GreenPolyProducts/openbabel
5
0 Fork 0
mirror of https://github.com/openbabel/openbabel.git synced 2026-11-01 08:28:03 -06:00
Code Issues Packages Projects Releases Wiki Activity
Files
master
openbabel/test
T
History
Geoff Hutchison 492707e172 Fix BGF overflow reported by @rphang 
Potential heap-buffer-overflow at bgfformat.cpp:172
CONECT 3 in a 2-atom file previously accepted
Now checks against NumAtoms() since it's unsigned

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
2026-08-18 15:02:36 -04:00
..
cdjson
Update ChemDoodle JSON format for rapidjson
2018-02-11 15:03:57 +00:00
cmltest
Remove executable bit from the text files
2014-02-24 23:39:54 +02:00
files
Fix BGF overflow reported by @rphang
2026-08-18 15:02:36 -04:00
fuzz
Bounds check number of bonds before writing
2026-05-26 07:48:06 -04:00
inchi
Add .gitattributes and renormalize EOL
2022-06-10 17:24:09 +09:00
pcjson
Update PubChem JSON format for rapidjson
2018-02-11 15:04:15 +00:00
pdb_ligands_sdf
Fix some broken structures
2019-07-23 21:39:50 -04:00
rinchi
Update docstring, and add tests for rxn->rinchi
2017-10-19 07:19:12 +01:00
testgauss
G09test (#2385)
2022-06-09 18:50:33 -04:00
addhtest.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
aliastest.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
aligntest.cpp
Everything else
2019-04-04 20:20:04 +01:00
aromatest.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
aromatic.pl
Moved aromatest to aromatic (makes for better summmary output from "make check")
2006-05-11 17:42:50 +00:00
atom.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
automorphismtest.cpp
Initial changes
2013-05-13 21:47:31 +01:00
bond.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
buildertest.cpp
Add an implementation of Dale codes for larger macrocycles
2026-05-17 08:35:49 -04:00
canonconsistenttest.cpp
Canonconsistent and canonstable tests updated to new framework.
2013-05-27 21:13:00 +01:00
canonfragmenttest.cpp
style: comment out unused parameters
2026-05-08 14:52:25 +09:00
canonstabletest.cpp
Merge branch 'master' of github.com:openbabel/openbabel into maybe_unused
2026-05-19 14:06:59 -04:00
cansmi.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
cansmiles_shuffle.sh
Change references to babel to obabel
2019-09-10 16:06:48 +01:00
carspacegrouptest.cpp
Everything else
2019-04-04 20:20:04 +01:00
charge_gasteiger.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
charge_mmff94.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
cifspacegrouptest.cpp
Fix unit tests (#2876)
2026-05-08 22:45:46 -04:00
cistranstest.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
CMakeLists.txt
Fix BGF overflow reported by @rphang
2026-08-18 15:02:36 -04:00
cml.sh
* test/cml.sh: Use /bin/bash to run, not /bin/sh as "source" is a
2008-01-04 17:58:39 +00:00
cmlreadfile.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
conversion.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
conversiontest.cpp
add mol to cdxml test
2018-05-24 13:39:35 +08:00
datatest.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
distgeomtest.cpp
Add a new test inspired by 2803
2026-05-18 19:08:26 -04:00
ffgaff.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
ffghemical.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
ffmmff94.cpp
Fix results to match revised data
2026-08-07 18:03:12 -04:00
ffuff.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
formalcharge.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
format.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
formula.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
fuzzregresstest.cpp
Fix BGF overflow reported by @rphang
2026-08-18 15:02:36 -04:00
gen3dtest.cpp
Fix OOM / crash with hypervalent, high permutation molecules
2026-05-20 15:17:28 -04:00
generate.sh
Merged revisions 3335-3337 via svnmerge from
2009-10-01 11:28:50 +00:00
graphsymtest.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
gziptest.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
implicitHtest.cpp
style: comment out unused parameters
2026-05-08 14:52:25 +09:00
inchi2.pl
Merged revisions 1900-1914 via svnmerge from
2007-04-13 18:57:13 +00:00
inchi.pl
Merged revisions 1900-1914 via svnmerge from
2007-04-13 18:57:13 +00:00
inchiwrite.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
internalcoord.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
invalidsmarts.cpp
Everything else
2019-04-04 20:20:04 +01:00
invalidsmiles.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
isomorphismtest.cpp
Everything else
2019-04-04 20:20:04 +01:00
iterators.cpp
Fix ring iterations w/no rings
2020-11-02 14:19:46 -05:00
ketformattest.cpp
Add test, move KET alias expansion to the final reader mutation in
2026-05-19 10:57:14 +03:00
logp_psa.cpp
Switch internal use of IsNear / IsNearZero to std::fabs
2026-05-19 10:31:36 -04:00
lssrtest.cpp
refactor: replace std::random_shuffle with std::shuffle
2026-05-19 10:14:31 +09:00
maereadertest.cpp
Add maeparser support to openbabel (#2)
2019-06-08 12:54:10 -07:00
math.cpp
Refactor to remove many internal deprecated warnings
2026-05-23 14:07:45 -04:00
mmff94validate.cpp
Update website to openbabel.org (long overdue).
2010-10-10 01:24:39 +00:00
mol.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
