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/schroedinger-coordgenlibs-1.4.2/CoordgenConfig.hpp
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenFragmentBuilder.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenFragmentBuilder.h
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenFragmenter.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenFragmenter.h
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenMacrocycleBuilder.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenMacrocycleBuilder.h
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenMinimizer.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenMinimizer.h
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenTemplates.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/CoordgenTemplates.h
Examining data/schroedinger-coordgenlibs-1.4.2/example_dir/example.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMaeReading.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizer.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizer.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerAtom.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerAtom.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerBendInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerBond.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerBond.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerClashInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerConstraintInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerEZConstrainInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerFragment.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerFragment.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerMarchingSquares.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerMarchingSquares.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerMaths.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerMolecule.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerMolecule.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerResidue.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerResidue.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerResidueInteraction.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerResidueInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerRing.cpp
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerRing.h
Examining data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizerStretchInteraction.h
Examining data/schroedinger-coordgenlibs-1.4.2/test/test_coordgen.cpp

FINAL RESULTS:

data/schroedinger-coordgenlibs-1.4.2/sketcherMinimizer.cpp:3527:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    auto pFile = fopen(filename.c_str(), "r");

ANALYSIS SUMMARY:

Hits = 1
Lines analyzed = 20479 in approximately 0.54 seconds (37827 lines/second)
Physical Source Lines of Code (SLOC) = 17218
Hits@level = [0]   0 [1]   0 [2]   1 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   1 [1+]   1 [2+]   1 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 0.0580788 [1+] 0.0580788 [2+] 0.0580788 [3+]   0 [4+]   0 [5+]   0
Dot directories skipped = 2 (--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.