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/macromoleculebuilder-3.2+dfsg/include/AddBackboneOxygenForces.h
Examining data/macromoleculebuilder-3.2+dfsg/include/AddNASTForces.h
Examining data/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/BaseInteractionParameterReader.h
Examining data/macromoleculebuilder-3.2+dfsg/include/BasePairContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/BasePairingBonds.h
Examining data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h
Examining data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClassTwoTransformForces.h
Examining data/macromoleculebuilder-3.2+dfsg/include/CalcTransformCorrection.h
Examining data/macromoleculebuilder-3.2+dfsg/include/CenterOfMass.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ConstraintContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ContactContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/DensityContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/DensityForce.h
Examining data/macromoleculebuilder-3.2+dfsg/include/DensityMap.h
Examining data/macromoleculebuilder-3.2+dfsg/include/DisplacementContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ElectrostaticPotentialGridForce.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ErrorManager.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ExportMacros.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ExtraMath.h
Examining data/macromoleculebuilder-3.2+dfsg/include/GeometricCenter.h
Examining data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h
Examining data/macromoleculebuilder-3.2+dfsg/include/KBBackboneTorsionForce.h
Examining data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Ligands.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Ligands.sam.h
Examining data/macromoleculebuilder-3.2+dfsg/include/MobilizerContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/MoleculeContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/MonoAtoms.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Mutation.h
Examining data/macromoleculebuilder-3.2+dfsg/include/NTC_FORCE_CLASS.h
Examining data/macromoleculebuilder-3.2+dfsg/include/NTC_PARAMETER_READER.h
Examining data/macromoleculebuilder-3.2+dfsg/include/NtCBackboneTorsionForce.h
Examining data/macromoleculebuilder-3.2+dfsg/include/NtCForces.h
Examining data/macromoleculebuilder-3.2+dfsg/include/NtCInteractionParameterReader.h
Examining data/macromoleculebuilder-3.2+dfsg/include/NtC_Class_Container.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ParameterReader_wrapper.h
Examining data/macromoleculebuilder-3.2+dfsg/include/PeriodicParameterReaderUpdater.h
Examining data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h
Examining data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h
Examining data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergyWriter.h
Examining data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h
Examining data/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h
Examining data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Repel.h
Examining data/macromoleculebuilder-3.2+dfsg/include/ResidueStretchContainer.h
Examining data/macromoleculebuilder-3.2+dfsg/include/RigidifyFormedHelices.h
Examining data/macromoleculebuilder-3.2+dfsg/include/SetChiMobility.h
Examining data/macromoleculebuilder-3.2+dfsg/include/SetSingleBondMobility.h
Examining data/macromoleculebuilder-3.2+dfsg/include/StackingForceSubsystem.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Sterics.h
Examining data/macromoleculebuilder-3.2+dfsg/include/TetherForce.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Threading.h
Examining data/macromoleculebuilder-3.2+dfsg/include/UnitCellParameters.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Utils.h
Examining data/macromoleculebuilder-3.2+dfsg/include/WadleyKeatingDuartePyleTorsionForce.h
Examining data/macromoleculebuilder-3.2+dfsg/include/Water.h
Examining data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h
Examining data/macromoleculebuilder-3.2+dfsg/include/superimposer.h
Examining data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/AtomSpringContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/BaseInteractionParameterReader.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/CCP4Reader.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/DensityContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/MobilizerContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/NTC_PARAMETER_READER.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/NtCForces.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/NtCInteractionParameterReader.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/RNABuilder.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/TwoTransformForces.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/Utils.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/add.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/loadTorqueTheta.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/main.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/superimposer.cpp
Examining data/macromoleculebuilder-3.2+dfsg/src/test.2.cpp
FINAL RESULTS:
data/macromoleculebuilder-3.2+dfsg/include/AddBackboneOxygenForces.h:44:33: [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.
int addForces (CompoundSystem & system, SimbodyMatterSubsystem & matter , DuMMForceFieldSubsystem & backboneOxygenForces, ParameterReader & myParameterReader, MagnesiumIon myMagnesiumIon )
data/macromoleculebuilder-3.2+dfsg/include/AddBackboneOxygenForces.h:64:33: [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.
int addForces (CompoundSystem & system, SimbodyMatterSubsystem & matter , DuMMForceFieldSubsystem & backboneOxygenForces, ParameterReader & myParameterReader, Biopolymer & myChain ,int firstResidueIndex , int lastResidueIndex )
data/macromoleculebuilder-3.2+dfsg/include/AddNASTForces.h:48:33: [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.
int addForces (CompoundSystem & system, SimbodyMatterSubsystem & matter , DuMMForceFieldSubsystem & nastForces, ParameterReader & myParameterReader, Biopolymer & myChain )
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:131:48: [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.
int initializeBiopolymer(CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:215:65: [4] (shell) system:
This causes a 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 constrainRigidSegmentsToGround(CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state, ConstraintToGroundContainer & myConstraintToGroundContainer, bool toGround, ResidueID rootResidue );
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:217:123: [4] (shell) system:
This causes a 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 multiplySmallGroupInertia( ResidueID residueID, String atomName, double multiplier, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state);
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:218:82: [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.
