pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-03 21:44:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
Release_2025_09
rdkit/Code/GraphMol/test_data
History
Greg Landrum 82e8f673b7 Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930) 
* Fixes a bug with chirality perception of T-shaped centers in very large rings

* remove those files from the chemdraw tests
should be added later once we figure out and fix what the problem on the chemdraw side is (it is not directly connected to this PR)

* be more systematic about the tolerance values
carry the same tolerances over into the bond wedging code

* re-enable those chemdraw tests

* typo
2025-11-27 17:22:10 +01:00
..
CDX
Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)
2025-08-29 04:39:22 +02:00
CDXML
Expose CDX support to FileParsers and ChemDraw to SWIG (#8681)
2025-08-29 04:39:22 +02:00
1a9u.sdf
Fixes #607 (#1075)
2016-09-23 04:57:07 +02:00
1a9u.zwitterion.sdf
Fixes #607 (#1075)
2016-09-23 04:57:07 +02:00
adjustqueryprops_fivering_1.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_fivering_2.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_fivering_3.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_fivering_4.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_fivering_5.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_fivering_6.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_MDLfivering_1.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_MDLfivering_2.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_MDLfivering_3.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
adjustqueryprops_MDLfivering_4.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
canon_reorder1.mol
update coords
2015-01-09 09:58:20 +01:00
canon_reorder2.mol
update coords
2015-01-09 09:58:20 +01:00
canonSmiles.long.smi
Unset executable flag
2019-10-10 20:18:43 +09:00
canonSmiles.past_problems.smi
Unset executable flag
2019-10-10 20:18:43 +09:00
canonSmiles.smi
Unset executable flag
2019-10-10 20:18:43 +09:00
canonSmiles.v1.pkl
initial import
2006-05-06 22:20:08 +00:00
canonSmiles.v2.pkl
initial import
2006-05-06 22:20:08 +00:00
ChEBI_50252.mol
Fixes #298
2014-07-23 05:31:16 +02:00
chembl1203199.mol
Bugfix in SmilesWrite and some additional tests for getMolFrags function
2015-04-16 10:53:20 +02:00
CHEMBL501674_3D.mol
- make bond stereo detection in rings consistent (#1727)
2018-02-01 04:28:10 +01:00
CHEMBL501674.mol
- make bond stereo detection in rings consistent (#1727)
2018-02-01 04:28:10 +01:00
chi3d_r1_bad.mol
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
chi3d_r1.mol
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
chi3d_r2.mol
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
chi3d_s1.mol
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
chi3d_s2.mol
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
compounds.smi
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
cyclohexene_3D.mol
- make bond stereo detection in rings consistent (#1727)
2018-02-01 04:28:10 +01:00
dummyArom.mol
fixes to issues 2196817 and 2208994
2008-10-30 06:56:39 +00:00
github72.2.mol
Fixes #72
2013-08-25 06:36:10 +02:00
github72.3.mol
Fixes #72
2013-08-25 06:36:10 +02:00
github72.mol
Fixes #72
2013-08-25 06:36:10 +02:00
github87.2.mol
Fixes #87
2013-08-21 08:20:19 +02:00
github87.mol
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
github443.min.mol
Fixes #443
2015-03-05 06:38:38 +01:00
github443.mol
Fixes #443
2015-03-05 06:38:38 +01:00
github1936.mol
Fixes #1936 (#1945)
2018-07-05 11:53:54 -04:00
github2224_1.mol
Fixes #2224 (#2234)
2019-01-21 11:31:02 -05:00
github8689_2.sdf
Fixes #8689 (#8738)
2025-09-03 12:15:09 +02:00
Github8323.sdf
Fixes #7983 (#8342)
2025-03-20 07:40:33 +01:00
iChi1a.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi1b.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi1c.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi1d.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi1e.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi2a.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi2b.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi2c.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi2d.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi2e.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi3a.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi3b.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi3c.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi4a.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi4b.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi4c.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
iChi4d.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
Issue266.mol
