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e35f7db0093afaeda39155f9ea232a8daa47c525
rdkit/Code/GraphMol/FileParsers/test_data
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Yakov Pechersky 0986d22c58 Deterministic kekulize, independent of atom and bond order (#9125) 
* Make kekulization deterministic

* Add tautomer order-independence regression (python)

* Adjust tautomer tests for deterministic kekulization

* Update graphmol wedged-bond kekulization checks

* SmilesParse: update aromatic bond index expectations

* SmilesParse: refresh cxsmilesTest expected files

* Depictor: update testDepictor expected MolBlocks

* Depictor: update depictorCatch expectations

* Depictor Wrap: update expected MolBlock for pyDepictor

* MarvinParse: update testMrvToMol expected outputs

* FileParsers: refresh testAtropisomers expected outputs

* FileParsers: update tests for deterministic kekulization

* MolDraw2D: refresh brittle bond assertions

* RascalMCES: update expected cluster size

* MinimalLib: make cffi wedging check order-independent

* documentation fix

* MinimalLib: update Kekulé bond table in aligned-coords test

* Hoist duplicated lambdas to TEST_CASE scope

* Remove unused originalWedges variable

* Remove redundant bounds check; clarify wedge-end preference

* Pre-sort allAtms by wedge-end + rank

* Use mol.atomNeighbors() for neighbor iteration

* Check inAllAtms before linear-scanning done

* Drop redundant optsV/wedgedOptsV sorts

* Remove unused Canon.h include

* Add canonical parameter to Kekulize; skip ranking during sanitization

* Test canonical re-kekulization preserves stereo across atom orderings

* MinimalLib: update Kekulé bond orders in invertedWedges

* Change Kekulize canonical default to false, expose in Python wrappers

* keep rank order, push_back

* Revert "RascalMCES: update expected cluster size"

This reverts commit a81bb39495.

* docstring change

* expose new flag to python wrapper

* document changes in ReleaseNotes.md

* revert minimallib test changes again

* canonical = true defaults

* Revert "revert minimallib test changes again"

This reverts commit 039e1d84da.

* Reapply "RascalMCES: update expected cluster size"

This reverts commit 7b83a7a3e8.

