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ec74cd3761e31e82c6f808ebbaec1570064d48de
rdkit/Code/GraphMol
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Paolo Tosco ec74cd3761 Added OptimizeMoleculeConfs with pre-generated force-field (#2401) 
* - added two convenience functions to allow miniming all molecule confs with a pre-generated force-field (e.g., to use constraints)
- removed a lot of code duplication between Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h Code/GraphMol/ForceFieldHelpers/UFF/UFF.h
- homogenized the nonBondedThreshold to 100.0 across all MMFF functions

* - avoided code duplication
- added tests
- added PRECONDITION clauses
2019-05-19 15:34:06 +02:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Fixes #2427 (#2429)
2019-05-15 04:46:06 +02:00
ChemTransforms
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Depictor
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Descriptors
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
DistGeomHelpers
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
FileParsers
make this work when iostreams is being used
2019-05-09 08:12:19 +02:00
FilterCatalog
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Fingerprints
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
FMCS
A bit of not-particularly-related cleanup
2019-04-24 14:30:54 +02:00
ForceFieldHelpers
Added OptimizeMoleculeConfs with pre-generated force-field (#2401)
2019-05-19 15:34:06 +02:00
FragCatalog
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
libs
initial import
2006-05-06 22:20:08 +00:00
MMPA
Fixes #2437 (#2438)
2019-05-10 08:25:31 +02:00
MolAlign
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolCatalog
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolChemicalFeatures
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolDraw2D
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolHash
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolInterchange
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
MolStandardize
Fixes #2411 and #2414 (#2412)
2019-04-19 21:51:41 -04:00
MolTransforms
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
PartialCharges
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ReducedGraphs
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
RGroupDecomposition
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ShapeHelpers
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
SLNParse
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
SmilesParse
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
StructChecker
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Subgraphs
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Substruct
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
SubstructLibrary
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -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
Fixes #2441 (#2443)
2019-05-09 11:25:40 -04:00
AddHs.cpp
fixes #908 (#2328)
2019-03-10 21:43:20 -04:00
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
Fixes #2258 (#2286)
2019-02-22 07:30:31 -07:00
Atom.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
atomic_data.cpp
Add an allowed valence of 3 for Al (#2425)
2019-05-09 10:49:14 -04:00
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
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
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
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
Bond.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -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
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
Canon.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
catch_sgroups.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
catch_tests.cpp
Fixes #2437 (#2438)
2019-05-10 08:25:31 +02:00
Chirality.cpp
Fixes #2422
2019-04-26 16:43:35 +02:00
Chirality.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
CMakeLists.txt
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
Conformer.cpp
Merge branch 'master' into modern_cxx
2017-10-05 05:58:38 +02:00
Conformer.h
Fixes #2441 (#2443)
2019-05-09 11:25:40 -04:00
ConjugHybrid.cpp
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
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
Issue #2403: Speed up SSSR symmetrization (#2410)
2019-04-18 07:11:15 +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
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
Fixes #1703 (#1714)
2018-01-08 20:06:42 -05:00
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
correct mistake in halogen cleanup and add test cases, fix for #2020 (#2021)
2018-09-05 16:13:50 +02:00
MolOps.h
Allow components of the MolStandardize code to be initialized from streams (#2385)
2019-04-03 04:48:05 +02:00
molopstest.cpp
Issue #2403: Speed up SSSR symmetrization (#2410)
2019-04-18 07:11:15 +02:00
MolPickler.cpp
Fixes #2441 (#2443)
2019-05-09 11:25:40 -04:00
MolPickler.h
Fixes #2441 (#2443)
2019-05-09 11:25:40 -04:00
MonomerInfo.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
new_canon.cpp
Fixes #2437 (#2438)
2019-05-10 08:25:31 +02:00
new_canon.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
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
Fixes #2299 (#2300)
2019-03-01 13:22:01 -05:00
QueryAtom.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryBond.cpp
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
QueryBond.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryOps.cpp
Some optimization of the queries constructed from SMARTS (#1940)
2018-06-30 20:22:06 -04:00
QueryOps.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
querytest.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
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
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
Resonance.cpp
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
Resonance.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
RingInfo.cpp
a number of other small changes from manually reviewing the PR
2017-04-22 17:24:57 +02:00
RingInfo.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
Rings.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
ROMol.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
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
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
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
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
StereoGroup.h
add export flags for the MolStandardize library (#2072)
2018-09-29 07:43:07 +02:00
SubstanceGroup.cpp
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -04:00
SubstanceGroup.h
rename SGroup -> SubstanceGroup (#2375)
2019-03-30 14:53:24 -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
testCanon.cpp
Address compile warnings & trivial improvements (#2097)
2018-10-12 06:39:32 -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 #2441 (#2443)
2019-05-09 11:25:40 -04:00
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