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1d018746787421c6dd7b2c38844ec599270dffdf
rdkit/Code/GraphMol
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Greg Landrum 1d01874678 improvements to the Uncharge functionality (#2374) 
* modify the uncharger to be use a canonical atom ordering

* add doCanonical cleanup parameter
make canonical ordering the default
document the change

* Add neutralization of additonal negative groups (not just acids).
This may not be the right thing to do.

* expose the new parameter to python

* changes in response to review
2019-03-29 21:02:55 -04:00
..
Basement/FeatTrees
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
ChemReactions
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
ChemTransforms
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
Depictor
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
Descriptors
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
DistGeomHelpers
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
FileParsers
#2329 wrap detect atom stereochemistry (#2351)
2019-03-19 10:54:28 +01:00
FilterCatalog
Patch/pains updates (#2272)
2019-03-18 13:42:31 -04:00
Fingerprints
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
FMCS
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
ForceFieldHelpers
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
FragCatalog
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
libs
initial import
2006-05-06 22:20:08 +00:00
MMPA
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
MolAlign
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
MolCatalog
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
MolChemicalFeatures
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
MolDraw2D
Exposes substructlibrary to swig (#2337)
2019-03-12 16:35:22 +01:00
MolHash
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
MolInterchange
Address compile warnings & trivial improvements (#2097)
2018-10-12 06:39:32 -04:00
MolStandardize
improvements to the Uncharge functionality (#2374)
2019-03-29 21:02:55 -04:00
MolTransforms
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
PartialCharges
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
ReducedGraphs
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
RGroupDecomposition
fixes an r-group symmetrization problem (#2324)
2019-03-08 09:11:15 -05:00
ShapeHelpers
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00
SLNParse
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
SmilesParse
- small fixes to get DLLs to build on Windows (#2356)
2019-03-18 05:33:39 +01:00
StructChecker
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
Subgraphs
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
Substruct
Add options for substructure searching (#2254)
2019-02-08 09:10:10 -05:00
SubstructLibrary
- small fixes to get DLLs to build on Windows (#2356)
2019-03-18 05:33:39 +01:00
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
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
Wrap
#2329 wrap detect atom stereochemistry (#2351)
2019-03-19 10:54:28 +01:00
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
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
atomic_data.cpp
Fixes #1668 (#1669)
2017-12-21 05:45:24 +01:00
atomic_data.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
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
Fixes #1903 (#1971)
2018-07-25 09:14:17 +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
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
2018-01-07 14:19:47 -05:00
Bond.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
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
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
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
Fix #2042 allowing python/c++ randomizer smiles generator (#2059)
2018-10-08 11:09:42 +02:00
catch_sgroups.cpp
Support for parsing/writing SGroups in SD Mol files. (#2138)
2019-01-22 15:42:27 +01:00
catch_tests.cpp
fixes #908 (#2328)
2019-03-10 21:43:20 -04:00
Chirality.cpp
Removes an extra debugging cerr statment (#2360)
2019-03-22 15:50:04 +01:00
Chirality.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
CMakeLists.txt
Support for parsing/writing SGroups in SD Mol files. (#2138)
2019-01-22 15:42:27 +01:00
Conformer.cpp
Merge branch 'master' into modern_cxx
2017-10-05 05:58:38 +02:00
Conformer.h
Fix 2D/3D interpretation of V2000 ctabs (#2083)
2018-10-03 21:05:33 +02:00
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
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +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
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
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
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
#2329 wrap detect atom stereochemistry (#2351)
2019-03-19 10:54:28 +01:00
molopstest.cpp
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
MolPickler.cpp
[WIP] property custom handlers (#2293)
2019-03-28 17:21:00 +01:00
MolPickler.h
[WIP] property custom handlers (#2293)
2019-03-28 17:21:00 +01:00
MonomerInfo.h
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
new_canon.cpp
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
new_canon.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
PeriodicTable.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
PeriodicTable.h
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
QueryAtom.cpp
Fixes #2299 (#2300)
2019-03-01 13:22:01 -05:00
QueryAtom.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
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
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
QueryOps.cpp
Some optimization of the queries constructed from SMARTS (#1940)
2018-06-30 20:22:06 -04:00
QueryOps.h
Build warnings revisited (#2318)
2019-03-08 16:42:54 +01:00
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
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
RingInfo.cpp
a number of other small changes from manually reviewing the PR
2017-04-22 17:24:57 +02:00
RingInfo.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
Rings.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
ROMol.cpp
Support for parsing/writing SGroups in SD Mol files. (#2138)
2019-01-22 15:42:27 +01:00
ROMol.h
Added exports (#2242)
2019-01-25 04:38:13 +01:00
RWMol.cpp
Support for parsing/writing SGroups in SD Mol files. (#2138)
2019-01-22 15:42:27 +01:00
RWMol.h
Fixes #2144 (#2147)
2018-11-18 10:41:33 -05:00
SanitException.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
sanitTest.cpp
moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)
2018-10-11 17:35:23 -04:00
Sgroup.cpp
Support for parsing/writing SGroups in SD Mol files. (#2138)
2019-01-22 15:42:27 +01:00
Sgroup.h
Add a read-only Python wrapper for SGroups (#2343)
2019-03-15 08:50:32 -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
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 #2266 (#2269)
2019-02-15 10:35:09 -05:00
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
[WIP] property custom handlers (#2293)
2019-03-28 17:21:00 +01:00
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
Add a read-only Python wrapper for SGroups (#2343)
2019-03-15 08:50:32 -04:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00