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42782d31cfd0f6cb2b3fa5e6acc1907eb46e3da2
rdkit/Code/GraphMol
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David Cosgrove 42782d31cf Change IUPAC metal->non-metal single bonds to dative (#6038) 
* Change atom to metal bonds from single to dative if appropriate.

* Pedantic change whilst I was in the area.

* Reinstate all tests, leave in debugging writes to see failing tests.

* Re-did it.  Failing tests now pass.

* Move any positive charge from the non-metal to the metal.
Fix expected test results.

* Write dative bond to JSON.

* Bump currentRDKitJSONVersion to 11, but allow parser to still read 10.

* Only move 1 unit of charge at a time from non-metal to metal.

* Greg's hack to not do it for O+ and N+ etc.
Explicitly exclude H, He, F, Ne from dative bonds.
Fix tests.

* Update expected PostGres json version to 11.

* suggestions for PR

* Correct comment.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
2023-02-06 04:37:32 +01:00
..
Abbreviations
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Propagate query features from reacting molecules to products (#6021)
2023-01-28 04:47:46 +01:00
ChemTransforms
Fixes #6034 (#6035)
2023-02-02 05:00:47 +01:00
CIPLabeler
Add a timeout protection for CIP calculations (#5772)
2022-12-09 05:28:38 +01:00
Depictor
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
Deprotect
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
Descriptors
Fixes #5941 (#5942)
2023-01-14 08:54:30 -05:00
DetermineBonds
fixes #5902 (#5926)
2023-01-11 09:43:05 +01:00
DistGeomHelpers
cleanup a compiler warning (#6016)
2023-02-01 04:31:45 +01:00
FileParsers
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
FilterCatalog
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
Fingerprints
Expose fingerprint generator options to python (#6024)
2023-02-01 04:29:22 +01:00
FMCS
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
ForceFieldHelpers
Create getExperimentalTorsions() function (#5969)
2023-01-25 12:15:04 +01:00
FragCatalog
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
GenericGroups
make the catch tests build faster (#5284)
2022-05-17 04:39:33 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
windows.h header should be lowercase to avoid issues when (#5712)
2022-10-31 06:43:57 +01:00
MolAlign
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
MolCatalog
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
MolChemicalFeatures
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
MolDraw2D
fixes #6054 (#6055)
2023-02-05 08:14:56 +01:00
MolEnumerator
Propagate query features from reacting molecules to products (#6021)
2023-01-28 04:47:46 +01:00
MolHash
stop caching ring-finding results (#5955)
2023-01-11 09:32:54 -05:00
MolInterchange
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
MolStandardize
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
MolTransforms
Fix Flake8 erorrs (#4252)
2022-03-10 06:55:18 +01:00
PartialCharges
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ReducedGraphs
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RGroupDecomposition
Refactor RGD moving function implementations from header to source files (#5958)
2023-01-20 15:01:45 +01:00
ScaffoldNetwork
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
ShapeHelpers
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
SLNParse
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
SmilesParse
Allow SMARTS of zero order bonds to match zero order bonds (#6037)
2023-02-02 05:05:11 +01:00
StructChecker
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Subgraphs
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Substruct
Fixes #888 (#6018)
2023-01-30 17:18:22 +01:00
SubstructLibrary
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
TautomerQuery
Support Python 3.11 (#5994)
2023-01-24 18:16:26 +01:00
test_data
Fix a problem with pickling molecules with more than 255 rings (#5992)
2023-01-30 23:24:00 -05:00
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
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
AddHs.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
AdjustQuery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
Aromaticity.cpp
run clang_format (#5676)
2022-11-01 04:14:26 +01:00
Atom.cpp
Fixes #5849 (#5861)
2022-12-28 20:10:13 +00:00
Atom.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
atomic_data.cpp
extend the allowed valences of the alkali earths (#5786)
2022-11-25 04:50:36 +01:00
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
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
Canon.h
swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00
catch_adjustquery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
catch_canon.cpp
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
catch_chirality.cpp
Fix #6011 and #6012 (#6013)
2023-01-26 19:26:19 +01:00
catch_graphmol.cpp
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
catch_moliterators.cpp
- added equality operator to CXXAtomIter and CXXBondIter classes such that they can used with implicit loop STL algorithms (#5995)
2023-01-20 15:00:32 +01:00
catch_sgroups.cpp
Addresses #4434 (#4435)
2021-08-24 05:10:06 +02:00
Chirality.cpp
Expose additional functionality to SWIG wrappers (#5614)
2022-10-04 05:04:28 +02:00
Chirality.h
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
CMakeLists.txt
Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557)
2022-10-06 05:46:08 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
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
stop caching ring-finding results (#5955)
2023-01-11 09:32:54 -05:00
FindStereo.cpp
Fix #6011 and #6012 (#6013)
2023-01-26 19:26:19 +01:00
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
Run clang-tidy (readability-braces-around-statements) (#4977)
2022-03-10 08:00:10 +01:00
MolOps.cpp
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
MolOps.h
Change IUPAC metal->non-metal single bonds to dative (#6038)
2023-02-06 04:37:32 +01:00
molopstest.cpp
fix + test (#5100)
2022-03-17 04:53:17 +01:00
MolPickler.cpp
Fix a problem with pickling molecules with more than 255 rings (#5992)
2023-01-30 23:24:00 -05:00
MolPickler.h
Fixes https://github.com/rdkit/rdkit/issues/4621 (#5623)
2022-10-06 16:45:14 +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
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +02:00
new_canon.h
New version of AssignStereochemistry (#5442)
2022-09-06 12:53:02 +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
add #include <utility> (#5060)
2022-03-17 04:56:34 +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
Fixes #5930 (#5931)
2023-01-07 05:13:00 +01:00
QueryOps.h
Fixes #5210 (#5408)
2022-07-11 11:20:03 +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
Fix #4071 (#4080)
2021-04-23 16:45:54 -04:00
resMolSupplierTest.cpp
Fix a hang in ResonanceMolSupplier when the computed ceMap is empty (#5701)
2022-10-28 19:47:06 +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
stop caching ring-finding results (#5955)
2023-01-11 09:32:54 -05:00
RingInfo.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Fix some minor leaks (#6029)
2023-01-31 17:30:34 +01:00
ROMol.h
- added equality operator to CXXAtomIter and CXXBondIter classes such that they can used with implicit loop STL algorithms (#5995)
2023-01-20 15:00:32 +01:00
RWMol.cpp
Fix memory safety issues found by OSS-Fuzz (#4983)
2022-02-06 05:06:38 +01:00
RWMol.h
fix doxygen comments (#5254)
2022-07-11 13:55:35 +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
add info to debug (#5526)
2022-09-06 13:03:08 +02:00
StereoGroup.h
add info to debug (#5526)
2022-09-06 13:03:08 +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
Fixes a couple of query-related bugs (#3398)
2020-09-17 08:16:43 +02:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Drop usage of CIP information from the canonicalization code (#5385)
2022-07-13 05:40:23 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
add boost::serialization support to ROMol (#5249)
2022-05-07 11:11:53 +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
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00