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John Mayfield dd475b3677 Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730) 
* Set _SmilesStart when parsing SMARTS.

* SmartsWriter should also invert first atoms, like SMILES.

* Update test cases now these SMILES match themselves as SMARTS.

* rerun bison

* cleanup a possible repeated define

* When an atom moves from the first to second position winding should flip in SMARTS (i.e. same as SMILES).

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>
2023-10-05 06:02:49 +02:00
..
Abbreviations
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
add missing Python parameter and reformat (#6707)
2023-09-15 09:02:27 +02:00
ChemTransforms
Fail CI builds on compiler warnings + some fixes (#6675)
2023-09-02 04:38:45 +02:00
CIPLabeler
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
Depictor
Add trans layout for double bonds in rings (#6709)
2023-09-25 13:19:35 +02:00
Deprotect
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
Descriptors
Fail CI builds on compiler warnings + some fixes (#6675)
2023-09-02 04:38:45 +02:00
DetermineBonds
Use the connect-the-dots algorithm by default in DetermineBonds (#6740)
2023-09-26 06:10:20 +02:00
DistGeomHelpers
add option to use sequential random seeds in the conformer generator (#6639)
2023-08-19 19:19:56 +02:00
FileParsers
Fixes #6703 (#6705)
2023-09-28 05:16:17 +02:00
FilterCatalog
switch from boost::any to std::any (#6662)
2023-08-25 17:55:33 +02:00
Fingerprints
avoid leaking memory in case exceptions are thrown while generating FPs (#6630)
2023-08-15 04:59:14 +02:00
FMCS
Fail CI builds on compiler warnings + some fixes (#6675)
2023-09-02 04:38:45 +02:00
ForceFieldHelpers
fixes #6728 (#6755)
2023-09-27 17:01:53 +02:00
FragCatalog
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
GeneralizedSubstruct
Fail CI builds on compiler warnings + some fixes (#6675)
2023-09-02 04:38:45 +02:00
GenericGroups
clear up some compiler warnings (#6627)
2023-08-15 04:43:51 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
export Mrv{File,Block}IsReaction to python (#6701)
2023-09-08 11:06:17 +02:00
MMPA
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolAlign
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolCatalog
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
MolChemicalFeatures
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
MolDraw2D
extract continuous lines from the conrec code (#6676)
2023-09-15 09:00:26 +02:00
MolEnumerator
Support TautomerQuery and MolBundle queries in the cartridge (#6393)
2023-08-23 06:32:06 +02:00
MolHash
Fixes #6505 (#6506)
2023-07-14 06:58:19 +02:00
MolInterchange
switch from boost::any to std::any (#6662)
2023-08-25 17:55:33 +02:00
MolStandardize
fix some more leaks (#6684)
2023-09-04 06:38:01 +02:00
MolTransforms
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
PartialCharges
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RascalMCES
Fail CI builds on compiler warnings + some fixes (#6675)
2023-09-02 04:38:45 +02:00
ReducedGraphs
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RGroupDecomposition
Extract the core matching logic into a separate function (#6754)
2023-09-28 15:21:22 +02:00
ScaffoldNetwork
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
ShapeHelpers
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
SLNParse
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
SmilesParse
Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730)
2023-10-05 06:02:49 +02:00
StructChecker
refactor(python): replace deprecated unittest methods (#6304)
2023-07-14 07:51:15 +02:00
Subgraphs
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Substruct
Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730)
2023-10-05 06:02:49 +02:00
SubstructLibrary
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
TautomerQuery
RGD with matching on tautomers of core (#6611)
2023-08-29 08:50:14 +02:00
test_data
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Wrap
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
AddHs.cpp
Add hasQueryHs (#6702)
2023-09-15 08:59:56 +02:00
AdjustQuery.cpp
Add a new parameter to mol_adjust_query_properties for generic query parameters (#6332)
2023-08-03 15:41:43 +02:00
Aromaticity.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Atom.cpp
Remove check for ring information from Atom::Match (#6063)
2023-02-08 04:30:05 +01:00
Atom.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
atomic_data.cpp
Fixes #6638 (#6656)
2023-08-26 05:26:04 +02:00
atomic_data.h
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
AtomIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Bond.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
Bond.h
add #include <utility> (#5060)
2022-03-17 04:56:34 +01:00
BondIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
BondIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
bulktest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Canon.cpp
Fixes #6633 (#6643)
2023-08-23 06:18:14 +02:00
Canon.h
Add a "rootedAtAtom" to MolToSmarts (#6581)
2023-08-19 19:17:45 +02:00
catch_adjustquery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
catch_canon.cpp
