); // molecular force field
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:25:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:27:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:28:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
new VTKEventReporter(system, 0.020));
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:30:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:32:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:36:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleLoadRNA.cpp:37:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:16:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MultibodySystem& system,
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:20:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system),
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:20:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system),
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:31:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:41:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MultibodySystem& system;
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:55:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system; // molecule-specialized simbody System
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:56:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:57:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:58:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TinkerDuMMForceFieldSubsystem dumm(system); // molecular force field
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:83:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein1);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:84:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein2, Vec3(0.5, 0.5, 0) );
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:89:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
WritePdbReporter writePdbReporter(system, pdbStream, 0.010);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:92:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(&writePdbReporter);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:94:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventHandler(new VelocityRescalingThermostat(system, 293.15, 0.020));
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:94:82: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventHandler(new VelocityRescalingThermostat(system, 293.15, 0.020));
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:96:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:98:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:100:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State& state = system.updDefaultState();
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:105:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 100.0);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:111:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
integratorPtr = new RungeKuttaMersonIntegrator(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:114:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
integratorPtr = new VerletIntegrator(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:117:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
integratorPtr = new CPodesIntegrator(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:120:61: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
integratorPtr = new ExplicitEulerIntegrator(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:127:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper timeStepper(system, study);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:13:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:14:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:15:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:18:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TinkerDuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:37:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(sodium1, Vec3(-0.3, 0, 0.3));
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:39:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(chloride1, Vec3(0, -0.3, 0));
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:43:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(new VTKEventReporter(system,
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:43:72: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(new VTKEventReporter(system,
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:46:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:48:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:52:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/examplesNotReadyYet/ExampleSodiumChloride.cpp:53:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/include/molmodel/internal/AtomSubsystem.h:140:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
explicit AtomSubsystem(SimTK::MultibodySystem& system);
data/molmodel-3.0~svn842/include/molmodel/internal/Compound.h:1045:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setMultibodySystem(MultibodySystem& system);
data/molmodel-3.0~svn842/include/molmodel/internal/DuMMForceFieldSubsystem.h:1397:62: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
explicit Amber99ForceSubsystem(MolecularMechanicsSystem& system)
data/molmodel-3.0~svn842/include/molmodel/internal/DuMMForceFieldSubsystem.h:1398:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: DuMMForceFieldSubsystem(system)
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:69:70: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
explicit MassCenterMotionRemover(const MolecularMechanicsSystem& system,
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:72:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system), linearMomOnly(false),
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:72:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system), linearMomOnly(false),
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:188:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
{ system.removeSystemRigidBodyMomentum(state, linearMomOnly); }
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:200:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
{ system.moveSystemMassCenter(state, comPos); }
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:215:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
{ return (system.calcSystemMassCenterLocation(state) - comPos).norm(); }
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:223:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/include/molmodel/internal/MassCenterMotionRemover.h:232:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MolecularMechanicsSystem& system;
data/molmodel-3.0~svn842/include/molmodel/internal/PDBReader.h:59:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void createCompounds(CompoundSystem& system, const String & chainsPrefix);
data/molmodel-3.0~svn842/include/molmodel/internal/PDBReader.h:70:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real createState(const CompoundSystem& system, State& state) const;
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:48:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system,
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:52:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system),
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:52:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system),
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:60:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:64:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (SimTK::CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c)
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:65:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getCompound(c).writePdb(state, outputStream, nextAtomSerialNumber);
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicPdbWriter.h:82:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system;
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicVmdReporter.h:47:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system,
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicVmdReporter.h:53:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system),
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicVmdReporter.h:53:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(system),
data/molmodel-3.0~svn842/include/molmodel/internal/PeriodicVmdReporter.h:62:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system;
data/molmodel-3.0~svn842/include/molmodel/internal/Protein.h:1062:60: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
explicit Protein( const Sequence& seq, CompoundSystem& system, Transform transform = Transform() )
data/molmodel-3.0~svn842/include/molmodel/internal/Protein.h:1065:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(*this, transform);
data/molmodel-3.0~svn842/include/molmodel/internal/VelocityRescalingThermostat.h:108:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(const MolecularMechanicsSystem& system,
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:72:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:73:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:74:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TinkerDuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:220:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methanol1, Vec3(-0.5, 2, 0));
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:226:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(*myWaterVec[i],Vec3( 1.0*i/200.0-2.000, 3 *cos(1.0*i/50 *360*Deg2Rad ), 3 *sin(1.0*i/50 *360*Deg2Rad )));
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:231:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myMagnesiumIonVec[i],Vec3(i,0,0));