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>
2026-03-19 08:43:13 +01:00
..
atropisomers
Deterministic kekulize, independent of atom and bond order (#9125)
2026-03-19 08:43:13 +01:00
macromols
Handle chiral atoms with 2 hydrogens in SCSR parser (#8939)
2026-01-29 08:08:14 +01:00
sgroupFragments
fragmentation of mol loses any sgroups (#7056)
2024-01-25 13:32:55 +01:00
wedgeTests
cleanup of stereogroups and wedges for non-chiral sites (#9051)
2026-01-30 04:20:32 +01:00
1CRN.pdb
very minimal testing of pdb reading/writing
2013-10-11 16:58:20 +02:00
1kv1.maegz
Keep PDB info from Maestro files if available (#2619)
2019-08-23 14:00:52 -07:00
1ps3_zn.pdb
[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)
2017-11-15 06:53:31 +01:00
2c92_hypervalentH.pdb
[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)
2017-11-15 06:53:31 +01:00
2dej_APW.pdb
[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)
2017-11-15 06:53:31 +01:00
2FVD.pdb
PDB reader/writer fixes;
2013-10-25 05:02:09 +02:00
2NW4.pdb
Fixes #234
2014-03-17 08:33:07 +01:00
2vnf_bindedHOH.pdb
[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)
2017-11-15 06:53:31 +01:00
4BNA.pdb
Expanded sequence support (#1140)
2016-11-04 04:29:26 +01:00
4TNA.pdb
Expanded sequence support (#1140)
2016-11-04 04:29:26 +01:00
3505.mol2
allow the cleanup step of Mol2 parsing to be disabled (#1898)
2018-06-09 05:44:10 +02:00
acd_few.tdt
initial import
2006-05-06 22:20:08 +00:00
acetate.xyz
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
AtomProps1.mol
support parsing atom properties; fix ordering "bug" in property parsing
2009-05-11 15:27:39 +00:00
AtomProps2.mol
support parsing atom properties; fix ordering "bug" in property parsing
2009-05-11 15:27:39 +00:00
AtomQuery1.mol
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
AtomQuery2.mol
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
AtomQuery3.mol
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
bad_ppty.mae
Rework MaeMolSupplier, fix #2617 (#2620)
2019-12-03 15:04:23 +01:00
badringstereochem2.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
badringstereochem3.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
badringstereochem.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
badSubstPyridine.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
benzene.mae
Improve MaeMolSupplier API (#6053)
2023-02-08 04:31:51 +01:00
benzene.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
BlankPropLines.sdf
support skip lines in ctabs;
2012-10-10 10:16:13 +00:00
bond-query2.mol
Fixes #266
2014-05-22 17:34:06 +02:00
bond-query3.mol
Fixes #266
2014-05-22 17:34:06 +02:00
bond-query4.mol
Fixes #269
2014-05-23 08:26:26 +02:00
bond-query5.mol
Fixes #269
2014-05-23 08:26:26 +02:00
bond-query6.mol
Fixes #269
2014-05-23 08:26:26 +02:00
bond-query.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
bondorder0.mol
fix and test issue 2337369
2008-11-24 07:40:53 +00:00
bondorder9.mol
fix and test issue 2337369
2008-11-24 07:40:53 +00:00
Canion.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
cdk2_stereo.csv
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
CH2.mol
initial pass at this
2013-07-15 17:04:15 +02:00
CH3.mol
initial pass at this
2013-07-15 17:04:15 +02:00
CH.mol
initial pass at this
2013-07-15 17:04:15 +02:00
CH.v3k.mol
initial pass at this
2013-07-15 17:04:15 +02:00
ChainBondQuery.mol
start to add better support for MDL mol files.
2007-07-19 16:41:11 +00:00
chargedAmidine.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
chargedAmidineEC.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
chargedAmidineRWH.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
chebi_15469.v3k.mol
add (non-standard) handling of R groups to v3k mol parser
2014-01-08 05:22:15 +01:00
chebi_57262.v3k.2.mol
more isotope fixing
2014-01-08 06:51:48 +01:00
chebi_57262.v3k.mol
more isotope fixing
2014-01-08 06:51:48 +01:00
chiral1.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