void multiplySmallGroupInertia( double multiplier, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state) ;
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:278:77: [4] (shell) system:
This causes a 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 constrainRigidSegmentsToGroundForAllChains(CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state, ConstraintToGroundContainer & myConstraintToGroundContainer ) ;
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:435:56: [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.
int initializeBiopolymers(CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:452:64: [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.
int initializeBiopolymer(String chainID, CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:480:58: [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.
void writePdb(State & state, CompoundSystem & system, std::ostream& outputStream, int modelNumber=1, bool calcEnergy=false, int satisfiedBasePairs=0, int unSatisfiedBasePairs=0);
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:511:85: [4] (shell) system:
This causes a 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 multiplySmallGroupInertia(const double multiplier, CompoundSystem & system,SimbodyMatterSubsystem & matter,State & state);
data/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:552:70: [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.
void constrainRigidSegmentsToGroundForAllChains(CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state, ConstraintToGroundContainer & myConstraintToGroundContainer );
data/macromoleculebuilder-3.2+dfsg/include/ConstraintContainer.h:36:111: [4] (shell) system:
This causes a 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 applyConstrainChainRigidSegments (BiopolymerClassContainer & biopolymerClassContainer, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state);
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:43:60: [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.
VelocityRescalingThermostatImpl(const MultibodySystem& system, Real temperature) :
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:44:13: [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(system), temperature(temperature) {
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:44:20: [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(system), temperature(temperature) {
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:53:23: [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/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:64:9: [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::Acceleration);
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h: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.
const MultibodySystem& system;
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:72:81: [4] (shell) system:
This causes a 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::VelocityRescalingThermostat(const MultibodySystem& system, Real temperature, Real rescalingInterval) : PeriodicEventHandler(rescalingInterval) {
data/macromoleculebuilder-3.2+dfsg/include/HarmonicVelocityRescalingThermostat.h:73:48: [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, temperature);
data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h: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.
LigandDroplet(CompoundSystem &system
data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h:88:28: [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.
for (int i =0 ; i< system.getNumCompounds(); i++)
data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h:91:17: [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.
totalAtoms += system.updCompound(Compound::Index(i)).getNAtoms();
data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h:98:21: [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/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h:100:22: [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.
for (int j = 0; j< system.updCompound(Compound::Index(i)).getNAtoms(); j++)
data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h:102:28: [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.
Compound & myCompound = system.updCompound(Compound::Index(i));
data/macromoleculebuilder-3.2+dfsg/include/LigandDroplet.h:152:13: [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(*myWaterVec[myWaterIndex],myTransform);//Vec3(xi*arista-dropletRadius+dropletCenter[0],yi*arista-dropletRadius+dropletCenter[1],zi*arista-dropletRadius+dropletCenter[2]));
data/macromoleculebuilder-3.2+dfsg/include/MonoAtoms.h:32:50: [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.
void initialize(CompoundSystem & system, bool readPreviousFrameFile, String previousFrameFileName, bool matchExact, bool matchIdealized);
data/macromoleculebuilder-3.2+dfsg/include/PeriodicParameterReaderUpdater.h:52:31: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicParameterReaderUpdater.h:56:11: [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), myAllTwoTransformLinearSprings(myAllTwoTransformLinearSprings), interval(interval)
data/macromoleculebuilder-3.2+dfsg/include/PeriodicParameterReaderUpdater.h:56:18: [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), myAllTwoTransformLinearSprings(myAllTwoTransformLinearSprings), interval(interval)
data/macromoleculebuilder-3.2+dfsg/include/PeriodicParameterReaderUpdater.h:92:27: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:52:31: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:62:11: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:62:18: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:73:17: [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.
system.realize(state, Stage::Position);
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h: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.
for (SimTK::Compound::Index c(0); c < system.getNumCompounds(); ++c)
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:78:4: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:91:42: [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.
cout<<"REMARK Energy ="<<system.calcEnergy(state)<<endl;
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:104:27: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:29:31: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:33:11: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:33:18: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:41:9: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:47:55: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h: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.getCompound(c).writePdb(state, outputStream, nextAtomSerialNumber);
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:59:52: [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.
outputStream <<"REMARK Energy = "<<system.calcEnergy(state) <<std::endl;
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:65:27: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:27:31: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:40:27: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:53:31: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:57:11: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:57:18: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:65:9: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:71:55: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:72:4: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:89:27: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h:27:31: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h:37:11: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h:37:18: [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/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.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/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:6:55: [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.
static int RandomizeRNACoordinates (CompoundSystem & system, State & state,SimbodyMatterSubsystem & matter , ParameterReader & myParameterReader, RNA & myChain)
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:14:5: [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/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:15:5: [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::Dynamics);
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:16:23: [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.
float oldEnergy = system.calcPotentialEnergy(state);
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:17:23: [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.
float newEnergy = system.calcPotentialEnergy(state);
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:25:57: [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.
for (SimTK::CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c)
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:26:10: [4] (shell) system:
This causes a new 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, myoutfile ,Transform(Vec3(0)));
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:110:5: [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::Dynamics);
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:111:23: [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.
float newEnergy = system.calcPotentialEnergy(state);
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:129:61: [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/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:130:14: [4] (shell) system:
This causes a new 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,myoutfile ,Transform(Vec3(0)));
data/macromoleculebuilder-3.2+dfsg/include/Repel.h:171:67: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int initializeBiopolymersAndCustomMolecules(CompoundSystem & system);
data/macromoleculebuilder-3.2+dfsg/include/Repel.h:184:55: [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.