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:234:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myMolecule);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:241:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (makeWaterDroplet) WaterDroplet myReturnInt(system,dumm,forces);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:244:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:246:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:247:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state,Stage::Position);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:275:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VTKVisualizer display(system, 0.1);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:278:99: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VelocityRescalingThermostat * myVelocityRescalingThermostat = new VelocityRescalingThermostat(system, myTemperature, myReportingInterval);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:280:69: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PeriodicPdbWriter * myPeriodicPdbWriter = new PeriodicPdbWriter(system,output,myReportingInterval);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:282:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventHandler(myVelocityRescalingThermostat);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:283:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultSubsystem().addEventReporter(myPeriodicPdbWriter);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:290:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:302:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:310:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (int i = 0; i< system.getNumCompounds(); i++)
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:313:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updCompound(Compound::Index(i)).writePdb(study.getState(),outputFrame,Vec3(0));
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:322:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system,study);
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:323:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ts.initialize(system.getDefaultState());
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:347:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (int i = 0; i< system.getNumCompounds(); i++)
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:350:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updCompound(Compound::Index(i)).writePdb(currentState,outputFrame,Vec3(0));
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:11:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem& system;
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:37:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Impl(MultibodySystem& system)
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:38:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: system(system)
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:38:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: system(system)
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:87:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MobilizedBody& body = system.getMatterSubsystem().getMobilizedBody(bodyIx);
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:121:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MobilizedBody& body = system.getMatterSubsystem().getMobilizedBody(bodyIx);
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:143:47: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
AtomSubsystem::AtomSubsystem(MultibodySystem& system)
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:145:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
adoptSubsystemGuts( new AtomSubsystem::Impl(system) );
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:146:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptSubsystem(*this);
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:150:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return updRep().system;
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:153:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return getRep().system;
data/molmodel-3.0~svn842/src/AtomSubsystem.cpp:166:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return updRep().system.updMatterSubsystem();
data/molmodel-3.0~svn842/src/Compound.cpp:1543:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void Compound::setMultibodySystem(MultibodySystem& system) {
data/molmodel-3.0~svn842/src/Compound.cpp:1544:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
updImpl().setMultibodySystem(system);
data/molmodel-3.0~svn842/src/CompoundRep.h:124:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setMultibodySystem(MultibodySystem& system)
data/molmodel-3.0~svn842/src/CompoundRep.h:126:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ownerSystem = &system;
data/molmodel-3.0~svn842/src/PDBReader.cpp:257:45: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy ( tp->res_name, term.res_name );
data/molmodel-3.0~svn842/src/PDBReader.cpp:359:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void createCompounds( CompoundSystem& system, const String & chainsPrefix = "" ) {
data/molmodel-3.0~svn842/src/PDBReader.cpp:482:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(compounds[i]);
data/molmodel-3.0~svn842/src/PDBReader.cpp:486:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real createState(const CompoundSystem& system, State& state) const {
data/molmodel-3.0~svn842/src/PDBReader.cpp:548:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return ObservedPointFitter::findBestFit(system, state, bodyList, stationList, targetList, tolerance);
data/molmodel-3.0~svn842/src/PDBReader.cpp:566:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void PDBReader::createCompounds(CompoundSystem& system, const String & chainsPrefix = "" ) {
data/molmodel-3.0~svn842/src/PDBReader.cpp:567:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
impl->createCompounds(system, chainsPrefix);
data/molmodel-3.0~svn842/src/PDBReader.cpp:570:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real PDBReader::createState(const CompoundSystem& system, State& state) const {
data/molmodel-3.0~svn842/src/PDBReader.cpp:571:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return impl->createState(system, state);
data/molmodel-3.0~svn842/src/PeriodicVmdReporter.cpp:52:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/src/PeriodicVmdReporter.cpp:60:61: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (SimTK::CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c)
data/molmodel-3.0~svn842/src/PeriodicVmdReporter.cpp:61:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getCompound(c).writePdb(state, pdbString, nextAtomSerialNumber);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:45:70: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VelocityRescalingThermostatImpl(const MolecularMechanicsSystem& system)
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:46:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: system(system), Tb(NaN), numExcludedDofs(-1)
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:46:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: system(system), Tb(NaN), numExcludedDofs(-1)
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:65:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const Real ke = system.calcKineticEnergy(state);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:71:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:84:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Dynamics); // TODO: shouldn't be needed
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:85:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getMatterSubsystem().multiplyByMInv(state, impulse, du);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:87:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:93:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:99:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MolecularMechanicsSystem& system;
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:108:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(const MolecularMechanicsSystem& system, Real bathTemperature,
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:111:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
impl = new VelocityRescalingThermostatImpl(system);
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:1040:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(void) sprintf( lineBuffer, "%s", line.c_str() );
data/molmodel-3.0~svn842/src/mol.cpp:152:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (name, "%s:%s:%c", model->name, struc->name, chain_id);
data/molmodel-3.0~svn842/src/mol.cpp:155:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (name, "%s:%s:solv:%c", model->name, struc->name, chain_id);
data/molmodel-3.0~svn842/src/mol.cpp:276:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (struct_name, "%s_struct", name);
data/molmodel-3.0~svn842/src/mol.cpp:1066:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (tp->res_name, term->res_name);
data/molmodel-3.0~svn842/src/mol.cpp:1326:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (atom_name, " %s", s);
data/molmodel-3.0~svn842/src/mol.cpp:1552:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (residues[n++], s);
data/molmodel-3.0~svn842/src/mol.cpp:1976:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (name, s);
data/molmodel-3.0~svn842/src/mol.cpp:2177:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy( dest, source );
data/molmodel-3.0~svn842/src/mol.cpp:2219:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (tf, format);
data/molmodel-3.0~svn842/src/mol.cpp:2253:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf (str, tf, ia);
data/molmodel-3.0~svn842/src/mol.cpp:2254:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (msg, "%s%s", msg, str);
data/molmodel-3.0~svn842/src/mol.cpp:2262:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf (str, tf, fa);