chiral1a.mol
initial import
2006-05-06 22:20:08 +00:00
chiral2.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
chiral2a.mol
initial import
2006-05-06 22:20:08 +00:00
chiral3.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
chiral3a.mol
initial import
2006-05-06 22:20:08 +00:00
chiral4.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
chiral4a.mol
initial import
2006-05-06 22:20:08 +00:00
chiral5.mol
initial import
2006-05-06 22:20:08 +00:00
chiral_3h.mol
handle isotopic H better from ctabs
2013-08-23 12:59:09 +02:00
chiral_flag.mol
Fix #64
2013-07-09 07:19:24 +02:00
chiral_phosphorous.1.mol
fix and test issue 3376319
2011-07-23 16:53:04 +00:00
chiral_phosphorous.2.mol
fix and test issue 3376319
2011-07-23 16:53:04 +00:00
chiral_phosphorous.3.mol
fix and test issue 3376319
2011-07-23 16:53:04 +00:00
chiral_phosphorous.4.mol
fix and test issue 3376319
2011-07-23 16:53:04 +00:00
ChiralityAndBondDir1a.mol
merge the changes from the CanonicalizerRework30Nov branch in.
2008-01-30 14:53:04 +00:00
ChiralityAndBondDir1b.mol
merge the changes from the CanonicalizerRework30Nov branch in.
2008-01-30 14:53:04 +00:00
ChiralityAndBondDir2a.mol
merge the changes from the CanonicalizerRework30Nov branch in.
2008-01-30 14:53:04 +00:00
ChiralityAndBondDir2b.mol
merge the changes from the CanonicalizerRework30Nov branch in.
2008-01-30 14:53:04 +00:00
cistrans.1.mol
continue fix and test for sf.net issue 1718794
2007-05-14 17:41:17 +00:00
cistrans.1a.mol
continue fix and test for sf.net issue 1718794
2007-05-14 17:41:17 +00:00
cistrans.2.mol
continue fix and test for sf.net issue 1718794
2007-05-14 17:41:17 +00:00
cistrans.2a.mol
continue fix and test for sf.net issue 1718794
2007-05-14 17:41:17 +00:00
cistrans.3.mol
continue fix and test for sf.net issue 1718794
2007-05-14 17:41:17 +00:00
cmpd1.tpl
Unset executable flag
2019-10-10 20:18:43 +09:00
cmpd2.tpl
Unset executable flag
2019-10-10 20:18:43 +09:00
colchicine.mol.png
Molecule metadata in PNGs (#3316)
2020-08-25 07:51:18 +02:00
colchicine.mrv.png
Molecule metadata in PNGs (#3316)
2020-08-25 07:51:18 +02:00
colchicine.no_metadata.png
Molecule metadata in PNGs (#3316)
2020-08-25 07:51:18 +02:00
colchicine.png
Molecule metadata in PNGs (#3316)
2020-08-25 07:51:18 +02:00
combined.mol
expand capabilities of v3k ctab parser
2010-06-02 17:55:35 +00:00
conflicting-list-query.mol
start to add better support for MDL mol files.
2007-07-19 16:41:11 +00:00
CrBz2.mol
initial pass at ZBO support.
2013-11-30 06:58:03 +01:00
CrBz.mol
initial pass at ZBO support.
2013-11-30 06:58:03 +01:00
CrossedDoubleBondWithChiralNbr2.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CrossedDoubleBondWithChiralNbr2.sdf.expected.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CrossedDoubleBondWithChiralNbr.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CrossedDoubleBondWithChiralNbr.sdf.expected.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Cubane.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CubaneNoWedges.cxsmi
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
CubaneWedges.cxsmi
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
D_in_CTAB.mol
fix and test Issue 3557675
2012-08-15 04:21:33 +00:00
dative_bonds_one.mol
Add support for dative bonds. (#1190)
2016-12-14 09:44:18 +01:00
dative_bonds_two.mol
Add support for dative bonds. (#1190)
2016-12-14 09:44:18 +01:00
DativeBond2000.mol
Add support for dative bonds in MOL files (#6566)
2023-07-21 08:43:23 +02:00
dbtranslateCharged.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
dbtranslateUncharged.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
dbtranslateUnchargedRing.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
earlyEOF.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
empty2.sdf
fix and test GitHub issue 19
2013-04-21 05:22:57 +00:00
empty.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
empty.smi
Unset executable flag
2019-10-10 20:18:43 +09:00