void initializeMoleculesAndBonds(CompoundSystem & system, DuMMForceFieldSubsystem & dumm, SimbodyMatterSubsystem & matter);
data/macromoleculebuilder-3.2+dfsg/include/Repel.h:187:50: [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.
void setInterfaceMobilizers(CompoundSystem & system, SimbodyMatterSubsystem & matter, State & state);
data/macromoleculebuilder-3.2+dfsg/include/Repel.h:196:47: [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.
void createMultibodyTree(CompoundSystem & system, State & state);
data/macromoleculebuilder-3.2+dfsg/include/RigidifyFormedHelices.h:88:26: [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.
CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/include/RigidifyFormedHelices.h:137:17: [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 = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/include/RigidifyFormedHelices.h:138:16: [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.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/include/StackingForceSubsystem.h:18:48: [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/macromoleculebuilder-3.2+dfsg/include/StackingForceSubsystem.h:19:39: [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.
Vector_<SpatialVec>& forces = system.updRigidBodyForces(state,
data/macromoleculebuilder-3.2+dfsg/include/StackingForceSubsystem.h:39:48: [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/macromoleculebuilder-3.2+dfsg/include/StackingForceSubsystem.h:56:39: [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.
ExampleSubsystem(MultibodySystem& system) {
data/macromoleculebuilder-3.2+dfsg/include/StackingForceSubsystem.h:58:9: [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.addForceSubsystem(*this);
data/macromoleculebuilder-3.2+dfsg/include/WadleyKeatingDuartePyleTorsionForce.h:130:33: [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.
int addForces (CompoundSystem & system, SimbodyMatterSubsystem & matter , DuMMForceFieldSubsystem & wkdpForces, ParameterReader & myParameterReader, Biopolymer & myChain )
data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:40:42: [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 addWaterMolecules(CompoundSystem & system, DuMMForceFieldSubsystem &dumm, SimbodyMatterSubsystem& matter, BiopolymerClassContainer & myBiopolymerClassContainer);
data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:42:93: [4] (shell) system:
This causes a 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 multiplySmallGroupInertia(double smallGroupInertiaMultiplier, CompoundSystem & system, SimbodyMatterSubsystem& matter, State & state) ;
data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:50:38: [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.
void adopt( CompoundSystem & system, bool readPreviousFrameFile);
data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:61:42: [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 addWaterMolecules(CompoundSystem & system, DuMMForceFieldSubsystem &dumm, SimbodyMatterSubsystem& matter, BiopolymerClassContainer & myBiopolymerClassContainer );
data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:63:93: [4] (shell) system:
This causes a 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 multiplySmallGroupInertia(double smallGroupInertiaMultiplier, CompoundSystem & system, SimbodyMatterSubsystem& matter, State & state) ;
data/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:71:38: [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.
void adopt( CompoundSystem & system, bool readPreviousFrameFile);
data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:94:20: [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/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:95:34: [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/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.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/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:97:47: [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.
HuntCrossleyContact myHuntCrossleyContact(system);
data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:101:36: [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/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:129:5: [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(myMoleculeA);
data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:131:5: [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(myMoleculeB);
data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:132:5: [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/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:134:19: [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/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.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.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:930:61: [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.
int BiopolymerClass::initializeBiopolymer(CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1018:9: [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(myBiopolymer ,Transform(myRotation, (initialDisplacementVec3/1)) );} // used to convert to nm, now using nm directly.
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1020:9: [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(myBiopolymer ,Vec3(biopolymerClassIndex,biopolymerClassIndex,biopolymerClassIndex )*initialSeparation/1); // used to convert to nm, now using nm directly
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1711:71: [4] (shell) system:
This causes a 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 BiopolymerClass::constrainRigidSegmentsToGround(CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state, ConstraintToGroundContainer & myConstraintToGroundContainer , bool toGround = true, ResidueID baseResidue = ResidueID() ) {
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1886:123: [4] (shell) system:
This causes a 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 BiopolymerClass::multiplySmallGroupInertia(ResidueID residueID, String atomName, double multiplier, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state) {
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1891:17: [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 = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1892:17: [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.
system.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1896:85: [4] (shell) system:
This causes a 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 BiopolymerClass::multiplySmallGroupInertia(double multiplier, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state) {
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1902:62: [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.
multiplySmallGroupInertia(i,"CG2",multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1903:62: [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.
multiplySmallGroupInertia(i,"OG1",multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1907:62: [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.
multiplySmallGroupInertia(i,"CG2",multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1908:62: [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.
multiplySmallGroupInertia(i,"CD" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1912:62: [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.
multiplySmallGroupInertia(i,"CD1",multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1913:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"CD2" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1917:62: [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.
multiplySmallGroupInertia(i,"OG" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1922:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"ND2" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1926:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"NE2" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1930:62: [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.
multiplySmallGroupInertia(i,"NZ" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1934:62: [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.
multiplySmallGroupInertia(i,"CD" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1938:62: [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.
multiplySmallGroupInertia(i,"CE" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1941:62: [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.