fix and test issue 266
2012-11-17 07:39:39 +00:00
Issue2313979.sdf
fix and test Issue2313979
2008-12-02 08:50:51 +00:00
Issue2316677.mol
fix and test sf.net issue 2787221
2009-05-05 12:54:41 +00:00
Issue2705543.1.mol
just for backup
2009-03-27 16:12:54 +00:00
Issue2705543.1h.mol
resolves issue 2705543
2009-03-28 06:43:04 +00:00
Issue2705543.2.mol
just for backup
2009-03-27 16:12:54 +00:00
Issue2705543.2h.mol
resolves issue 2705543
2009-03-28 06:43:04 +00:00
Issue2788233.mol
fix and test sf.net Issue2788233
2009-06-01 13:04:33 +00:00
Issue2951221.1.mol
chirality support in the fix for issue 2951221
2010-02-14 06:39:51 +00:00
Issue2951221.2.mol
chirality support in the fix for issue 2951221
2010-02-14 06:39:51 +00:00
Issue2951221.3.mol
chirality support in the fix for issue 2951221
2010-02-14 06:39:51 +00:00
Issue3185548.2.mol
further ring-finding algorithmic changes to fix issue 3185548
2011-02-19 04:35:53 +00:00
Issue3185548.mol
initial fix for Issue3184458, more work should still be done here.
2011-02-18 06:31:31 +00:00
Issue3480481.mol
fix and test Issue 3480481
2012-02-18 05:34:34 +00:00
Issue3525076.sdf
fix and test issue 3525076
2012-05-10 05:35:20 +00:00
Issue3549146.mol
fix and test Issue3549146
2012-07-26 14:34:35 +00:00
mol_with_confs.pkl
Allow partial deserialization of molecules (#4040)
2021-04-24 07:22:55 +02:00
mol_with_double_confs.pkl
Allow partial deserialization of molecules (#4040)
2021-04-24 07:22:55 +02:00
mol_with_pickle_error.mol
Fix a problem with pickling molecules with more than 255 rings (#5992)
2023-01-30 23:24:00 -05:00
mol_with_sgroups_and_stereo.pkl
fix a problem with reading older pickles (#7180)
2024-02-22 14:03:45 +01:00
nontetrahedral_3d.sdf
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
pains.smi
RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
2015-07-14 10:31:31 -04:00
perchlorate1.mol
initial import
2006-05-06 22:20:08 +00:00
pubchem_87396055.sdf
add a test (still fails)
2016-03-09 07:27:11 +01:00
sgroups_and_marvin_metal.mol
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
sgroups_and_remove_atoms_1.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_atoms_2.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_atoms_3.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_atoms_4.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_atoms_5.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_atoms_6.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_atoms_7.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_and_remove_Hs_1.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_copolymer2.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
sgroups_copolymer.mol
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
stereochem.sdf
Fixes github1497 (#1555)
2017-09-11 08:37:32 -04:00
stereoOrder1.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
substructLibV1.pkl
Minor tweaks to SubstructLibrary (#3564)
2020-12-09 19:42:38 -05:00
water_coords2.trc
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords2.trx
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords_bad2.trc
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords_bad2.trx
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords_bad.trc
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords_bad.trx
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords.trc
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
water_coords.trx
- initial work to put the Trajectory code into a separate object
2016-05-09 19:05:15 +01:00
wedging_problems1.mol
fix start/end atoms when wedging bonds (#2861)
2019-12-27 07:21:49 -05:00
wedging_problems2.mol
fix start/end atoms when wedging bonds (#2861)
2019-12-27 07:21:49 -05:00
zero_chiral_volume_1.sdf
Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)
2025-11-27 17:22:10 +01:00
zero_chiral_volume_2.60.mol
Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)
2025-11-27 17:22:10 +01:00
zero_chiral_volume_2.80.mol
Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)
2025-11-27 17:22:10 +01:00
zero_chiral_volume_simple.mol
Fixes a bug with chirality perception of T-shaped centers in very large rings (#8930)
2025-11-27 17:22:10 +01:00
zinc3850436.mol
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
zinc3850436piece.mol
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
zinc4235774.mol
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
zinc4235774a.mol
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
zinc6624278.mol
this version passes the ZINC natural-products torture test
2012-06-28 06:45:42 +00:00
zinc8221201.mol
this version passes the ZINC natural-products torture test
2012-06-28 06:45:42 +00:00
zinc13403961piece.mol
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00