data/molmodel-3.0~svn842/src/mol.cpp:2263:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (msg, "%s%s", msg, str);
data/molmodel-3.0~svn842/src/mol.cpp:2271:8: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf (str, tf, fa);
data/molmodel-3.0~svn842/src/mol.cpp:2272:8: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (msg, "%s%s", msg, str);
data/molmodel-3.0~svn842/src/mol.cpp:2280:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf (str, tf, ia);
data/molmodel-3.0~svn842/src/mol.cpp:2281:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (msg, "%s%s", msg, str);
data/molmodel-3.0~svn842/src/mol.cpp:2289:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf (str, tf, sa);
data/molmodel-3.0~svn842/src/mol.cpp:2290:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (msg, "%s%s", msg, str);
data/molmodel-3.0~svn842/tests/TestBodyIds.cpp:15:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestBodyIds.cpp:16:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestBodyIds.cpp:19:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestBodyIds.cpp:37:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(proteins[0]);
data/molmodel-3.0~svn842/tests/TestBodyIds.cpp:38:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound( proteins[1], Vec3(-2, 0, 0) );
data/molmodel-3.0~svn842/tests/TestBodyIds.cpp:42:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:23:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:24:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:25:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Amber99ForceSubsystem amber99(system);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:28:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(compound);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:29:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:30:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:31:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:46:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:47:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:48:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Amber99ForceSubsystem amber99(system);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:54:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(compound, adoptTransform);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:63:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:64:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:65:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:80:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:81:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:82:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Amber99ForceSubsystem amber99(system);
data/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp:88:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(compound, adoptTransform);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:51:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TestSystem() : system(), matter(system), dumm(system)
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:51:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TestSystem() : system(), matter(system), dumm(system)
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:51:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TestSystem() : system(), matter(system), dumm(system)
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:58:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.updDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:58:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.updDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:59:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system.calcPotentialEnergy(system.getDefaultState());
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:59:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system.calcPotentialEnergy(system.getDefaultState());
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:64:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.updDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:64:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.updDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:65:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system.getRigidBodyForces(system.getDefaultState(), Stage::Dynamics)[body];
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:65:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system.getRigidBodyForces(system.getDefaultState(), Stage::Dynamics)[body];
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:68:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& getSystem() const {return system;}
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:69:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem& updSystem() {return system;}
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:78:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:101:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(na, Vec3(distance, 0, 0));
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:102:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(cl);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:103:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:107:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:107:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:206:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(argon1);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:207:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(argon2, Vec3(distance, 0, 0));
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:208:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:212:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:212:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:318:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(o2Molecule);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:319:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:323:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:323:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:423:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:560:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(water);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:561:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:563:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:563:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:637:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:637:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:765:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(h2O2);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:766:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:770:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:770:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:775:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.getDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:775:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.getDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:781:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getDefaultState(),
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:782:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getRigidBodyForces(system.getDefaultState(), Stage::Dynamics),
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:782:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getRigidBodyForces(system.getDefaultState(), Stage::Dynamics),
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:786:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.getDefaultState(),
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:884:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestDuMMForces.cpp:884:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.updDefaultState() = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp:17:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp:18:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp:19:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp:20:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp:27:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myMagnesiumIonVec[i],Vec3(0,0,i));
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:49:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:50:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:51:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:52:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:57:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna);
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:58:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:68:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:71:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system);
data/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp:74:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:41:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:42:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:43:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:44:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:61:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(serine);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:63:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:64:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:66:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:75:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(study.getState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestGbsa.cpp:76:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real energy = system.calcPotentialEnergy(study.getState());
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:42:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:43:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:44:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:175:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myRNA);