empty.xyz
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
esters_end.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
esters.prop_name_trunc.sdf
[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)
2017-11-15 06:53:31 +01:00
esters.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
ethane.xyz
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
EZ_mol2_issue114.mol2
Fixed GitHub Issue #114
2013-10-05 11:10:32 +01:00
FeCO5.mol
initial pass at ZBO support.
2013-11-30 06:58:03 +01:00
fewSmi.2.csv
Unset executable flag
2019-10-10 20:18:43 +09:00
fewSmi.csv
Unset executable flag
2019-10-10 20:18:43 +09:00
first_200.tpsa.csv
Unset executable flag
2019-10-10 20:18:43 +09:00
fusedRing.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
github82.1.mol
Fixes #82
2013-08-23 09:18:04 +02:00
github88.v3k.mol
Fixes #88
2013-08-21 20:45:54 +02:00
github88.v3k.sdf
Fixes #88
2013-08-21 20:45:54 +02:00
github186.mol
Fixes #186
2014-01-11 06:01:30 +01:00
github187.2.mol
Fixes #187
2014-01-11 05:38:11 +01:00
github187.mol
Fixes #187
2014-01-11 05:38:11 +01:00
github187.v3k.mol
Fixes #187
2014-01-11 05:38:11 +01:00
github188_2.mol
ok, this time it is a proper fix
2016-03-29 13:09:22 +02:00
github188.mol
Fixes #188
2016-03-29 10:58:56 +02:00
github189.mol
Fixes #189
2014-03-13 05:23:56 +01:00
github191.1.mol
Fixes #191
2014-01-12 05:42:50 +01:00
github191.2.mol
Fixes #191
2014-01-12 05:42:50 +01:00
github192.mol
the fix for #188 also
2016-03-29 13:19:10 +02:00
github196.mol
Fixes #196
2014-01-16 02:07:03 -05:00
github210.mol
Fixes #210
2014-02-03 05:25:27 +01:00
github271.mol
[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)
2017-11-15 06:53:31 +01:00
github360.mol
Fixes #360
2014-10-25 12:13:01 +02:00
github438_1.mol2
Fixes #438
2015-02-21 14:20:47 +01:00
github438_2.mol2
Fixes #438
2015-02-21 14:20:47 +01:00
github741.mol
Fixes #741
2016-02-13 05:38:03 +01:00
github741.v3k.mol
Fixes #741
2016-02-13 05:38:03 +01:00
github1023.pdb
fixes #1023 (#1027)
2016-08-18 16:29:29 -04:00
github1029.1.pdb
Fix two problems with the PDB parsing (#1341)
2017-03-04 12:34:27 -05:00
github1029.1jld_chaina.pdb
Fix two problems with the PDB parsing (#1341)
2017-03-04 12:34:27 -05:00
github1029.1jld.pdb
Fix two problems with the PDB parsing (#1341)
2017-03-04 12:34:27 -05:00
github1034.1.mol
Fixes #1034: squiggle bonds are now preserved if no sanitization is done (#1043)
2016-08-30 16:02:31 +02:00
github1034.2.mol
Fixes #1034: squiggle bonds are now preserved if no sanitization is done (#1043)
2016-08-30 16:02:31 +02:00
github1049.1.mol
Fixes #1049 (#1050)
2016-09-01 09:22:17 +02:00
github1049.2.mol
Fixes #1049 (#1050)
2016-09-01 09:22:17 +02:00
github1251.mol
Fixes #1251 (#1252)
2017-01-09 16:29:06 -05:00
github1340.1jld_snip.pdb
Fix two problems with the PDB parsing (#1341)
2017-03-04 12:34:27 -05:00
github2000.2.sdf
fixes #2000 (#2001)
2018-08-12 17:10:09 -04:00
github2000.sdf
fixes #2000 (#2001)
2018-08-12 17:10:09 -04:00
github2040_1.mol
Fixes #2040 (#2085)
2018-10-08 22:27:48 +02:00
github2225_1.mol
Fix #2225 (#2228)
2019-01-17 11:44:23 -05:00
github2225_2.mol
Fix #2225 (#2228)
2019-01-17 11:44:23 -05:00
github2229_1.mol
Fixes #2229 (#2235)
2019-01-22 10:53:48 -05:00
github2285.sdf
Add test for issue #2285, fix molbundle test (#2301)
2019-02-28 13:47:03 -05:00
github7306.mol
Fixes #7306 (#7510)
2024-07-01 05:00:24 +02:00
github8823.sdf
Fix a couple issues related to atom list handling in V3000 mol blocks (#8824)
2025-10-09 05:26:01 +02:00
Github164.mol
Fixes #164
2013-12-31 08:27:09 +01:00
Github611.mol
add test for #611
2015-09-10 16:01:15 +02:00
H3BNH3.mol
add support for the ZCH and HYD elements in mol files
2013-12-07 17:40:04 +01:00
highlySymmetricGuanidine.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
issue123.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
issue142a.mol
initial import
2006-05-06 22:20:08 +00:00
issue145.mol
initial import
2006-05-06 22:20:08 +00:00
issue148.mol
