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GreenPolyProducts/openbabel

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History

Noel O'Boyle 71128d38a8 Revert "Remove outdated stereo code"

2019-04-07 17:57:22 +01:00

..

Update ChemDoodle JSON format for rapidjson

2018-02-11 15:03:57 +00:00

Remove executable bit from the text files

2014-02-24 23:39:54 +02:00

Merge pull request #1831 from JasonYCHuang/fix-cdxml-upside-down-format

2019-03-02 17:56:31 -05:00

Fix #1785 by using the correct values for the average atomic mass when setting/reading isotope values

2018-03-17 17:05:14 +00:00

Update PubChem JSON format for rapidjson

2018-02-11 15:04:15 +00:00

Update docstring, and add tests for rxn->rinchi

2017-10-19 07:19:12 +01:00

aligntest.cpp

Port remaining instances of IsHydrogen(). Part Two.

2017-06-19 21:09:21 +01:00

aromatest.cpp

Remove test cases that are no longer aromatic

2017-09-14 21:14:06 +01:00

aromatic.pl

Moved aromatest to aromatic (makes for better summmary output from "make check")

2006-05-11 17:42:50 +00:00

atom.cpp

Starting on the old tests...

2013-06-06 21:30:53 +01:00

automorphismtest.cpp

Initial changes

2013-05-13 21:47:31 +01:00

bond.cpp

5 more tests.

2013-06-08 12:25:52 +01:00

buildertest.cpp

For right now, turn off distance geometry building by default.

2016-03-02 15:04:55 -05:00

canonconsistenttest.cpp

Canonconsistent and canonstable tests updated to new framework.

2013-05-27 21:13:00 +01:00

canonfragmenttest.cpp

Update the canonfragment test as the atom numbers have changed.

2017-05-19 08:56:24 +01:00

canonstabletest.cpp

Canonconsistent and canonstable tests updated to new framework.

2013-05-27 21:13:00 +01:00

cansmi.cpp

5 more tests.

2013-06-08 12:25:52 +01:00

cansmiles_shuffle.sh

New test file to exercise the SMILES canonicalizer.

2009-07-18 22:53:35 +00:00

carspacegrouptest.cpp

Improve space group support in .car files

2013-09-12 08:46:16 -04:00

charge_gasteiger.cpp

5 more tests.

2013-06-08 12:25:52 +01:00

charge_mmff94.cpp

switch lineend stream to work on stream, not streambuf

2015-06-12 00:22:34 -04:00

cifspacegrouptest.cpp

Make sure new test is run.

2018-04-23 15:59:58 -04:00

cistranstest.cpp

Replace instances of IsCarbon().

2017-06-18 10:26:57 +01:00

CMakeLists.txt

Merge pull request #1948 from baoilleach/cmakewarnings

2019-03-21 20:49:30 +00:00

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

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

conversion.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

conversiontest.cpp

add mol to cdxml test

2018-05-24 13:39:35 +08:00

datatest.cpp

Add missing include

2017-06-27 21:26:48 +01:00

ffgaff.cpp

gaff.prm and bondtyp.txt are updated in order to reproduce the atom types based on the Wang et al. Vol. 25, No. 9 . Journal of computational Chemistry. 2004

2016-03-14 13:45:21 +01:00

ffghemical.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

ffmmff94.cpp

Starting on the old tests...

2013-06-06 21:30:53 +01:00

ffuff.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

formalcharge.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

format.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

formula.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

generate.sh

Merged revisions 3335-3337 via svnmerge from

2009-10-01 11:28:50 +00:00

graphsymtest.cpp

Rename Get/SetImplicitHydrogen to Get/SetImplicitHCount

2017-05-19 09:01:13 +01:00

gziptest.cpp

Fix failing gziptest due to MOL2 file. MOL2 needs (a lot) more work but this is sufficient to keep the tests passing.

2017-05-19 08:59:52 +01:00

implicitHtest.cpp

Update tests: cistrans, graphsym, implicitH, lssr

2013-05-27 21:34:49 +01:00

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

Update website to openbabel.org (long overdue).

2010-10-10 01:24:39 +00:00

internalcoord.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

invalidsmarts.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

invalidsmiles.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

isomorphismtest.cpp

Update test to check only one bijection is found

2019-02-27 10:13:35 +00:00

iterators.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

logp_psa.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

lssrtest.cpp

Update tests: cistrans, graphsym, implicitH, lssr

2013-05-27 21:34:49 +01:00

math.cpp

Minor fix for Linux compilation

2013-06-08 21:24:50 +01:00

mmff94validate.cpp

Update website to openbabel.org (long overdue).