multiplySmallGroupInertia(i,"CB" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1944:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"NH1" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1945:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"NH2" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1949:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"CG1" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1950:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
multiplySmallGroupInertia(i,"CG2" ,multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2684:71: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int BiopolymerClassContainer::initializeBiopolymers(CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2701:81: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
returnValue = (biopolymerClassMapIterator->second).initializeBiopolymer(system,
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2723:86: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int BiopolymerClassContainer::initializeBiopolymer(String chainID, CompoundSystem & system,
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2736:34: [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.
if (bpc.initializeBiopolymer(system, myProteinCapping, matchExact,
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2978:73: [4] (shell) system:
This causes a 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 BiopolymerClassContainer::writePdb(State & state, CompoundSystem & system, std::ostream& outputStream, int modelNumber, bool calcEnergy, int satisfiedBasePairs, int unSatisfiedBasePairs) // get the latter two from ParameterReader
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:2983:5: [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::Dynamics);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3009:44: [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.
outputStream <<"REMARK Energy = "<<system.calcEnergy(state) <<std::endl;
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3010:58: [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.
outputStream <<"REMARK Angular, Linear Momentum = "<<system.calcSystemRigidBodyMomentum(state)<<endl;
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3765:95: [4] (shell) system:
This causes a 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 BiopolymerClassContainer::multiplySmallGroupInertia( double multiplier, CompoundSystem & system,SimbodyMatterSubsystem & matter,State & state) {
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3768:84: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(biopolymerClassMapIterator->second). multiplySmallGroupInertia(multiplier,system,matter,state);
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3941:20: [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/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3943:36: [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/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3945:34: [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/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3946:34: [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/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3949:34: [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.
myPDBReader.createCompounds( system, chainsPrefix );
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3951:68: [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.
cout<<__FILE__<<":"<<__LINE__<<" system.getNumCompounds() = "<<system.getNumCompounds() <<endl;
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3975:34: [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.
int myNumChainsFromSystem = system.getNumCompounds() / myPdbStructure.getNumModels() ;
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3979:68: [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.
cout<<__FILE__<<":"<<__LINE__<<" system.getNumCompounds() = "<<system.getNumCompounds() <<endl;
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3990:82: [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.
cout<<__FILE__<<":"<<__FUNCTION__<<":"<<__LINE__<<" Processing chain >"<<system.getCompound(c).getPdbChainId()<<"< ."<<endl;
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3991:36: [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.
if (Molecule::isInstanceOf(system.getCompound(c) ))
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:3993:66: [4] (shell) system:
This causes a 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 Molecule & myMolecule = Molecule::downcast(system.getCompound(c));
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:4306:92: [4] (shell) system:
This causes a 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 BiopolymerClassContainer::constrainRigidSegmentsToGroundForAllChains(CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state, ConstraintToGroundContainer & myConstraintToGroundContainer ) {
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:4313:58: [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.
myBiopolymerClass.constrainRigidSegmentsToGround(system, matter,state, myConstraintToGroundContainer );
data/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp:71:139: [4] (shell) system:
This causes a 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 ConstraintToGroundContainer::applyConstrainChainRigidSegments (BiopolymerClassContainer & biopolymerClassContainer, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state){
data/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp:74:125: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
biopolymerClassContainer.updBiopolymerClass(constrainChainRigidSegmentsVector[i].chainID).constrainRigidSegmentsToGround( system, matter, state, *this , constrainChainRigidSegmentsVector[i].toGround, constrainChainRigidSegmentsVector[i].residueID);
data/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:323:46: [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 MonoAtoms::initialize (CompoundSystem & system, bool readPreviousFrameFile, String previousFrameFileName, bool matchExact, bool matchIdealized) {
data/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:331:20: [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.
adoptCompounds(system,readPreviousFrameFile );
data/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:335:55: [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.
void MonoAtomsContainer::initialize (CompoundSystem & system , bool readPreviousFrameFile, String previousFrameFileName, bool matchExact, bool matchIdealized ) {
data/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:343:46: [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.
(*monoAtomsMapIterator).second.initialize(system, readPreviousFrameFile, previousFrameFileName, matchExact, matchIdealized);
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:22:87: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
SimTK::PeriodicPdbAndEnergyWriter::PeriodicPdbAndEnergyWriter( const CompoundSystem& system,
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:30:18: [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/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:30:25: [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.
system(system),
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.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.realize(state, Stage::Dynamics);
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:56:57: [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.
for (SimTK::CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c)
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:57:10: [4] (shell) system:
This causes a new 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,Transform(Vec3(0)));//, nextAtomSerialNumber);
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:62:57: [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.
for (SimTK::CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c)
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:63:10: [4] (shell) system:
This causes a new 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, fbstream,Transform(Vec3(0)));
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:77:36: [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.
double myPotentialEnergy = system.calcPotentialEnergy(state);
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:85:34: [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.
double myKineticEnergy = system.calcKineticEnergy(state);
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:90:27: [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.
double myEnergy = system.calcEnergy(state);
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:96:58: [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.
outputStream <<"REMARK Angular, Linear Momentum = "<<system.calcSystemRigidBodyMomentum(state)<<endl;
data/macromoleculebuilder-3.2+dfsg/src/RNASample.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/macromoleculebuilder-3.2+dfsg/src/RNASample.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/macromoleculebuilder-3.2+dfsg/src/RNASample.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/macromoleculebuilder-3.2+dfsg/src/RNASample.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.adoptCompound(myMagnesiumIonVec[i],Vec3(i,0,0));
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:133:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:134:52: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:147:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.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.
