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1b79e6014cf374d53ce6f3afb1081fb3cb2bde88
rdkit/Code/GraphMol
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David Cosgrove 1b79e6014c Resolve clashing atom labels in 2D drawing (#8074) 
* Move atom labels round if they clash.

* Tidy.

* Re-work orientation logic.
Remove virtual fns from AtomSymbol.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
2024-12-19 08:54:33 +01:00
..
Abbreviations
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Fix some minor issues reported by ubsan and the compiler (#8015)
2024-11-28 07:28:31 +01:00
ChemTransforms
Revert "Expose molzip functionality to MinimalLib (#7959)"
2024-11-28 08:46:41 +01:00
CIPLabeler
Fix some minor issues reported by ubsan and the compiler (#8015)
2024-11-28 07:28:31 +01:00
Depictor
Remove explicit default constructor from Compute2DCoordParameters (#8046)
2024-11-28 08:30:39 +01:00
Deprotect
Fixes #7989 Incorrect benzyl deprotection reaction (#7990)
2024-11-28 07:17:01 +01:00
Descriptors
One final round of mem errors (#7943)
2024-11-28 07:13:18 +01:00
DetermineBonds
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
DistGeomHelpers
fixes #8001 (#8002)
2024-11-28 07:24:07 +01:00
FileParsers
remove no-op macros and dead code (pt 1) (#8012)
2024-11-28 07:30:39 +01:00
FilterCatalog
One final round of mem errors (#7943)
2024-11-28 07:13:18 +01:00
Fingerprints
Fixed #7986 (#7987)
2024-11-29 10:43:56 +01:00
FMCS
remove no-op macros and dead code (pt 1) (#8012)
2024-11-28 07:30:39 +01:00
ForceFieldHelpers
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-25 05:08:01 +02:00
FragCatalog
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
GeneralizedSubstruct
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
GenericGroups
New tests for specical query atoms and atropisomers (#7010)
2024-01-11 05:54:14 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MarvinParse
Fixes #8023 (#8024)
2024-11-28 07:29:09 +01:00
MMPA
Fix shifting of a potentially negative number (#8014)
2024-11-28 07:30:26 +01:00
MolAlign
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-25 05:08:01 +02:00
MolCatalog
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-25 05:08:01 +02:00
MolChemicalFeatures
fix GCC 13.2 warnings about redundant move in return statement (#7029)
2024-01-09 09:29:33 +01:00
MolDraw2D
Resolve clashing atom labels in 2D drawing (#8074)
2024-12-19 08:54:33 +01:00
MolEnumerator
Fix some mem errors in 2024.09.1 (#7867)
2024-10-25 05:05:36 +02:00
MolHash
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
MolInterchange
Fix #8027 (#8031)
2024-12-19 08:52:04 +01:00
MolProcessing
Fix some more mem errors in 2024.09.1 (#7899)
2024-10-25 05:08:01 +02:00
MolStandardize
Expose tautomer scoring functions to python (#7994)
2024-11-28 07:25:01 +01:00
MolTransforms
Fix inversion of stereo with canonicalizeConformer (#7878)
2024-10-25 05:28:25 +02:00
PartialCharges
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
RascalMCES
Synthon fingerprint search (#8025)
2024-11-29 13:20:15 +01:00
ReducedGraphs
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
RGroupDecomposition
Restore "oops, exponential is a pain" code snippet in the RGD algorithm (#7898)
2024-10-25 05:30:05 +02:00
ScaffoldNetwork
Allow inclusion of molecule names in ScaffoldNetwork (#7956)
2024-11-28 07:13:54 +01:00
ShapeHelpers
Fix inversion of stereo with canonicalizeConformer (#7878)
2024-10-25 05:28:25 +02:00
SLNParse
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
SmilesParse
[fix] issue #7572, precondition rootAtAtom if more than one fragment exists (#7811)
2024-11-28 07:31:39 +01:00
StructChecker
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
Subgraphs
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
Substruct
Fix some minor issues reported by ubsan and the compiler (#8015)
2024-11-28 07:28:31 +01:00
SubstructLibrary
remove no-op macros and dead code (pt 1) (#8012)
2024-11-28 07:30:39 +01:00
SynthonSpaceSearch
Synthon fingerprint search (#8025)
2024-11-29 13:20:15 +01:00
TautomerQuery
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
test_data
Fixes #7501 dative bonds in cdxml (#7757)
2024-08-28 05:59:43 +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
Fix #4570 Segfault on Property Getters/Setters (#8042)
2024-12-19 08:53:39 +01:00
AddHs.cpp
MergeQueryHs better detects hydrogens in OR queries (#8043)
2024-11-28 07:30:55 +01:00
AdjustQuery.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
Aromaticity.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
Atom.cpp
Fixes #7873 (#7885)
2024-10-25 05:08:53 +02:00
Atom.h
Fixes #7873 (#7885)
2024-10-25 05:08:53 +02:00
atomic_data.cpp
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
atomic_data.h
Switch to isoelectronic valence model (#7491)
2024-06-25 15:38:49 +02:00
AtomIterators.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Atropisomers.cpp
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
Atropisomers.h
Support atropisomers in the conformer generator (#7098)
2024-02-06 15:48:25 +01:00
Bond.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
Bond.h
A collection of small improvements from Roger S (#7566)
2024-06-26 08:29:57 +02:00
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
