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a75018fe385b0a36901bcb074ebbca0c4e84a9d5
rdkit/Code/GraphMol
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Greg Landrum a75018fe38 Cleanups and additional tests to improve test coverage (#2852) 
* disable builds of the StructChecker code by default

* operator"" _smarts() doesn't need to catch sanitization errors

* remove unused function

* turn back on some tests that shouldn't have been disabled

* Remove unused code from SMARTS parser and simplify a bit

SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API

* Removes obsolete special case code for SMARTS

This was relevant when organic atoms in SMARTS queries were stored as two-part queries.

* improve SMARTS testing

make sure we can generate SMARTS from all the examples and then parse that again.

* Fixes #2814

* Fixes #2815

* some additional smarts tests to improve coverage

* test copy ctor and getPos

* remove obsolete test_list files

* include tests for the morgan invariant generators

* more cleanups and coverage improvements

* remove files that were mistakenly added
2020-01-09 16:07:55 -05:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
ChemTransforms
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
Depictor
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
Descriptors
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
DistGeomHelpers
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
FileParsers
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
FilterCatalog
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
Fingerprints
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
FMCS
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ForceFieldHelpers
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
FragCatalog
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
MolAlign
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
MolCatalog
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
MolChemicalFeatures
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
MolDraw2D
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
MolHash
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
MolInterchange
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
MolStandardize
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
MolTransforms
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
PartialCharges
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
ReducedGraphs
Fixes #2516 (#2519)
2019-06-28 09:57:00 -04:00
RGroupDecomposition
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ShapeHelpers
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
SLNParse
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
SmilesParse
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
StructChecker
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
Subgraphs
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
Substruct
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
SubstructLibrary
Expose SubstructLibrary serialization stream (#2853)
2020-01-08 07:44:37 +01:00
test_data
fix start/end atoms when wedging bonds (#2861)
2019-12-27 07:21:49 -05:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Wrap
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
AddHs.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
AdjustQuery.cpp
Fixes #1943 (#1954)
2018-07-16 10:27:08 -04:00
Aromaticity.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
Atom.cpp
Fixes #2775 (#2776)
2019-11-14 16:58:30 +01:00
Atom.h
Fix typo (#2862)
2019-12-31 06:43:27 +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
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
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
blah.hpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
Bond.cpp
Cleanup some unintended consequences of #2553 (#2735)
2019-10-25 04:31:06 +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
Fix some chirality issues in SMARTS writing/parsing (Issues #2565 & #2568) (#2570)
2019-10-03 15:33:46 +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 #2782 (#2783)
2019-11-15 16:46:55 +01:00
Chirality.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
Chirality.h
Assign stereo bond labels in molecules read from SMARTS (#2623)
2019-08-23 14:07:46 -07:00
CMakeLists.txt
Cleanups and additional tests to improve test coverage (#2852)
2020-01-09 16:07:55 -05:00
Conformer.cpp
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
Conformer.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ConjugHybrid.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
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
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
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
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
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
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
MolOps.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
molopstest.cpp
Integrate Unique Ring Families from RingDecomposerLib (#2558)
2019-07-30 06:41:55 -04:00
MolPickler.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
MolPickler.h
Tidy Up (#2834)
2019-12-18 16:44:55 +01:00
MonomerInfo.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
new_canon.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
new_canon.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
PeriodicTable.cpp
Fixes #2784 (#2787)
2019-11-15 07:53:42 -05:00
PeriodicTable.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryAtom.cpp
Fixes #2604 (#2689)
2019-10-13 09:33:10 -04:00
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
Fixes #2604 (#2689)
2019-10-13 09:33:10 -04:00
QueryOps.h
merge
2019-10-25 04:48:08 +02:00
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
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 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
Fix typo [ci skip]
2019-10-17 17:45:50 +09:00
RingInfo.cpp
Use query molecule rather than ambiguous SMARTS for MCS matching (#2759)
2019-12-16 04:57:54 +01:00
RingInfo.h
Use query molecule rather than ambiguous SMARTS for MCS matching (#2759)
2019-12-16 04:57:54 +01:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.h
Fix typo [ci skip]
2019-10-17 17:45:50 +09:00
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
Tidy Up (#2834)
2019-12-18 16:44:55 +01:00
sanitTest.cpp
Do not catch exceptions by value
2019-10-10 20:22:17 +09:00
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
[WIP] Make StructureGroups editable from Python (#2692)
2019-10-15 22:32:26 -04:00
test1.cpp
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
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
Resolves #2823 (#2863)
2019-12-29 06:25:52 +01:00
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