State & state = system.updDefaultState();
data/macromoleculebuilder-3.2+dfsg/src/RNASample.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.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:152:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:159:5: [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();//realizeTopolgy is special. invoke explicitly.
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:160:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.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.realizeTopology();//realizeTopolgy is special. invoke explicitly.
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:170:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:189:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:199:5: [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(); // realizeTopolgy is special. invoke explicitly.
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:200:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:203:99: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:204:5: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:206:38: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:230:85: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PeriodicPdbAndCOMWriter * myPeriodicPdbWriter = new PeriodicPdbAndCOMWriter(system,outputFrame,myReportingInterval,matter,myMolecule,dumm,residueList);
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:231:9: [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.updDefaultSubsystem().addEventReporter(myPeriodicPdbWriter);
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:232:24: [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,study);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:117:244: [4] (shell) system:
This causes a 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 ConstrainedDynamics::constraintsAndRestraints (ParameterReader & myParameterReader,BiopolymerClassContainer & myBiopolymerClassContainer,GeneralForceSubsystem & forces,SimbodyMatterSubsystem & matter, State & state, CompoundSystem & system) {
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:137:119: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
myParameterReader.constraintToGroundContainer.applyConstrainChainRigidSegments ( myBiopolymerClassContainer, system, matter, state);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:306:24: [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.
state = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:307:16: [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.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:344:25: [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.
state = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:345:17: [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.
system.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:380:84: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int ConstrainedDynamics::initializeBiopolymersAndCustomMolecules(CompoundSystem & system){
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:386:62: [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.
_parameterReader->moleculeClassContainer.adoptCompounds (system);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:391:86: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
returnValue = _parameterReader->myBiopolymerClassContainer.initializeBiopolymers(system,
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:441:72: [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.
void ConstrainedDynamics::initializeMoleculesAndBonds(CompoundSystem & system, DuMMForceFieldSubsystem & dumm, SimbodyMatterSubsystem & matter){
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:442:55: [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.
_parameterReader->myMonoAtomsContainer.initialize(system , _parameterReader->readPreviousFrameFile, _parameterReader->previousFrameFileName, _parameterReader->matchExact, _parameterReader->matchIdealized );
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:447:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_parameterReader->waterDropletContainer.addWaterMolecules(system, dumm, matter, _parameterReader->myBiopolymerClassContainer);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:453:52: [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.
_parameterReader->waterDropletContainer.adopt (system,_parameterReader->readPreviousFrameFile);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:482:67: [4] (shell) system:
This causes a 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 ConstrainedDynamics::setInterfaceMobilizers(CompoundSystem & system, SimbodyMatterSubsystem & matter, State & state){
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:490:73: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
cout<<__FILE__<<":"<<__LINE__<<" system.getNumRealizeCalls () = "<< system.getNumRealizeCalls () <<endl;
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:492:13: [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.
state = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:494:5: [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/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:538:64: [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.
void ConstrainedDynamics::createMultibodyTree(CompoundSystem & system, State & state){
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:539:67: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
cout<<__FILE__<<":"<<__LINE__<<" Calling modelOneCompound "<< system.getNumCompounds()<<" times."<<endl;
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:540:50: [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.
for (CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c) {
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:541:38: [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.
String currentChain = String(system.getCompound(c).getPdbChainId());
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:545:13: [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.modelOneCompound(c,tempMobilizerType );
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:549:13: [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.modelOneCompound(c, tempMobilizerType ); // for non-biopolymers, use the default behavior, which is for root atom to be connected with a Free mobilizer.
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:553:13: [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.
state = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:554:5: [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/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1030:20: [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/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1032:35: [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/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1033:34: [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/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1036:45: [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.
initializeBiopolymersAndCustomMolecules(system);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1037:33: [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.
initializeMoleculesAndBonds(system, dumm, matter);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1042:25: [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.
createMultibodyTree(system, state);
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:1043:66: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_parameterReader->myBiopolymerClassContainer.writePdb(state, system, filestream);
data/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:38:9: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (access((directoryPath ).c_str(), R_OK) == 0) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:81:108: [4] (shell) system:
This causes a 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 WaterDropletContainer::multiplySmallGroupInertia(double smallGroupInertiaMultiplier, CompoundSystem & system, SimbodyMatterSubsystem& matter, State & state) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:83:80: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
waterDropletVector[i].multiplySmallGroupInertia(smallGroupInertiaMultiplier, system, matter,state);
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:87:65: [4] (shell) system:
This causes a 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 WaterDropletContainer::addWaterMolecules( CompoundSystem & system, DuMMForceFieldSubsystem &dumm, SimbodyMatterSubsystem& matter, BiopolymerClassContainer & myBiopolymerClassContainer) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:89:45: [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.
waterDropletVector[i].addWaterMolecules( system, dumm, matter, myBiopolymerClassContainer);
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:139:99: [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.
void WaterDroplet::multiplySmallGroupInertia(double smallGroupInertiaMultiplier, CompoundSystem & system, SimbodyMatterSubsystem& matter, State & state) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:147:25: [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.
state = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:148:17: [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.
