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5dfd67a22a0405eb62c3f7589a976107700fdfd2
rdkit/Code/GraphMol
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Greg Landrum 5dfd67a22a Add new mol hashing code (#2636) 
* copy in, get building, add some basic tests

* complete the testing
Except for regiosiomers, which do not work

* regioisomers work now

* backup commit; things work

* remove last of NM macros from hashfunctions.cpp

* remove last of NM macros from hashfunctions.cpp

* remove dependency on the abstraction layer

* typo

* start using namespaces
clang-format

* switch to using enums for the HashFunctions and StripTypes

* Add initial python wrapper (and tests)

* move the new hashing code to the MolHash library

still may want to revise the naming of this

* Setup deprecation of the older hashing code

* better release notes text

* change in response to review
2019-09-24 07:55:21 -04:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Assign stereo bond labels in molecules read from SMARTS (#2623)
2019-08-23 14:07:46 -07:00
ChemTransforms
Preserve bond direction in fragmentOnBonds (#2484)
2019-06-10 13:08:50 -04:00
Depictor
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
Descriptors
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
DistGeomHelpers
Allow providing a bounds matrix to EmbedMol (#2560)
2019-07-30 06:43:42 -04:00
FileParsers
Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646)
2019-09-20 09:13:19 -04:00
FilterCatalog
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
Fingerprints
Fixes #2614 (#2616)
2019-08-19 12:42:40 -04:00
FMCS
Remove arbitrary lower bound on the number of steps. [closes #2581] (#2583)
2019-08-06 16:31:17 +02:00
ForceFieldHelpers
Fix/mmff threadsafety issues (#2518)
2019-07-12 06:45:47 +02:00
FragCatalog
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
libs
initial import
2006-05-06 22:20:08 +00:00
MMPA
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
MolAlign
Branch/vf2 optimisations (#2500)
2019-06-30 04:49:24 +02:00
MolCatalog
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
MolChemicalFeatures
Fixes #2603 (#2613)
2019-08-19 13:43:11 -04:00
MolDraw2D
draw zero-order bonds (#2630)
2019-08-28 18:11:12 -04:00
MolHash
Add new mol hashing code (#2636)
2019-09-24 07:55:21 -04:00
MolInterchange
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
MolStandardize
optimization of the MolStandardize code (#2621)
2019-08-28 18:08:29 -04:00
MolTransforms
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
PartialCharges
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
ReducedGraphs
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
RGroupDecomposition
Dev/rgroup handle ties in symmetry matching (#2628)
2019-09-11 16:15:14 -04:00
ShapeHelpers
Branch/vf2 optimisations (#2500)
2019-06-30 04:49:24 +02:00
SLNParse
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
SmilesParse
Assign stereo bond labels in molecules read from SMARTS (#2623)
2019-08-23 14:07:46 -07:00
StructChecker
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
Subgraphs
Fixes #2647 (#2651)
2019-09-23 18:14:50 +02:00
Substruct
E/Z and CIS/TRANS stereo bonds are incorrectly matched (#2596)
2019-08-21 16:35:35 +02:00
SubstructLibrary
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
test_data
Fixes #2224 (#2234)
2019-01-21 11:31:02 -05:00
testExecs
initial import
2006-05-06 22:20:08 +00:00
Trajectory
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Wrap
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
AddHs.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
AdjustQuery.cpp
Fixes #1943 (#1954)
2018-07-16 10:27:08 -04:00
Aromaticity.cpp
Fix github1928 (#1946)
2018-07-14 12:32:38 -04:00
Atom.cpp
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
Atom.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
atomic_data.cpp
A collection of bug fixes (#2608)
2019-08-15 04:53:23 +02:00
atomic_data.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
AtomIterators.cpp
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
AtomIterators.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
blah
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
blah.hpp
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
Bond.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
Bond.h
Fixes #2450 (#2457)
2019-05-22 09:23:44 -04:00
BondIterators.cpp
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
BondIterators.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
bulktest.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
Canon.cpp
Use the same criteria to flip chiral atoms in SMILES parsing/writing (Fixes #1028) (#2600)
2019-08-15 07:47:27 +02:00
Canon.h
Use the same criteria to flip chiral atoms in SMILES parsing/writing (Fixes #1028) (#2600)
2019-08-15 07:47:27 +02:00
catch_sgroups.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
catch_tests.cpp
Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646)
2019-09-20 09:13:19 -04:00
Chirality.cpp
Fixes: Atoms in non-standard valences not being properly written to mol blocks (#2646)
2019-09-20 09:13:19 -04:00
Chirality.h
Assign stereo bond labels in molecules read from SMARTS (#2623)
2019-08-23 14:07:46 -07:00
CMakeLists.txt
Add new mol hashing code (#2636)
2019-09-24 07:55:21 -04:00
Conformer.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
Conformer.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
ConjugHybrid.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
cptest.cpp
Fixes #2144 (#2147)
2018-11-18 10:41:33 -05:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
Add new mol hashing code (#2636)
2019-09-24 07:55:21 -04:00
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
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
itertest.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
Kekulize.cpp
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
Matrices.cpp
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
memtest1.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
MolBundle.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolDiscriminators.cpp
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
MolOps.cpp
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
MolOps.h
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
molopstest.cpp
Integrate Unique Ring Families from RingDecomposerLib (#2558)
2019-07-30 06:41:55 -04:00
MolPickler.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
MolPickler.h
Fixes #2441 (#2443)
2019-05-09 11:25:40 -04:00
MonomerInfo.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
new_canon.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
new_canon.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
PeriodicTable.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
PeriodicTable.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryAtom.cpp
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryAtom.h
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryBond.cpp
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryBond.h
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryOps.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
QueryOps.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
querytest.cpp
Fix/rgroup sdf isotope (#2449)
2019-06-04 15:41:20 +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
initial import
2006-05-06 22:20:08 +00:00
Renumber.cpp
Fixes #1735 (#1743)
2018-02-15 05:39:02 +01:00
resMolSupplierTest.cpp
- fixes ResonanceMolSupplier bug in perceiving conjugated groups (#2517)
2019-07-23 08:03:24 -04:00
Resonance.cpp
- fixes ResonanceMolSupplier bug in perceiving conjugated groups (#2517)
2019-07-23 08:03:24 -04:00
Resonance.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
RingInfo.cpp
Integrate Unique Ring Families from RingDecomposerLib (#2558)
2019-07-30 06:41:55 -04:00
RingInfo.h
Integrate Unique Ring Families from RingDecomposerLib (#2558)
2019-07-30 06:41:55 -04:00
Rings.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
ROMol.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
ROMol.h
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
RWMol.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
RWMol.h
Fixes #2144 (#2147)
2018-11-18 10:41:33 -05:00
SanitException.h
Allow identification of chemistry problems (#2587)
2019-08-28 14:15:55 -07:00
sanitTest.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
StereoGroup.cpp
Python wrap enhanced stereo setters (#2509)
2019-07-03 10:24:26 +02:00
StereoGroup.h
Python wrap enhanced stereo setters (#2509)
2019-07-03 10:24:26 +02:00
SubstanceGroup.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
SubstanceGroup.h
Fixes #2450 (#2457)
2019-05-22 09:23:44 -04:00
test1.cpp
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
test_list.py
Issue1071/yapf (#1078)
2016-09-23 04:58:46 +02:00
test-valgrind.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
testChirality.cpp
Fixes #2422
2019-04-26 16:43:35 +02:00
testMolBundle.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
testPickler.cpp
Fixes #2466 and #2465 (#2467)
2019-05-30 18:45:57 +02:00
testPicklerGlobalSettings.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
testSGroup.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00