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rdkit/Code/GraphMol
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Greg Landrum 73d26036de Support enumerating some mol file features into MolBundles (#3257) 
* backup

* compiles

* progress, but not there yet

* basics now working

* start towards adding another test

* test having two variation points

* add actual enumeration and the corresponding tests

* docs and cleanup

* cleanups to get the mac build working

* attempt to get win32 dll builds to work

* dlls are fun

* Add FixedMolSizeMolBundle class

* changes in response to review

Also: add warnings for bad input in ParseV3000Array

* a bit of refactoring

* additional testing

* does not work, backup

* LINKNODES work now

* cleanup

* allow silencing reaction validation warnings during initialization

* docs

* fix (and test) handling of empty enumerations

* silence warnings when doing alchemy

* first pass at a Python wrapper for the enumerator

* Add Java wrappers for MolBundle and the MolEnumerator

* cleanup some comment formatting
2020-07-11 12:54:23 +02:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
ChemTransforms
Add cxsmiles query atoms to CTAB parsers and writers (#3261)
2020-07-03 12:51:19 -04:00
CIPLabeler
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
Depictor
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
Descriptors
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
DistGeomHelpers
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
FileParsers
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
FilterCatalog
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Fingerprints
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
FMCS
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
ForceFieldHelpers
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
FragCatalog
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolAlign
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
MolCatalog
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolChemicalFeatures
Address build warnings (#3082)
2020-04-17 14:40:15 +02:00
MolDraw2D
Annotation clashes with symbols on small drawings. #3262 (#3263)
2020-07-03 14:54:21 +02:00
MolEnumerator
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
MolHash
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
MolInterchange
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolStandardize
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
MolTransforms
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
PartialCharges
Cleanup some cmake dependencies (#3077)
2020-04-17 14:34:23 +02:00
ReducedGraphs
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
RGroupDecomposition
RGroupDecomposition restructuring (#3270)
2020-07-08 11:47:00 -04:00
ScaffoldNetwork
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
ShapeHelpers
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
SLNParse
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
SmilesParse
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
StructChecker
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Subgraphs
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Substruct
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
SubstructLibrary
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
TautomerQuery
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
test_data
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
Wrap
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
AddHs.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
AdjustQuery.cpp
Add cxsmiles query atoms to CTAB parsers and writers (#3261)
2020-07-03 12:51:19 -04:00
Aromaticity.cpp
Fixes #2895 (#2906)
2020-01-26 07:41:51 -05:00
Atom.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Atom.h
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
atomic_data.cpp
Fixes #2784 (#2787)
2019-11-15 07:53:42 -05:00
atomic_data.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
AtomIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
AtomIterators.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Bond.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Bond.h
Fixes #2450 (#2457)
2019-05-22 09:23:44 -04:00
BondIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
BondIterators.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
bulktest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Canon.cpp
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
Canon.h
Modernization: use nullptr (#3143)
2020-05-25 09:40:01 +02:00
catch_adjustquery.cpp
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
catch_graphmol.cpp
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
catch_main.cpp
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
catch_sgroups.cpp
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
Chirality.cpp
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
Chirality.h
Add new CIP labelling algorithm (#3234)
2020-07-07 20:34:33 +02:00
CMakeLists.txt
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
ConjugHybrid.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
Speed up ring finding by skipping nodes not in rings (#3254)
2020-06-26 05:42:34 +02:00
GraphMol.cpp
first pass, using google style
2015-11-14 14:58:11 +01:00
GraphMol.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
hanoitest.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Matrices.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
memtest1.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
MolBundle.h
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
MolDiscriminators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.h
Adds more options to adjustQueryProperties (#3235)
2020-06-22 09:17:50 -04:00
molopstest.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
MolPickler.cpp
Add cxsmiles query atoms to CTAB parsers and writers (#3261)
2020-07-03 12:51:19 -04:00
MolPickler.h
Add cxsmiles query atoms to CTAB parsers and writers (#3261)
2020-07-03 12:51:19 -04:00
MonomerInfo.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
new_canon.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
new_canon.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
PeriodicTable.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
PeriodicTable.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
QueryBond.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryBond.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
QueryOps.cpp
Add cxsmiles query atoms to CTAB parsers and writers (#3261)
2020-07-03 12:51:19 -04:00
QueryOps.h
Tautomer search (#3205)
2020-06-24 17:27:40 +02:00
querytest.cpp
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
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
Fixes #1735 (#1743)
2018-02-15 05:39:02 +01:00
resMolSupplierTest.cpp
- fixes GitHub #3048 (#3081)
2020-04-17 14:19:53 +02:00
Resonance.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Resonance.h
- fixes #3041 (#3045)
2020-04-01 10:00:22 +02:00
RingInfo.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
RingInfo.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
ROMol.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
RWMol.cpp
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
RWMol.h
Fixes #2144 (#2147)
2018-11-18 10:41:33 -05:00
SanitException.h
Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)
2020-04-01 14:30:07 +02:00
sanitTest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
StereoGroup.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
StereoGroup.h
clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190)
2020-05-28 09:07:58 +02:00
SubstanceGroup.cpp
Cleanup warnings from clang-10 (#3238)
2020-06-19 17:16:22 -04:00
SubstanceGroup.h
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
test1.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testMolBundle.cpp
Support enumerating some mol file features into MolBundles (#3257)
2020-07-11 12:54:23 +02:00
testPickler.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
testPicklerGlobalSettings.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
testSGroup.cpp
Allow SubstanceGroups to survive molecule edits (#3170)
2020-05-19 17:35:08 +02:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00