initial import
2006-05-06 22:20:08 +00:00
Issue142b.mol
initial import
2006-05-06 22:20:08 +00:00
Issue142d.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
Issue180.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
Issue226.sdf
initial import
2006-05-06 22:20:08 +00:00
Issue264-1.mol
initial import
2006-05-06 22:20:08 +00:00
Issue264-2.mol
initial import
2006-05-06 22:20:08 +00:00
Issue269.mol
support additional trans-uranic elements (#1134)
2016-11-03 11:48:31 -04:00
Issue381.sdf
initial import
2006-05-06 22:20:08 +00:00
Issue399a.mol
initial import
2006-05-06 22:20:08 +00:00
Issue1965035.mol
fix and test issue 1965035
2008-05-16 05:35:50 +00:00
Issue3009836.1.mol
fix issue 3009836; partial fix for issue 3009911
2010-06-01 17:54:49 +00:00
Issue3009836.2.mol
fix issue 3009836; partial fix for issue 3009911
2010-06-01 17:54:49 +00:00
Issue3009836.3.mol
fix issue 3009836; partial fix for issue 3009911
2010-06-01 17:54:49 +00:00
Issue3228150.full.sdf
partial fix for Issue3228150
2011-03-25 03:26:03 +00:00
Issue3228150.sdf
partial fix for Issue3228150
2011-03-25 03:26:03 +00:00
Issue3374639.1.mol
fix and test Issue3374639
2011-07-22 10:55:40 +00:00
Issue3374639.2.mol
fix and test Issue3374639
2011-07-22 10:55:40 +00:00
Issue3374639.full.mol
fix and test Issue3374639
2011-07-22 10:55:40 +00:00
Issue3375647.1.mol
fix and tests sf.net issue3375647
2011-07-22 15:53:05 +00:00
Issue3375647.2.mol
fix and tests sf.net issue3375647
2011-07-22 15:53:05 +00:00
Issue3375684.1.mol
fix and tests Issue3375684
2011-07-23 03:49:36 +00:00
Issue3375684.2.mol
another piece of Issue3375684
2011-07-23 04:47:17 +00:00
Issue3392107.1.mol
fix and test issue 3392107. Add first pass at being able to write atom list queries to mol files
2011-08-16 06:03:27 +00:00
Issue3399798.2.mol2
fix and test Issue3399798
2011-08-30 09:13:07 +00:00
Issue3399798.mol2
fix and test Issue3399798
2011-08-30 09:13:07 +00:00
Issue3432136_1.mol
initial pass at fixing issue 3432136
2011-11-03 04:13:02 +00:00
Issue3432136_1.v3k.mol
initial pass at fixing issue 3432136
2011-11-03 04:13:02 +00:00
Issue3432136_2.mol
initial pass at fixing issue 3432136
2011-11-03 04:13:02 +00:00
Issue3432136_2.v3k.mol
Add SCSR parsing to RDKit (#8147)
2025-05-14 13:37:59 +02:00
Issue3477283.mol
fix and test issue 3477283
2012-01-22 09:40:54 +00:00
Issue3482695.sdf
fix and test issue 3482695
2012-02-02 03:28:48 +00:00
Issue3514824.2.mol
fix and test issue 3514824
2012-04-10 04:14:52 +00:00
Issue3514824.cdxml
ChemDraw Document and read/write support for the RDKit (#8620)
2025-07-04 06:36:10 +02:00
Issue3514824.mol
fix and test issue 3514824
2012-04-10 04:14:52 +00:00
Issue3525000.sdf
fix and test issue 3525000
2012-05-09 13:13:46 +00:00
Issue3525000b.sdf
a bit more robustification around issue 3525000b
2012-05-09 13:41:22 +00:00
Issue3525673.sdf
fix and test issue 3525673
2012-05-12 05:31:54 +00:00
Issue3525799.mol
fix issues 3525799 and 3526810
2012-05-18 05:56:45 +00:00
largemol.mol
initial fix and tests for issue 3154208
2011-01-10 07:11:44 +00:00
list-query-long.mol
fix and test issue2413431
2008-12-10 09:09:02 +00:00
list-query.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
lists_plus_values.mol
robustify multiple query handling
2009-05-28 14:14:15 +00:00
lonePairMol.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
m_with_enh_stereo.sdf
Fixes #5165 (#5209)
2022-04-17 17:35:43 +02:00
manycharges.mol
Check in a bunch of changes to fix radical handling.
2008-09-23 06:02:02 +00:00
missingCR.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
mol1.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
mol_noatoms.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
mol_nomol.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
mol_with_enhanced_stereo_2_And_groups.sdf
Fixes #5165 (#5209)
2022-04-17 17:35:43 +02:00
MolFileChgBug.mol
fix and test SF.net bug 1603923
2006-11-27 17:53:02 +00:00
mrv-sma-bad.mol
Adds case for testing invalid smarts in MRV SMA tags