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:176:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:177:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:179:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const State& state = system.getDefaultState();
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:180:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp:185:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper myTimeStepper(system,study);
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:46:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:47:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:48:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:58:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(m1, v1);
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:61:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(c1, Vec3(2, 0.00, -3.5));
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:64:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:66:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp:67:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:51:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:52:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:53:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:58:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methane1, Vec3( 0, 0, 0));
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:59:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methane2, Vec3( 0.4, 0, 0));
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:66:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:68:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:71:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system, 0.1);
data/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp:74:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:92:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:93:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:94:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:96:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:97:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
HuntCrossleyContact contact(system);
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:137:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methanol1, Vec3(-0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:138:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methanol2, Vec3( 0, 0, 0));
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:139:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methanol3, Vec3( 0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:141:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:143:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:146:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system, 0.1);
data/molmodel-3.0~svn842/tests/TestMethanol.cpp:150:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:48:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system; // molecule-specialized simbody System
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:49:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:50:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system); // molecular force field
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:56:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(mg1, Vec3(-0.5, 1, 0));
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:58:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:59:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const State& state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:61:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:62:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Vec3 mg1Force = system.getRigidBodyForces(state, Stage::Dynamics)
data/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp:69:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real potentialEnergy = system.calcPotentialEnergy(state) * JouleToCalorie;
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:104:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
nDim(dim), system(), matter(system), forces(system), atoms(system), mass(1.0)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:104:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
nDim(dim), system(), matter(system), forces(system), atoms(system), mass(1.0)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:104:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
nDim(dim), system(), matter(system), forces(system), atoms(system), mass(1.0)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:104:68: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
nDim(dim), system(), matter(system), forces(system), atoms(system), mass(1.0)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:147:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:149:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.2) );
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:153:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(reporter);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:155:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:162:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
INTEGRATOR integ(system);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:164:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:265:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem& updSystem() {return system;}
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:266:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MultibodySystem& getSystem() const {return system;}
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:292:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem system;
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:328:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:340:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:342:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real energy = system.calcKineticEnergy(state);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:365:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(), matter(system), forces(system), atoms(system)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:365:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(), matter(system), forces(system), atoms(system)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:365:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(), matter(system), forces(system), atoms(system)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:365:57: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(), matter(system), forces(system), atoms(system)
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:435:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:445:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:447:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.20) );
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:451:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(reporter);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:453:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:461:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:481:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:499:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
INTEGRATOR integ(system);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:501:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:566:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem& updSystem() {return system;}
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:567:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const MultibodySystem& getSystem() const {return system;}
data/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp:583:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem system;
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:48:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system; // molecule-specialized simbody System
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:49:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:50:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system); // molecular force field
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:69:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(mg1, Vec3(-0.5, 0.6, 0.6));
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:71:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna, Vec3(-0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:75:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, of, 0.020));
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:75:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, of, 0.020));
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:76:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:77:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
new VelocityRescalingThermostat(system, 293.15, 0.050));
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:83:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:87:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:89:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.updDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:89:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(system.updDefaultState(), Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:90:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Vec3 mg1Force = system.getRigidBodyForces(system.updDefaultState(), Stage::Dynamics)
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:90:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Vec3 mg1Force = system.getRigidBodyForces(system.updDefaultState(), Stage::Dynamics)
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:98:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integrator(system);
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:99:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper timeStepper(system, integrator);
