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2b99ee477c19cb7bf4e826b386ab465cbc21bb2f
rdkit/Code/GraphMol/test_data
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Brian Kelley 2b99ee477c Allow fragments to be grouped in cdxml (#7529) 
* Allow fragments to be groups in CDXML

* Add support for grouped reactants

* run clang-format

* Change github issue to 7528

* Add documents to the code

* response to review, check grouped reactants in cdxml against rxn file

* Remove unused code

* Add missing file

---------

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
2024-06-23 07:02:19 +02:00
..
CDXML
Allow fragments to be grouped in cdxml (#7529)
2024-06-23 07:02:19 +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
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
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