2017-12-22 08:21:05 -05:00
mrv-sma.mol
Adds ability to read and parse marvin smarts in mol blocks
2017-12-22 08:20:31 -05:00
multiple_mols.png
Molecule metadata in PNGs (#3316)
2020-08-25 07:51:18 +02:00
Na.mol
initial pass at this
2013-07-15 17:04:15 +02:00
NCI_aids_few.mae
Add initial Maestro format Supplier using maeparser library (#1872)
2018-06-02 12:24:03 +02:00
NCI_aids_few.maegz
Add initial Maestro format Supplier using maeparser library (#1872)
2018-06-02 12:24:03 +02:00
NCI_aids_few.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
NCI_aids_few.sdf.gz
add the ForwardSDMolSupplier to allow use of gzipped sd files;
2009-05-14 18:07:57 +00:00
nonexistant.xyz
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
not-list-query.mol
start to add better support for MDL mol files.
2007-07-19 16:41:11 +00:00
Noxide.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
O2.sdf
[GSoC-2020] Generalized and Multithreaded File Reader (#3363)
2020-10-09 04:31:05 +02:00
outNCI_arom.sdf
Unset executable flag
2019-10-10 20:18:43 +09:00
parity.nitrogen.mol
support parity with implicit hs
2009-01-26 05:56:28 +00:00
parity.simple1.mol
add a few simple tests for the mol file parity handling
2009-01-21 06:05:13 +00:00
parity.simple2.mol
add a few simple tests for the mol file parity handling
2009-01-21 06:05:13 +00:00
parity.simpleH1.mol
add a few simple tests for the mol file parity handling
2009-01-21 06:05:13 +00:00
parity.simpleH2.mol
add a few simple tests for the mol file parity handling
2009-01-21 06:05:13 +00:00
parity.twoHs.mol
support parity with implicit hs
2009-01-26 05:56:28 +00:00
precision.v3k.mol
Custom decimal precision (#7229)
2024-03-17 06:03:03 +01:00
props_test.mae
Rework MaeMolSupplier, fix #2617 (#2620)
2019-12-03 15:04:23 +01:00
pyrazole_pyridine.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
pyridiniumPhenyl.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
query_A.mol
better handling of Q, A and * queries from CTABs
2009-05-28 04:37:12 +00:00
query_A.v3k.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
query_Q.mol
better handling of Q, A and * queries from CTABs
2009-05-28 04:37:12 +00:00
query_Q.v3k.mol
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
query_star.mol
better handling of Q, A and * queries from CTABs
2009-05-28 04:37:12 +00:00
radical.mol
Check in a bunch of changes to fix radical handling.
2008-09-23 06:02:02 +00:00
rdkit_chunk_boundary_bug.sdf
Fixes a boundary issue when indexing SDF (#9162)
2026-03-12 13:58:33 +01:00
rgroups1.mol
start to add better support for MDL mol files.
2007-07-19 16:41:11 +00:00
rgroups2.mol
start to add better support for MDL mol files.
2007-07-19 16:41:11 +00:00
rgroups3.mol
add more flexibility to the R group labelling from mol files
2010-03-10 05:14:52 +00:00
RingBondQuery.mol
start to add better support for MDL mol files.
2007-07-19 16:41:11 +00:00
ringcount_0.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
ringcount_2.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
ringcount_3.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
ringcount_4.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
ringcount_star2.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
ringcount_star3.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
ringcount_star.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
rxn1.mol
Fixes #118
2013-10-05 16:19:02 +02:00
s1p_chembldoc89753.txt
Fixes #9068: raise a ValueError when trying to set properties with empty names (#9085)
2026-02-09 05:58:25 +01:00
s58_rcsb.mol
- RCSB SDF files which feature right-justified element names can now be parsed (#994)
2016-07-27 14:49:52 +02:00
sdErrors1.sdf
initial import
2006-05-06 22:20:08 +00:00
sdErrors2.sdf
initial import
2006-05-06 22:20:08 +00:00
sdErrors3.sdf
initial import
2006-05-06 22:20:08 +00:00
sdErrors4.sdf
initial import
2006-05-06 22:20:08 +00:00
sgroup_ap_bug.mol