system.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:245:56: [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.
void WaterDroplet::addWaterMolecules( CompoundSystem & system, DuMMForceFieldSubsystem &dumm, SimbodyMatterSubsystem& matter, BiopolymerClassContainer & myBiopolymerClassContainer) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:281:33: [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.
for (int i =0 ; i< (int)system.getNumCompounds(); i++)
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:284:17: [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.
totalAtoms += system.updCompound(CompoundSystem::CompoundIndex(i)).getNumAtoms();
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:291:26: [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.
for (int i =0 ; i< (int)system.getNumCompounds(); i++)
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:293:25: [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.
for (int j = 0; j< system.updCompound(CompoundSystem::CompoundIndex(i)).getNumAtoms(); j++)
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:294:62: [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.
if (! (myBiopolymerClassContainer.hasChainID(system.updCompound(CompoundSystem::CompoundIndex(i)).getPdbChainId())))
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:297:28: [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.
Compound & myCompound = system.updCompound(CompoundSystem::CompoundIndex(i));
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:379:44: [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.
void WaterDroplet::adopt( CompoundSystem & system, bool readPreviousFrameFile) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:388:13: [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(waterVector[i]); // This should be moved to its own method
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:451:52: [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 WaterDropletContainer::adopt(CompoundSystem & system,bool readPreviousFrameFile) {
data/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:453:37: [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.
waterDropletVector[i].adopt(system,readPreviousFrameFile);
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:13:24: [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/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.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.
SimbodyMatterSubsystem matter(system);
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:15:38: [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/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:17:38: [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/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:43:9: [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(myMolecule,Vec3( 0,0,0));
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:50:9: [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/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:55:26: [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.
State & state = system.updDefaultState();
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:56:17: [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 = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:57:9: [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/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:58:32: [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 study(system,.002);
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:60:24: [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,study);
data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.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/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:97:34: [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/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:98:34: [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/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:99:47: [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.
HuntCrossleyContact myHuntCrossleyContact(system);
data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:103:36: [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/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:131:5: [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(myMoleculeA);
data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:133:5: [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(myMoleculeB);
data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:134:5: [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/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:136:19: [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/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.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.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:9:85: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (strcmp(&fsp[strlen(fsp)-3],".gz")==0 || strcmp(&fsp[strlen(fsp)-2],".Z")==0) { sprintf(s,"zcat %s",fsp);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:10:5: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
in=popen(s,"rb"); pipe=1;
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:12:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s,"bzcat %s",fsp); in=popen(s,"rb"); pipe=1;
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:12:32: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
sprintf(s,"bzcat %s",fsp); in=popen(s,"rb"); pipe=1;
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:40:19: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (mrch->nz==1) sprintf(s,"Read a %s %s %dx%d 2D %s MRC File\n", str2[ord+mord],str3[pipe],nx,ny,str[mrch->mode]);
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:14:24: [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/macromoleculebuilder-3.2+dfsg/src/protein-test.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.
SimbodyMatterSubsystem matter(system);
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:16:38: [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/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:18:38: [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/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:111:9: [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(tempMolecule,Vec3( 0,0,0));
data/macromoleculebuilder-3.2+dfsg/src/protein-test.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.modelCompounds();
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:123:26: [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.
State & state = system.updDefaultState();
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:124:17: [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 = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:125:9: [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/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:126:32: [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 study(system,.002);
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:133:24: [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,study);
data/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:148:9: [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/macromoleculebuilder-3.2+dfsg/src/protein-test.cpp:150:54: [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.
cout <<"REMARK Angular, Linear Momentum = "<<system.calcSystemRigidBodyMomentum(state)<<endl;
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:384:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:516:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:532:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:545:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:558:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:575:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:591:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:604:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:617:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:631:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:644:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:668:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:693:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:721:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:734:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:746:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:759:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:771:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:801:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:821:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:837:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:856:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:870:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:888:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:914:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:938:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:953:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:977:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:991:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1000:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1009:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1037:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1059:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1073:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1102:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1125:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1139:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1151:13: [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(rootMobilizer, bpc.updBiopolymerClass(chainID).getFirstResidueMobilizerType().c_str());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1154:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1169:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1199:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1214:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1245:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1270:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1293:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1308:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1334:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1357:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1371:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1396:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1408:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1420:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1432:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1444:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1456:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1481:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1493:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1520:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1560:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1574:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1588:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1600:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1639:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1653:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1667:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1679:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1721:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1735:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1749:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1761:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1799:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1812:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1826:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1838:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1846:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/python_wrapper.cpp:1854:13: [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(errorString, e.what());
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:14:24: [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/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.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.
SimbodyMatterSubsystem matter(system);
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:16:38: [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/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:18:38: [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/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:44:9: [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(myMolecule,Vec3( 0,0,0));
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:45:9: [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(myMolecule2,Vec3( 0,0,0));
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.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.modelCompounds();
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:57:26: [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.
State & state = system.updDefaultState();
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:60:17: [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 = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.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::Position);
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:62:32: [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 study(system,.002);
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:75:17: [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 = system.realizeTopology();
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.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.realize(state,Stage::Position);
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.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.