Fixes #6633 (#6643)
2023-08-23 06:18:14 +02:00
catch_chirality.cpp
Fixes #6703 (#6705)
2023-09-28 05:16:17 +02:00
catch_graphmol.cpp
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
catch_molbundle.cpp
Add support for generalized substructure searching (#6443)
2023-06-22 10:54:35 +02:00
catch_moliterators.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
catch_organometallics.cpp
Fail CI builds on compiler warnings + some fixes (#6675)
2023-09-02 04:38:45 +02:00
catch_pickles.cpp
make sure bond attachpt info is pickled (#6698)
2023-09-07 12:21:36 +02:00
catch_queries.cpp
Fixes #6106 (#6107)
2023-02-19 10:46:07 -05:00
catch_sgroups.cpp
Addresses #4434 (#4435)
2021-08-24 05:10:06 +02:00
Chirality.cpp
Fixes #6703 (#6705)
2023-09-28 05:16:17 +02:00
Chirality.h
Fixes #6239 (#6240)
2023-04-11 10:42:56 +02:00
CMakeLists.txt
Add support for Marvin files (#6575)
2023-09-01 04:50:34 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Allow some tolerance in flatness determination (#6696)
2023-09-07 16:50:56 +02:00
ConjugHybrid.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
cptest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
Do not include dative bonds in ring finding by default (#6231)
2023-03-30 18:09:24 +02:00
FindStereo.cpp
some modernization of the memory handing in the canonicalization code (#6763)
2023-10-03 12:07:14 +02:00
GraphMol.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
GraphMol.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
hanoitest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Fixes #5505: problems when kekulizing molecules with query bonds (#5550)
2022-09-13 14:49:45 +02:00
Matrices.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
memtest1.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolBundle.h
Fix some build warnings (#6618)
2023-08-11 06:04:55 +02:00
MolOps.cpp
fix order of cleanupOrganometallics() in sanitizeMol() (#6690)
2023-09-07 12:58:03 +02:00
MolOps.h
Add hasQueryHs (#6702)
2023-09-15 08:59:56 +02:00
molopstest.cpp
Add hasQueryHs (#6702)
2023-09-15 08:59:56 +02:00
MolPickler.cpp
make sure bond attachpt info is pickled (#6698)
2023-09-07 12:21:36 +02:00
MolPickler.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
MonomerInfo.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
MonomerInfo.h
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
new_canon.cpp
some modernization of the memory handing in the canonicalization code (#6763)
2023-10-03 12:07:14 +02:00
new_canon.h
some modernization of the memory handing in the canonicalization code (#6763)
2023-10-03 12:07:14 +02:00
NontetrahedralStereo.cpp
Initial support for non-tetrahedral stereochemistry (#5084)
2022-05-20 09:07:16 +02:00
PeriodicTable.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
PeriodicTable.h
Include element name in atomic data (#5524)
2022-09-06 14:35:29 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Enable optional visualization of complex query atoms in a more compact form (#6056)
2023-02-16 12:34:05 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
QueryOps.cpp
Support additional generic groups (#6570)
2023-08-10 06:36:38 +02:00
QueryOps.h
switch from boost::any to std::any (#6662)
2023-08-25 17:55:33 +02:00
querytest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RDKitBase.h
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
RDKitQueries.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
regress.txt
Unset executable flag
2019-10-10 20:18:43 +09:00
Renumber.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
resMolSupplierTest.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
Resonance.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
- Changed all unsigned to unsigned int for clarity (#6646)
2023-08-25 06:09:19 +02:00
RingInfo.h
- Changed all unsigned to unsigned int for clarity (#6646)
2023-08-25 06:09:19 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
ROMol.h
Issue 6411 ROMol hasquery (#6739)
2023-09-25 13:23:37 +02:00
RWMol.cpp
Fix vulnerabilities found by fuzzer. (#6579)
2023-08-06 06:33:08 +02:00
RWMol.h
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
SanitException.h
Run clang-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
sanitTest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
StereoGroup.cpp
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
StereoGroup.h
Optionally forward Enhanced Stereo Group ids (#6560)
2023-07-27 18:53:40 +02:00
SubstanceGroup.cpp
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
SubstanceGroup.h
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
test1.cpp
switch from boost::any to std::any (#6662)
2023-08-25 17:55:33 +02:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Switch to determining atom chiral types from pseudo 3D instead of bond dirs (#6456)
2023-07-04 04:48:55 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Reformat C/C++ code ahead of 2023.03 release (#6295)
2023-04-28 04:42:35 +02:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Allow removal of non-special H atoms in SGroups (#5399)
2022-07-07 11:05:18 +02:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
Fixes #6423 (#6424)
2023-06-06 17:39:56 +02:00