data/molmodel-3.0~svn842/tests/TestNucleotide2.cpp:100:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
timeStepper.initialize(system.updDefaultState());
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:87:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:88:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:89:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:103:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(oxygen1);
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:104:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(oxygen2, Vec3(0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:115:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methane, Vec3(0, 0.5, 0));
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:117:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:119:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:121:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:125:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system, 0.1);
data/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp:128:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:58:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:59:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:61:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:62:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:93:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound( protein, Vec3(1.5, 0, 0) );
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:104:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:108:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:111:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system, 0.1);
data/molmodel-3.0~svn842/tests/TestPartitioner.cpp:114:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:45:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:46:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:48:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:76:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(*ethaneI);
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:79:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:81:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp:83:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:49:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestProtein.cpp:50:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:51:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:53:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:69:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myMolecule,Vec3( 0,0,0));
data/molmodel-3.0~svn842/tests/TestProtein.cpp:76:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestProtein.cpp:81:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestProtein.cpp:82:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state,Stage::Position);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:83:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator study(system,.002);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:85:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system,study);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:112:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestProtein.cpp:113:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:114:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:115:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:128:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:130:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestProtein.cpp:132:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestProtein.cpp:135:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:136:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.005) );
data/molmodel-3.0~svn842/tests/TestProtein.cpp:139:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestProtein.cpp:149:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, study);
data/molmodel-3.0~svn842/tests/TestProteinDihedrals.cpp:12:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestProteinDihedrals.cpp:13:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestProteinDihedrals.cpp:14:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:102:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:103:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:104:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:110:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:140:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(ethane1, Transform(Vec3(-0.5, 0, 0)) * Transform(Rotation(0.1, YAxis)) );
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:143:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(ethane2, Vec3( 0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:150:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:151:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
new VelocityRescalingThermostat(system, 5000.0, 0.100));
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:154:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:163:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:165:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:169:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp:170:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/TestRna.cpp:49:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestRna.cpp:50:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestRna.cpp:51:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestRna.cpp:52:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestRna.cpp:58:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(rna);
data/molmodel-3.0~svn842/tests/TestRna.cpp:70:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestRna.cpp:72:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestRna.cpp:75:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system);
data/molmodel-3.0~svn842/tests/TestRna.cpp:78:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:52:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestSerine.cpp:53:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:54:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:55:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:60:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(serine);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:67:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestSerine.cpp:69:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestSerine.cpp:71:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Position);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:75:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:76:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.01) );
data/molmodel-3.0~svn842/tests/TestSerine.cpp:79:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestSerine.cpp:82:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, study);
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:58:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:59:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:60:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:66:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound( molecule );
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:68:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:70:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestSetTorsion.cpp:71:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeModel(state);
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:80:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:81:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:82:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:83:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:156:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:169:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:172:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:175:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system);
data/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp:178:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:96:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
EnergyMonitor(MultibodySystem& system) : PeriodicEventReporter(0.05), system(system), eventCount(0), sumEnergy(0.0), sumEnergySquared(0.0) {
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:96:75: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
EnergyMonitor(MultibodySystem& system) : PeriodicEventReporter(0.05), system(system), eventCount(0), sumEnergy(0.0), sumEnergySquared(0.0) {
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:96:82: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
EnergyMonitor(MultibodySystem& system) : PeriodicEventReporter(0.05), system(system), eventCount(0), sumEnergy(0.0), sumEnergySquared(0.0) {
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:102:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Dynamics);
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:103:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Real energy = system.calcKineticEnergy(state);
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:108:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
MultibodySystem& system;
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:12:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:13:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:14:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:87:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myRNA);
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:88:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds(); // finalize multibody system
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:89:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:90:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system);