TimeStepper ts(system,study);
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:101:9: [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/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:102:62: [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.
cout <<"REMARK Angular, Linear Momentum = "<<system.calcSystemRigidBodyMomentum(state)<<endl;
data/macromoleculebuilder-3.2+dfsg/include/RandomizeRNACoordinates.h:19:5: [3] (random) srand:
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.
srand(time(NULL)*time(NULL));
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:505:9: [3] (random) srand:
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.
srand (time(NULL)); // initialize rand()
data/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:238:21: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
char* myHome = getenv("HOME");
data/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:903:5: [3] (random) srand:
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.
srand((unsigned)time(0));
data/macromoleculebuilder-3.2+dfsg/include/AddBackboneOxygenForces.h:24:12: [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).
fb.open ((myParameterReader.tinkerParameterFileName).c_str(),ios::in);
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:93:17: [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 buffer [70];
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndCOMWriter.h:94:17: [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 (buffer,"ATOM 1 GC GC C 1 %8.3f%8.3f%8.3f",helix2GC[0]*10,helix2GC[1]*10,helix2GC[2]*10);
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergySingleFrameWriter.h:43:16: [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).
outputStream.open( outputFrameFileName);
data/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbSingleFrameWriter.h:67:16: [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).
outputStream.open( outputFrameFileName);
data/macromoleculebuilder-3.2+dfsg/include/Utils.h:166:31: [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).
residueNumber = atoi((inputString ).c_str()) ;
data/macromoleculebuilder-3.2+dfsg/include/Utils.h:181:31: [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).
residueNumber = atoi( ((inputString.substr(0, stringLength-1) ).c_str()));
data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:37:57: [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).
if (key == "-FRN") {firstResidueNumber = atoi(argv[q+1]);}
data/macromoleculebuilder-3.2+dfsg/parameterization/src/generate-base-pair-transform.cpp:38:57: [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 == "-SRN") {secondResidueNumber = atoi(argv[q+1]);}
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:711:49: [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).
ResidueInfo::Index myResidueIndex ( atoi(myAtomName.substr(0,pos).c_str()) );
data/macromoleculebuilder-3.2+dfsg/src/CCP4Reader.cpp:29:11: [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).
pFile = fopen ( "/usr/local/ccp4-6.1.2/examples/data/SSADinsulin.mtz" , "rb" );
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:847:25: [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).
int skipLines = atoi (mystring[0].c_str());
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:853:13: [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).
atoi (mystring[0].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:854:13: [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).
atoi (mystring[1].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:855:13: [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).
atoi (mystring[2].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:856:13: [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).
atoi (mystring[3].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:857:13: [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).
atoi (mystring[4].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:858:13: [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).
atoi (mystring[5].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:859:13: [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).
atoi (mystring[6].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:860:13: [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).
atoi (mystring[7].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:861:13: [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).
atoi (mystring[8].c_str())
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:888:14: [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).
if (atoi ((mystring[0].c_str())) != zIndex) {
data/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:414:3: [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).
atoi(moleculeBuildCommandVector[i][2].c_str()),
data/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:438:28: [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).
DuMM::AtomClassIndex(atoi(moleculeBuildCommandVector[i][2].c_str())), // force field atom class index
data/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:453:28: [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).
DuMM::AtomClassIndex(atoi(moleculeBuildCommandVector[i][4].c_str())), // force field atom class index
data/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:513:44: [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).
DuMM::AtomClassIndex myAtomClassIndex ( atoi(moleculeBuildCommandVector[i][4].c_str())); // force field atom class index
data/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:223:5: [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 temp [ PATH_MAX ];
data/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:479:8: [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).
fb.open ((tinkerParameterFileName).c_str(),ios::in);
data/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:3576:30: [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).
spiralPdbFile = fopen ("spiral.pdb","w");
data/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:59:8: [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).
fb.open("frame.pdb",ios::out);
data/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:61:69: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:62:69: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:63:69: [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/macromoleculebuilder-3.2+dfsg/src/RNASample.cpp:64:69: [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/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:558:13: [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).
_output.open(_parameterReader->outTrajectoryFileName.c_str(), ios_base::app);
data/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:445:36: [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).
baseInteger = (atoi(baseIntegerString.c_str()));
data/macromoleculebuilder-3.2+dfsg/src/coarseNucleicAcidTest.cpp:22:12: [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).
fb.open (("/Users/Sam/svn/RNAToolbox/include/resources/tinker_amber99_sam.prm"),ios::in);
data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:39:57: [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).
if (key == "-FRN") {firstResidueNumber = atoi(argv[q+1]);}
data/macromoleculebuilder-3.2+dfsg/src/generate-base-pair-transform.cpp:40:57: [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 == "-SRN") {secondResidueNumber = atoi(argv[q+1]);}
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:13:12: [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).