multicmltest.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
obbench.h
Add header with date/time to generated benchmark.txt
2010-03-23 21:59:57 +00:00
obmolbenchmark.cpp
* test/obbench.h: Macros for benchmarking. Tested on linux & win XP, should work on MacOSX.
2010-03-23 19:12:51 +00:00
obtest.cpp
style: comment out unused parameters
2026-05-08 14:52:25 +09:00
obtest.h
style: comment out unused parameters
2026-05-08 14:52:25 +09:00
pdbreadfile.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
periodictest.cpp
Specify includes for the periodicity tests
2020-01-25 15:37:51 -05:00
phmodel.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
README
* test/*: New test "harness" using Perl, if available to provide
2006-02-20 21:18:41 +00:00
regressionstest.cpp
Fix OOM / crash with hypervalent, high permutation molecules
2026-05-20 15:17:28 -04:00
residue.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
ringtest.cpp
Get rid of OBEdgeBase typedef.
2019-04-16 09:21:05 +01:00
rotortest.cpp
Switch internal use of IsNear / IsNearZero to std::fabs
2026-05-19 10:31:36 -04:00
roundtrip.cpp
Replace deprecated C headers with C++ alternatives
2021-06-16 18:06:56 +09:00
shuffletest.cpp
refactor: replace std::random_shuffle with std::shuffle
2026-05-19 10:14:31 +09:00
smartsparse.cpp
Everything else
2019-04-04 20:20:04 +01:00
smartstest.cpp
Fix memory leak in smartstest.cpp
2020-05-16 17:03:48 +00:00
smilesmatch.cpp
Add c standard libs required for g++ builds.
2019-04-06 16:40:50 +01:00
smilestest.cpp
Everything else
2019-04-04 20:20:04 +01:00
smileytest.cpp
Add SMILES read-only format using the Smiley parser. File extension is *.smy.
2012-11-25 21:12:48 +00:00
spectrophoretest.cpp
Everything else
2019-04-04 20:20:04 +01:00
squareplanartest.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
stereo_test_helpers.h
Add a new test inspired by 2803
2026-05-18 19:08:26 -04:00
stereoperceptiontest.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
stereotest.cpp
Merge branch 'master' of github.com:openbabel/openbabel into maybe_unused
2026-05-19 14:06:59 -04:00
strip.cpp
Update website to openbabel.org (long overdue).
2010-10-10 01:24:39 +00:00
tautomertest.cpp
Add override keyword
2022-07-28 12:29:24 +09:00
test_depiction.sh
Add OBDepict unit testing using ImageMagick utilities. It uses a shell script and is unix only for now but could easily be ported to windows using a .bat script.
2010-10-22 12:48:49 +00:00
test_pybel.py
fix(py): fix invalid escape sequence
2026-05-08 14:48:00 +09:00
test-set.sh
* test/*: Add many new unit test frameworks (atom, mol, bond,
2006-05-08 23:15:30 +00:00
testbabel.py
Add regression test for tetrazole pH model
2026-06-07 12:55:25 +01:00
testbindings.py
Add a unit test for OBConformerScore bindings
2026-05-14 14:30:22 -04:00
testcdjsonformat.py
Merge branch 'master' of github.com:openbabel/openbabel into fix-cdjson
2026-05-11 12:32:02 -04:00
testdistgeom.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testexample.py
fix(py): fix invalid escape sequence
2026-05-08 14:48:00 +09:00
testfastsearch.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testgauss.py
Fix small test failures from merging (#2490)
2022-06-10 11:15:57 -04:00
testkekule.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testketformat.py
Fix crashing test on Linux SWIG
2026-05-22 19:01:35 -04:00
testobconv_writers.py
refactor(python)!: drop python2
2026-05-18 19:09:04 +09:00
testpcjsonformat.py
fix(py): fix invalid escape sequence
2026-05-08 14:48:00 +09:00
testpdbformat.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testRInChI.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testroundtrip.py
refactor(python)!: drop python 3.3−
2026-05-18 19:09:04 +09:00
testsmartssym.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testsym.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
testunique.py
refactor(testbabel.run_exec): split argument beforehand
2026-05-20 03:48:14 +09:00
tetrahedraltest.cpp
Replace NULL with nullptr (C++11)
2020-05-07 07:24:29 +09:00
tetranonplanartest.cpp
style: comment out unused parameters
2026-05-08 14:52:25 +09:00
tetraplanartest.cpp
style: comment out unused parameters
2026-05-08 14:52:25 +09:00
uniqueidtest.cpp
Everything else
2019-04-04 20:20:04 +01:00
unitcell.cpp
Switch internal use of IsNear / IsNearZero to std::fabs
2026-05-19 10:31:36 -04:00
zipstream.cpp
Update website to openbabel.org (long overdue).
2010-10-10 01:24:39 +00:00

README 

    // Need to test:
    // atomic spin (i.e. radicals)
    // stereochemistry
    // bond types
    // atom types
    // fractional coordinate conversion
    // internal -> cartesian conversion
    // cartesian -> internal conversion
    // residue information
    // isotopes
    // chain information
    // chain perception
    // bond type perception
    // aromatic perception
    // ring perception
    // chirality perception
    // compress / uncompress
    // NumRotors

    // Builder utils
    // H->Methyl
    // Add hydrogens
    // SetHybAndGeom
    // SetLength
    // SetTorsion (obrotate)
    // Center
    // ToIntertialFrame
    // Rotate
    // Kekulize
    // Delete hydrogens
    // Add polar hydrogens
    // Add pH hydrogens
    // strip salts
    // obfit
Reference in new issue View Git Blame Copy Permalink