data/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp:91:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:53:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:54:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:55:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:72:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(methane, Vec3(-0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:73:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(ethane, Vec3( 0, 0, 0));
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:74:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein, Vec3( 0.5, 0, 0));
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:76:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:78:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:80:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system);
data/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp:84:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:21:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SaySomething(const CompoundSystem& system, const VelocityRescalingThermostat& rescaler, Real reportInterval)
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:22:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system), rescaler(rescaler) {}
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:22:59: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system), rescaler(rescaler) {}
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:25:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:29:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:31:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const Vec3 com = system.calcSystemMassCenterLocation(state);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:40:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:66:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:67:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:68:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:69:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:70:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:86:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(pdb4);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:87:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:97:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
*new MassCenterMotionRemover(system, 10);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:98:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(&remover);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:106:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
*new VelocityRescalingThermostat(system, temp, 0.1, 6);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:107:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(&rescaler);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:112:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:113:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.050) );
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:118:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new SaySomething(system,rescaler,1.));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:118:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new SaySomething(system,rescaler,1.));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:124:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:127:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:129:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:131:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:142:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:153:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:163:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:180:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator integ(system); integ.setAccuracy(1e-1);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:184:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:21:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static void removeSystemMomentum(const CompoundSystem& system, State& state);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:28:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SaySomething(CompoundSystem& system, Real reportInterval)
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:29:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system) {}
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:29:59: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system) {}
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:32:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:36:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:37:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const Real KE = system.calcKineticEnergy(state);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:48:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem& system;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:57:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
KillMomentum(CompoundSystem& system, Real interval)
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:58:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventHandler(interval), system(system) {}
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:58:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventHandler(interval), system(system) {}
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:68:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:70:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:74:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
removeSystemMomentum(system, state);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:75:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:80:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem& system;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:86:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:87:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:88:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:89:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:95:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(pdb);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:96:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:100:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
KillMomentum* killer = new KillMomentum(system, 10); // once per 10 ps
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:101:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(killer);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:103:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(system, temp, 0.1));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:103:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new VelocityRescalingThermostat(system, temp, 0.1));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:106:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:107:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, 0.010) );
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:109:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new SaySomething(system,1.));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:109:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new SaySomething(system,1.));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:114:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, pdbfile, 0.1));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:114:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(new PeriodicPdbWriter(system, pdbfile, 0.1));
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:115:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:118:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:120:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:140:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator integ(system); integ.setAccuracy(1e-2);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:143:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:169:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RemoveSystemMomentum(const CompoundSystem& system, const State& initState) :
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:170:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
OptimizerSystem(6), system(system), state(initState) {
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:170:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
OptimizerSystem(6), system(system), state(initState) {
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:173:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:176:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:183:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const CompoundSystem& system;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:188:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static void removeSystemMomentum(const CompoundSystem& system, State& state) {
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:189:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RemoveSystemMomentum objective(system,state);
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:194:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:203:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:51:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:52:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:53:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:54:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem artwork(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:59:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(serine);
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:66:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:68:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:71:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp:74:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:17:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
NoiseMaker(CompoundSystem& system, const Compound& compound, const Force::Thermostat& thermo,
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:19:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system), compound(compound),