remove no-op macros and dead code (pt 1) (#8012)
2024-11-28 07:30:39 +01:00
Canon.h
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
catch_adjustquery.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_canon.cpp
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
catch_chirality.cpp
Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)
2024-11-28 07:11:51 +01:00
catch_graphmol.cpp
Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)
2024-11-28 07:11:51 +01:00
catch_molbundle.cpp
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
catch_moliterators.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_molops.cpp
Throw when attempting to normalize a Zero RDGeom::Point (#8008)
2024-11-28 07:27:45 +01:00
catch_organometallics.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_periodictable.cpp
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +02:00
catch_pickles.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
catch_queries.cpp
switch to catch2 v3 (#6898)
2023-11-15 06:45:42 +01:00
catch_sgroups.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
Chirality.cpp
Need to reserve space before assignment (#7964)
2024-11-28 07:12:41 +01:00
Chirality.h
Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)
2024-11-28 07:11:51 +01:00
CMakeLists.txt
Throw when attempting to normalize a Zero RDGeom::Point (#8008)
2024-11-28 07:27:45 +01:00
Conformer.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
Conformer.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
ConjugHybrid.cpp
Fixes #7556 (#7646)
2024-07-22 16:34:08 +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
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
FindStereo.cpp
Fixes #7598 (#7604)
2024-07-15 14:15:32 -04:00
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 across everything (#7849)
2024-09-26 13:39:02 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +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 minimal build, allow building without boost::serialization (#6932)
2023-11-23 05:57:05 +01:00
MolOps.cpp
Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823)
2024-09-20 09:48:08 +02:00
MolOps.h
Revert "implemented JSON parsers for SanitizeFlags and RemoveHsParameters for CFFI and MinimalLib (#8000)"
2024-11-28 08:48:54 +01:00
molopstest.cpp
MergeQueryHs better detects hydrogens in OR queries (#8043)
2024-11-28 07:30:55 +01:00
MolPickler.cpp
GitHub 7865 haspropwithvaluequery leaks (#7872)
2024-11-28 07:14:35 +01:00
MolPickler.h
Revert "Expose propertyFlags to CFFI and MinimalLib (#7960)"
2024-11-28 08:49:49 +01:00
MolProps.cpp
Remove Descriptors as a dependency of many other RDKit libraries (#7700)
2024-08-13 13:22:43 +02:00
MonomerInfo.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
MonomerInfo.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
new_canon.cpp
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
new_canon.h
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
NontetrahedralStereo.cpp
Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)
2024-11-28 07:11:51 +01:00
PeriodicTable.cpp
Fixes #5210 (#5408)
2022-07-11 11:20:03 +02:00
PeriodicTable.h
Add missing GetRow method and fix Python parameter names (#7575)
2024-06-28 12:47:34 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
QueryOps.cpp
Adds HasPropWithValue Pickler (#7692)
2024-08-26 16:27:58 +02:00
QueryOps.h
GitHub 7865 haspropwithvaluequery leaks (#7872)
2024-11-28 07:14:35 +01:00
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 canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +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 across everything (#7849)
2024-09-26 13:39:02 +02:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
make sure outdated ring fusion information is recomputed before attempting to use it (#7274)
2024-03-20 09:37:10 +01:00
RingInfo.h
atropisomer handling added (#6903)
2023-12-22 04:58:18 +01:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Some modernization of core GraphMol classes (#7228)
2024-03-17 06:04:04 +01:00
ROMol.h
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +02:00
RWMol.cpp
fix #7782 (#7783)
2024-10-25 05:04:53 +02:00
RWMol.h
Run clang-format across everything (#7849)
2024-09-26 13:39:02 +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
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
StereoGroup.h
Fix canonicalization of stereogroups (#7041)
2024-10-25 05:09:30 +02:00
SubstanceGroup.cpp
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
SubstanceGroup.h
Fixes #5923 (#7039)
2024-01-19 18:43:30 +01:00
test1.cpp
Fix some mem errors in 2024.09.1 (#7867)
2024-10-25 05:05:36 +02:00
test_fixtures.h
Fixes #6944 (#6950)
2023-12-01 05:41:14 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
remove no-op macros and dead code (pt 1) (#8012)
2024-11-28 07:30:39 +01:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
remove no-op macros and dead code (pt 1) (#8012)
2024-11-28 07:30:39 +01:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Fixes #7064 (#7141)
2024-02-22 06:46:39 +01:00
UnitTestQueryMol.py
Reformat Python code for 2023.03 release (#6294)
2023-04-28 06:53:56 +02:00
WedgeBonds.cpp
Throw when attempting to normalize a Zero RDGeom::Point (#8008)
2024-11-28 07:27:45 +01:00