SGroups with more than one attachment point are now properly parsed (#3072)
2020-04-12 10:25:39 +02:00
simple_e.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
simple_either.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
simple_z.mol
Merge changes from the iterative chirality branch:
2008-09-19 09:40:15 +00:00
SimpleWiggleDoubleBond.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
SimpleWiggleDoubleBond.sdf.expected.sdf
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
SkipLines.sdf
support skip lines in ctabs;
2012-10-10 10:16:13 +00:00
stereo3d_1.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereo3d_2.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereo3d_cis.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereo3d_conflict.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereo3d_dblunknown.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereo3d_trans.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereo3d_unknown.mol
Make the defaults for some functions less error prone. (#1690)
2017-12-22 08:09:36 -05:00
stereochem.mae
Addresses issue #3815 (#3816)
2021-02-16 08:04:37 +01:00
strictLax1.sdf
- changed SDMolSupplier to be tolerant of spurious lines after
2015-05-10 22:30:11 +01:00
strictLax2.sdf
- changed SDMolSupplier to be tolerant of spurious lines after
2015-05-10 22:30:11 +01:00
subst1.mol
further improvements in handling queries from MDL mol files
2007-08-07 17:32:30 +00:00
subst2.mol
further improvements in handling queries from MDL mol files
2007-08-07 17:32:30 +00:00
subst3.mol
further improvements in handling queries from MDL mol files
2007-08-07 17:32:30 +00:00
subst4.mol
further improvements in handling queries from MDL mol files
2007-08-07 17:32:30 +00:00
sulfonAmide.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
Sulfonate.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
symmetricGuanidine.mol2
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
T_in_CTAB.mol
fix and test Issue 3557675
2012-08-15 04:21:33 +00:00
three_coordinate_chirality.1.mol
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
three_coordinate_chirality.2.mol
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
three_coordinate_chirality.3.mol
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
three_coordinate_chirality.4.mol
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
three_coordinate_chirality.5.mol
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
three_coordinate_chirality.6.mol
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
triazine.mol
Unset executable flag
2019-10-10 20:18:43 +09:00
two_centers_and.mol
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
two_centers_or.mol
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
unsanitary2.mol
initial import
2006-05-06 22:20:08 +00:00
unsanitary.mol
initial import
2006-05-06 22:20:08 +00:00
unsanitized_stereo.mol
Fixes #337
2014-10-04 14:44:42 +02:00
unsaturation.mol
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +00:00
v3k.1.mol
preliminary handling of v3000 mol blocks
2009-06-05 06:12:51 +00:00
v3k.2.mol
properly handle quoted NOT atom lists
2010-06-04 10:06:50 +00:00
v3k.3.mol
preliminary handling of v3000 mol blocks
2009-06-05 06:12:51 +00:00
v3k.4a.mol
preliminary handling of v3000 mol blocks
2009-06-05 06:12:51 +00:00
v3k.4b.mol
preliminary handling of v3000 mol blocks
2009-06-05 06:12:51 +00:00
v3k.5a.mol
fix and test sf.net issue 2804599
2009-06-11 04:55:44 +00:00
v3k.5b.mol
fix and test sf.net issue 2804599
2009-06-11 04:55:44 +00:00
v3k.6a.mol
fix and test sf.net issue 2804599
2009-06-11 04:55:44 +00:00
v3k.6b.mol
fix and test sf.net issue 2804599
2009-06-11 04:55:44 +00:00
v3k.crash1.mol
fix a v3k mol file problem
2010-02-15 12:43:38 +00:00
v3k.rbc.mol
expand capabilities of v3k ctab parser
2010-06-02 17:55:35 +00:00
wedged_single_to_double_bond.mol
Fixes Issue 1614 (#1781)
2018-04-01 17:48:36 +02:00
withHs.sdf
test the removeHs stuff a bit better
2007-08-13 03:59:58 +00:00