2010-10-10 01:24:39 +00:00

mol.cpp

Rename Get/SetImplicitHydrogen to Get/SetImplicitHCount

2017-05-19 09:01:13 +01:00

multicmltest.cpp

add test cases

2015-06-14 15:21:05 -04:00

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

Initial changes

2013-05-13 21:47:31 +01:00

obtest.h

add mol to cdxml test

2018-05-24 13:39:35 +08:00

pdbreadfile.cpp

More thoroughly test PDB element typing

2017-09-28 13:39:21 -04:00

phmodel.cpp

Get phmodel test to pass

2017-05-19 08:58:55 +01:00

README

* test/*: New test "harness" using Perl, if available to provide

2006-02-20 21:18:41 +00:00

regressionstest.cpp

Add basic tests

2019-02-27 20:15:55 +00:00

residue.cpp

Fix residue test to allow "UNL" as unknown ligand.

2014-03-15 15:26:03 -04:00

ringtest.cpp

Revert "Remove outdated stereo code"

2019-04-07 17:57:22 +01:00

rotortest.cpp

Add Susi Lehtola's patch (SF BUG 945) to use modulo 360 testing for angles, e.g. so that -179.8 is close to +180. This fixes the rotor test failure.

2015-05-31 13:08:49 +01:00

roundtrip.cpp

Update website to openbabel.org (long overdue).

2010-10-10 01:24:39 +00:00

shuffletest.cpp

Fix shuffletest failure caused by an example molecule with a tet stereo

2017-11-11 19:15:33 +00:00

smartsparse.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

smartstest.cpp

Prefer prefix ++/-- operators for non-primitive types.

2013-09-30 15:05:57 -04:00

smilesmatch.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

smilestest.cpp

Related to the previous commit. This test case no longer passes as this structure is no longer expected to have any stereo data associated with it when read from SMILES.

2017-11-19 20:00:06 +00:00

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

Finished with the new tests.

2013-06-05 21:58:22 +01:00

squareplanartest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

stereoperceptiontest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

stereotest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

strip.cpp

Update website to openbabel.org (long overdue).

2010-10-10 01:24:39 +00:00

tautomertest.cpp

Ensure tautomertest is exercised.

2015-08-08 00:42:57 -04:00

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

* Set svn:eol-style to native for all text files.

2010-06-03 14:29:31 +00:00

test-set.sh

* test/*: Add many new unit test frameworks (atom, mol, bond,

2006-05-08 23:15:30 +00:00

testbabel.py

Merge pull request #1948 from baoilleach/cmakewarnings

2019-03-21 20:49:30 +00:00

testbindings.py

Merge pull request #1951 from baoilleach/flags

2019-04-07 14:09:28 +01:00

testcdjsonformat.py

Update ChemDoodle JSON format for rapidjson

2018-02-11 15:03:57 +00:00

testexample.py

* Set svn:eol-style to native for all text files.

2010-06-03 14:29:31 +00:00

testfastsearch.py

Add regression test for fast tanimoto search

2015-05-22 10:53:27 -07:00

testkekule.py

Update Kekule test

2017-09-14 07:49:46 +01:00

testpcjsonformat.py

Update PubChem JSON format for rapidjson

2018-02-11 15:04:15 +00:00

testpdbformat.py

Convert tabs to spaces in testpdbformat.py

2017-05-17 10:56:23 -05:00

testRInChI.py

Minor updates to RInChI to get RXN tests to pass

2018-05-10 18:29:05 +01:00

testsmartssym.py

Potential ABI/API change: Check parsmart.h

2011-11-10 09:20:42 +00:00

testsym.py

Update test to reflect new behavior. Unspecified tet centers no longer set parity to '3' in MOL files. This can only happen if 'S' is specified on reading to force reperception.

2017-11-19 21:26:29 +00:00

testunique.py

* Set svn:eol-style to native for all text files.

2010-06-03 14:29:31 +00:00

tetrahedraltest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

tetranonplanartest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

tetraplanartest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

uniqueidtest.cpp

Finished with the new tests.

2013-06-05 21:58:22 +01:00

unitcell.cpp

Finished integration of all of the tests.

2013-06-08 20:38:01 +01:00

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