} else in=fopen(fsp,"rb"); if (in==NULL) {
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:41:7: [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.
else sprintf(s,"Read a %dx%dx%d 3D MRC File\n",nx,ny,nz);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:50:2: [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(s,"Incomplete data read %d/%d blocks\n",i,ny*nz); error(s,ERR_WARN);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:55:2: [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(s,"Incomplete data read %d/%d blocks\n",i,ny*nz); error(s,ERR_WARN); //printf ("ferror is %d", ferror(in));
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:80:2: [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(s,"Incomplete data read %d/%d blocks\n",i,ny*nz); error(s,ERR_WARN); //printf ("ferror is %d", ferror(in)); //printf ("feof is %d", feof(in));
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:95:2: [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(s,"Incomplete data read %d/%d blocks\n",i,ny*nz); error(s,ERR_WARN);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:104:2: [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(s,"Incomplete data read %d/%d blocks\n",i,ny*nz); error(s,ERR_WARN);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:108:2: [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(s,"Incomplete data read %d/%d blocks\n",i,ny*nz); error(s,ERR_ERROR);
data/macromoleculebuilder-3.2+dfsg/src/simple-benchmark.cpp:20:12: [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).
fb.open ("/Users/Sam/svn/RNAToolbox/include/resources/tinker_amber99_sam.prm",ios::in);
data/macromoleculebuilder-3.2+dfsg/include/UnitCellParameters.h:44:30: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const double getc() const {return c;};
data/macromoleculebuilder-3.2+dfsg/include/UnitCellParameters.h:59:64: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const double getMaxHalfWavelengthZ () {return (getc()*(getNc()-1));};// The longest half-wavelength is the width of the unit cell.
data/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:331:51: [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 ((proteinCapping) && ((sequence.substr((strlen(sequence.c_str())-1),1)).compare("P") == 0 )) {
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:228:245: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tempPosition = Vec3(xIndex * unitCellParameters.geta() + unitCellParameters.geta()*unitCellParameters.getaMin(), yIndex * unitCellParameters.getb() + unitCellParameters.getb()*unitCellParameters.getbMin(),zIndex * unitCellParameters.getc() + unitCellParameters.getc()*unitCellParameters.getcMin());
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:228:273: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tempPosition = Vec3(xIndex * unitCellParameters.geta() + unitCellParameters.geta()*unitCellParameters.getaMin(), yIndex * unitCellParameters.getb() + unitCellParameters.getb()*unitCellParameters.getbMin(),zIndex * unitCellParameters.getc() + unitCellParameters.getc()*unitCellParameters.getcMin());
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:356:143: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
distanceSquared = ySquaredplusXsquared + (zIndex2Corrected-zIndex1)*(zIndex2Corrected-zIndex1)*unitCellParameters.getc()*unitCellParameters.getc(); // add z^2
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:356:169: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
distanceSquared = ySquaredplusXsquared + (zIndex2Corrected-zIndex1)*(zIndex2Corrected-zIndex1)*unitCellParameters.getc()*unitCellParameters.getc(); // add z^2
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:421:79: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2;
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:425:49: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
double maxFrequencyZ = 1/unitCellParameters.getc()/2;
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:452:67: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
* sin(zIndex * unitCellParameters.getc() * myAmpFreqRandPhase.frequencyZ + myAmpFreqRandPhase.phaseZ) ;
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:517:177: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
myAmpFreqPhase.frequencyZ = 2*(double)SimTK::Pi* zIndex /( ((unitCellParameters.getNc()-1)*unitCellParameters.getc()*2) );
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:960:182: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
outFile << 10*unitCellParameters.geta()*(unitCellParameters.getNa() - 1) <<" " << 10*unitCellParameters.getb()*(unitCellParameters.getNb() - 1)<<" " <<10*unitCellParameters.getc()*(unitCellParameters.getNc() - 1) << " " << unitCellParameters.getAlpha() / SimTK::Pi * 180.0 << " " << unitCellParameters.getBeta() / SimTK::Pi * 180.0 << " " << unitCellParameters.getGamma() / SimTK::Pi * 180.0 <<std::endl;
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:1121:162: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
setPositiveZGradient (centralGridPoint,(getDensity(updGridPoint(GridIndices(xIndex, yIndex, zIndex+1))) -getDensity(centralGridPoint))/ unitCellParameters.getc());
data/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:1124:101: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
setPositiveZGradient (centralGridPoint,(0. -getDensity(centralGridPoint)) / unitCellParameters.getc() );
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:9:18: [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).
if (strcmp(&fsp[strlen(fsp)-3],".gz")==0 || strcmp(&fsp[strlen(fsp)-2],".Z")==0) { sprintf(s,"zcat %s",fsp);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:9:58: [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 (strcmp(&fsp[strlen(fsp)-3],".gz")==0 || strcmp(&fsp[strlen(fsp)-2],".Z")==0) { sprintf(s,"zcat %s",fsp);
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:11:20: [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 (strcmp(&fsp[strlen(fsp)-3],".bz")==0 || strcmp(&fsp[strlen(fsp)-4],".bz2")==0) {
data/macromoleculebuilder-3.2+dfsg/src/mrc.cpp:11:60: [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 (strcmp(&fsp[strlen(fsp)-3],".bz")==0 || strcmp(&fsp[strlen(fsp)-4],".bz2")==0) {
ANALYSIS SUMMARY:
Hits = 444
Lines analyzed = 34536 in approximately 2.58 seconds (13406 lines/second)
Physical Source Lines of Code (SLOC) = 23542
Hits@level = [0] 20 [1] 18 [2] 48 [3] 4 [4] 374 [5] 0
Hits@level+ = [0+] 464 [1+] 444 [2+] 426 [3+] 378 [4+] 374 [5+] 0
Hits/KSLOC@level+ = [0+] 19.7095 [1+] 18.8599 [2+] 18.0953 [3+] 16.0564 [4+] 15.8865 [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.