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:19:57: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventReporter(reportInterval), system(system), compound(compound),
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:26:42: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const SimbodyMatterSubsystem& matter = system.getMatterSubsystem();
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:29:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Dynamics);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:32:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const Real Es = system.calcEnergy(state);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:57:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem& system;
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:67:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ChangeTemperature(CompoundSystem& system,
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:70:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventHandler(reportInterval), system(system), thermostat(nht)
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:70:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
: PeriodicEventHandler(reportInterval), system(system), thermostat(nht)
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:78:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:88:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem& system;
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:96:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:98:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:99:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem decorations(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:103:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem forceField(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:106:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:113:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new ChangeTemperature(system, thermostat, 20));
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:113:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventHandler(new ChangeTemperature(system, thermostat, 20));
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:141:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(protein);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:144:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:146:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter(
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:147:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
new NoiseMaker(system, protein, thermostat, pdbOut, .05));
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:150:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer viz(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:151:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.addEventReporter( new Visualizer::Reporter(viz, /*0.020*/.5) );
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:165:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeTopology();
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:166:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.getDefaultState();
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:173:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realizeModel(state);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:177:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:181:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state, Stage::Velocity);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:209:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator integ(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp:212:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system, integ);
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:51:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:52:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:53:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:54:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DecorationSubsystem artwork(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:68:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound( sodium1, Vec3(-0.3, 0, 0) );
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:69:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound( sodium2, Vec3( 0.3, 0, 0) );
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:70:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:72:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:75:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Visualizer display(system);
data/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp:78:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
RungeKuttaMersonIntegrator study(system);
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:12:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CompoundSystem system;
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:13:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimbodyMatterSubsystem matter(system);
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:14:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GeneralForceSubsystem forces(system);
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:16:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DuMMForceFieldSubsystem dumm(system);
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:56:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.adoptCompound(myMolecule,Vec3( 0,0,0));
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:63:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.modelCompounds();
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:68:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
State state = system.realizeTopology();
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:69:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system.realize(state,Stage::Position);
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:70:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
VerletIntegrator study(system,.002);
data/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp:72:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeStepper ts(system,study);
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:78:29: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Random::Uniform random;
data/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp:80:30: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
impulse[i] = random.getValue();
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:121:21: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Random::Uniform random(-10.0, 10.0);
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:123:18: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Vec3 pos(random.getValue(), random.getValue(), random.getValue());
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:123:37: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Vec3 pos(random.getValue(), random.getValue(), random.getValue());
data/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp:123:56: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Vec3 pos(random.getValue(), random.getValue(), random.getValue());
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:124:25: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Random::Uniform random;
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:126:28: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
state.updU() = random.getValue();
data/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp:179:36: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
std::ofstream pdbFile; pdbFile.open("polyalanine.pdb");
data/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp:48:36: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
std::ofstream pdbFile; pdbFile.open(PdbFileName);
data/molmodel-3.0~svn842/include/molmodel/internal/AtomSubsystem.h:56:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char atomType[5];
data/molmodel-3.0~svn842/include/molmodel/internal/AtomSubsystem.h:57:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char residueType[5];
data/molmodel-3.0~svn842/include/molmodel/internal/Pdb.h:149:15: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char residueName[4],
data/molmodel-3.0~svn842/include/molmodel/internal/Pdb.h:275:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char residueName[4];
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:107:67: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (key == "-MT") {myUseMultithreadedComputation=atoi(argv[q+1]);}
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:108:67: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (key == "-ND") {numDivalents =atoi(argv[q+1]);}
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:109:67: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (key == "-NW") {numWater =atoi(argv[q+1]);}
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:110:67: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (key == "-WD") {makeWaterDroplet =atoi(argv[q+1]);}
data/molmodel-3.0~svn842/rna-dynamics/conf-explorer.2008.07.23.cpp:169:19: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
qvectorstream.open(qvectorfilename);
data/molmodel-3.0~svn842/src/DuMMForceFieldSubsystemRep.h:1263:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[100];
data/molmodel-3.0~svn842/src/DuMMForceFieldSubsystemRep.h:1264:14: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
std::sprintf(buf, "DuMMBody %d", bnum);
data/molmodel-3.0~svn842/src/PDBReader.cpp:145:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy ( hlist+num, &helix, sizeof(MolHelix) );
data/molmodel-3.0~svn842/src/PDBReader.cpp:198:25: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy ( list+num, &sheet, sizeof(MolSheet) );
data/molmodel-3.0~svn842/src/PDBReader.cpp:512:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char resName[32];
