Greg Landrum a102eaf932 Add options for substructure searching (#2254) ...

* first pass at adding a SubstructMatchParameter struct

* start moving the rest of the backend to use the parameters

* backend at least mostly moved over

* add aromaticMatchesConjugated
add tests

* switch over the MolBundle too
Add templates to reduce duplicated code

* support older compilers

let's see if it works...

* add SubstructMatchParameters to Python wrapper

* remove some deprecations and warnings

* damn compilers

* parameter support for bundles in python wrapper

* add the parameters to the java wrappers

* response to review

2019-02-08 09:10:10 -05:00

..

Basement/FeatTrees

moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)

2018-10-11 17:35:23 -04:00

ChemReactions

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

ChemTransforms

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

Depictor

Update build rules for coorgen & maeparser (#2184)

2019-01-06 06:28:00 +00:00

Descriptors

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

DistGeomHelpers

Fixes #2246 (#2248)

2019-02-04 10:32:33 -05:00

FileParsers

Fixes #2245 (#2250)

2019-01-31 00:03:39 -05:00

FilterCatalog

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

Fingerprints

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

FMCS

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

ForceFieldHelpers

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

FragCatalog

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

libs

initial import

2006-05-06 22:20:08 +00:00

MMPA

Rename the #define _DEBUG to MMPA_DEBUG as _DEBUG is defined bu MSVC whenever a Debug build is specifed, but that is not the intention here. (#2140)

2018-11-15 07:47:13 +01:00

MolAlign

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

MolCatalog

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

MolChemicalFeatures

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

MolDraw2D

Fixes #2220 (#2221)

2019-01-14 12:58:50 -05:00

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

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

MolTransforms

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

PartialCharges

moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074)

2018-10-11 17:35:23 -04:00

ReducedGraphs

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

RGroupDecomposition

RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups (#2202)

2019-01-02 17:57:34 +00:00

ShapeHelpers

ShapeTverskyIndex python function (#2156)

2018-11-08 07:42:10 -06:00

SLNParse

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

SmilesParse

Fix #2197 and #2237 (#2238)

2019-01-24 15:20:08 -05:00

StructChecker

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

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

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

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

Add options for substructure searching (#2254)

2019-02-08 09:10:10 -05:00

AddHs.cpp

Fixes #2224 (#2234)

2019-01-21 11:31:02 -05:00

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

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

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 #2224 (#2234)

2019-01-21 11:31:02 -05:00

Chirality.cpp

Fixes #1850 (#2087)

2018-10-04 08:29:50 -04:00

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

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

molopstest.cpp

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

MolPickler.cpp

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

MolPickler.h

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +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

Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)

2018-01-07 14:19:47 -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

Address compile warnings & trivial improvements (#2097)

2018-10-12 06:39:32 -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

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

Added exports (#2242)

2019-01-25 04:38:13 +01:00

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

Fix #2225 (#2228)

2019-01-17 11:44:23 -05:00

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

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

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

Fix (most of) mem problems (#2123)

2018-10-29 14:33:26 +00:00

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

Support for parsing/writing SGroups in SD Mol files. (#2138)

2019-01-22 15:42:27 +01:00

UnitTestQueryMol.py

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +02:00