data/molmodel-3.0~svn842/src/PDBReader.cpp:513:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(resName, "%d", res);
data/molmodel-3.0~svn842/src/Pdb.cpp:121:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char residueName[4],
data/molmodel-3.0~svn842/src/Pdb.cpp:1000:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char lineBuffer[300];
data/molmodel-3.0~svn842/src/PeriodicVmdReporter.cpp:65:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char lineBuffer[102];
data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp:863:33: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
implicitSolventResultsFile = fopen( resultsFileName.c_str(), "w" );
data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp:1014:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[bufferSize];
data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp:1024:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
infoFile = fopen( infoFileName.c_str(), "r" );
data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp:1032:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
infoFile = fopen( _defaultInfoFileName.c_str(), "r" );
data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp:1098:40: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
setOutputFileFrequency( atoi( value.c_str() ) );
data/molmodel-3.0~svn842/src/gbsa/CpuObc.cpp:816:33: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
implicitSolventResultsFile = fopen( resultsFileName.c_str(), "w" );
data/molmodel-3.0~svn842/src/gbsa/CpuObc.cpp:1029:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* logFile = fopen( "bF", "w" );
data/molmodel-3.0~svn842/src/gbsa/CpuObc.cpp:1373:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy( bornRadii, bornRadiiTemp, arraySzInBytes );
data/molmodel-3.0~svn842/src/gbsa/CpuObc.cpp:1374:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy( obcChain, obcChainTemp, arraySzInBytes );
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:322:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debugFile = fopen( debugFileName, "w" );
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:932:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char buffer[2048];
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:943:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen( fileName.c_str(), "r" );
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:1153:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen( fileName.c_str(), "w" );
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMWindowLinux.h:32:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN fopen
data/molmodel-3.0~svn842/src/imd.cpp:69:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *)&net,(void *)&n, sizeof(n));
data/molmodel-3.0~svn842/src/imd.cpp:166:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf+HEADERSIZE, indices, 4*n);
data/molmodel-3.0~svn842/src/imd.cpp:167:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf+HEADERSIZE+4*n, forces, 12*n);
data/molmodel-3.0~svn842/src/imd.cpp:178:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf+HEADERSIZE, energies, sizeof(IMDEnergies));
data/molmodel-3.0~svn842/src/imd.cpp:189:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf+HEADERSIZE, coords, 12*n);
data/molmodel-3.0~svn842/src/mol.cpp:142:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[80];
data/molmodel-3.0~svn842/src/mol.cpp:265:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char struct_name[500];
data/molmodel-3.0~svn842/src/mol.cpp:352:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tstr[4];
data/molmodel-3.0~svn842/src/mol.cpp:613:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chain_id, chain_ids[100];
data/molmodel-3.0~svn842/src/mol.cpp:922:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (hlist+num, helix, sizeof(MolHelix));
data/molmodel-3.0~svn842/src/mol.cpp:1016:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (list+num, sheet, sizeof(MolSheet));
data/molmodel-3.0~svn842/src/mol.cpp:1129:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1000];
data/molmodel-3.0~svn842/src/mol.cpp:1143:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen (file_name, "r");
data/molmodel-3.0~svn842/src/mol.cpp:1283:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1000];
data/molmodel-3.0~svn842/src/mol.cpp:1293:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *s, c, res_name[10], atom_name[10];
data/molmodel-3.0~svn842/src/mol.cpp:1308:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
num_atoms = atoi (line);
data/molmodel-3.0~svn842/src/mol.cpp:1482:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[80];
data/molmodel-3.0~svn842/src/mol.cpp:1531:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *s, str[80];
data/molmodel-3.0~svn842/src/mol.cpp:1583:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[80];
data/molmodel-3.0~svn842/src/mol.cpp:1658:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[80];
data/molmodel-3.0~svn842/src/mol.cpp:1708:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[80], aa_name[4];
data/molmodel-3.0~svn842/src/mol.cpp:1801:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
conn[n++] = atoi (s) - 1;
data/molmodel-3.0~svn842/src/mol.cpp:1821:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[80];
data/molmodel-3.0~svn842/src/mol.cpp:1828:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
*val = atoi (str);
data/molmodel-3.0~svn842/src/mol.cpp:1895:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[80];
data/molmodel-3.0~svn842/src/mol.cpp:1919:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1000];
data/molmodel-3.0~svn842/src/mol.cpp:1927:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen (file_name, "r");
data/molmodel-3.0~svn842/src/mol.cpp:1958:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *s, line[1000];
data/molmodel-3.0~svn842/src/mol.cpp:1960:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1000];
data/molmodel-3.0~svn842/src/mol.cpp:2206:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char des[3], msg[1000], gui_msg[1000], str[1000], tf[1000];
data/molmodel-3.0~svn842/src/mol.h:157:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char *mol_res_names[MOL_RESIDUE_MAX_NUM+1][3] = {
data/molmodel-3.0~svn842/src/mol.h:324:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
typedef char (MolResName)[4];
data/molmodel-3.0~svn842/src/mol.h:364:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char patterns[30][80];
data/molmodel-3.0~svn842/src/mol.h:370:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char id[3];
data/molmodel-3.0~svn842/src/mol.h:371:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char init_res_name[3];
data/molmodel-3.0~svn842/src/mol.h:374:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char term_res_name[3];
data/molmodel-3.0~svn842/src/mol.h:383:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char id[3];
data/molmodel-3.0~svn842/src/mol.h:385:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char init_res_name[3];
data/molmodel-3.0~svn842/src/mol.h:389:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char term_res_name[3];
data/molmodel-3.0~svn842/src/vmdsock.c:80:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char address[1030];
data/molmodel-3.0~svn842/src/vmdsock.c:95:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(address, "%d.%d.%d.%d",
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp:122:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pdbfile.open("c:/temp/output.pdb");
data/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:113:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pdbfile.open("c:/temp/output.pdb");
data/molmodel-3.0~svn842/src/About.cpp:124:14: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(value,v,maxlen-1);
data/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp:1060:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t bufferLen = strlen( buffer );
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:273:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for( int ii = (int) strlen( string ); ii < tab; ii++ ){
data/molmodel-3.0~svn842/src/gbsa/SimTKOpenMMUtilities.cpp:970:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
bufferLen = (int) strlen( buffer );
data/molmodel-3.0~svn842/src/mol.cpp:370:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(tstr) == 1) {
data/molmodel-3.0~svn842/src/mol.cpp:397:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(s) == 3) {
data/molmodel-3.0~svn842/src/mol.cpp:1219:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen (pdb_table[i].name);
data/molmodel-3.0~svn842/src/mol.cpp:1328:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (j = strlen(atom_name); j < 4; j++) {
data/molmodel-3.0~svn842/src/mol.cpp:1344:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (j = 0; j < strlen(atom_name); j++) {
data/molmodel-3.0~svn842/src/mol.cpp:1416:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i = 0, n = 0; i < strlen(s); i++) {
data/molmodel-3.0~svn842/src/mol.cpp:1848:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i = 0; i < strlen(line); ++i) {
data/molmodel-3.0~svn842/src/mol.cpp:2174:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int length = strlen( source );
data/molmodel-3.0~svn842/src/vmdsock.c:165:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return read(s->sd, buf, len);
data/molmodel-3.0~svn842/tests/adhoc/TestEthaneFromSimbody.cpp:860:9: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
getchar();
ANALYSIS SUMMARY:
Hits = 934
Lines analyzed = 66266 in approximately 1.92 seconds (34539 lines/second)
Physical Source Lines of Code (SLOC) = 40784
Hits@level = [0] 149 [1] 14 [2] 77 [3] 8 [4] 835 [5] 0
Hits@level+ = [0+] 1083 [1+] 934 [2+] 920 [3+] 843 [4+] 835 [5+] 0
Hits/KSLOC@level+ = [0+] 26.5545 [1+] 22.9011 [2+] 22.5579 [3+] 20.6699 [4+] 20.4737 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.