rdkit

mirror of https://github.com/rdkit/rdkit.git synced 2026-06-07 22:44:25 +08:00

Files

Brian Kelley d8722b1c64 First entry of the SubstructLibrary module (#1493 )

* First entry of the SubstructLibrary module

* Switch to shared_ptrs for memory safety

* run clang-format and add a test

* only build when threadsafe_sss is enabled, only test when test_multithreaded is enabled

* Adds PRECONDITION

* Adds exceptions for out of range errors

* Changes getQueryBits to makeQueryBits for clarity

* Adds API point to add Binary and Smiles directly

* Replaces 0 with NULL for clarity.

* Removes debugging code.

* Makes endIdx non-inclusive

* Adds substruct searching options

* Adds preconditions

* Small documentation cleanup and removes a line of code.

* Add DataStructs library dependency

* Actually uses passed in parameters

* Adds TrustedSmiles/Binary inputs

* Adds more api testing options/trusted smiles and binary inputs

* Finalizes API adds docs and doctests

* Minor copyright fixes and such

2017-07-19 10:39:42 +02:00

Basement/FeatTrees

first pass, using google style

2015-11-14 14:58:11 +01:00

ChemReactions

Fixes sanitizereaction throwing errors with unused rlabels in product template (#1451 )

2017-06-14 04:58:50 +02:00

ChemTransforms

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

Depictor

Support drawing reactions from C++ (#1444 )

2017-07-05 14:25:31 -04:00

Descriptors

assorted fixes to get the current master branch to build on Windows (#1495 )

2017-07-18 08:04:23 +02:00

DistGeomHelpers

Fix github1240 (#1396 )

2017-04-18 02:33:23 -04:00

FileParsers

Fixes lookup for HELM Monomer 'D' (#1477 )

2017-06-29 18:00:15 +02:00

FilterCatalog

fixes #1435 (#1437 )

2017-05-31 08:29:32 +02:00

Fingerprints

modify pattern fp order; update expected psql results (#1399 )

2017-04-19 11:57:48 -04:00

FMCS

Add the option to match formal charges to FMCS (#1311 )

2017-02-28 08:49:28 -05:00

ForceFieldHelpers

- Optimization of UFF and MMFF forcefields (#1218 )

2017-01-04 08:33:34 +01:00

FragCatalog

clear up a bunch of windows warnings (#1086 )

2016-10-04 06:46:07 -04:00

libs

initial import

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

MMPA

Dev/rdmmpa api update (#1291 )

2017-02-27 17:08:01 +01:00

MolAlign

Issue1071/yapf (#1078 )

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

MolCatalog

Issue1071/yapf (#1078 )

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

MolChemicalFeatures

Issue1071/yapf (#1078 )

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

MolDraw2D

assorted fixes to get the current master branch to build on Windows (#1495 )

2017-07-18 08:04:23 +02:00

MolDrawing

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

MolHash

Issue1071/yapf (#1078 )

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

MolTransforms

Fix/github1262 (#1265 )

2017-01-22 05:49:52 +01:00

PartialCharges

Issue1071/yapf (#1078 )

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

ReducedGraphs

Issue1071/yapf (#1078 )

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

ShapeHelpers

Issue1071/yapf (#1078 )

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

SLNParse

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

SmilesParse

Fixes #1472 (#1473 )

2017-06-29 20:51:44 -04:00

StructChecker

replace std::map::at with std::map::find

2016-11-14 16:17:38 +00:00

Subgraphs

Issue1071/yapf (#1078 )

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

Substruct

Add cis/trans tags to double bonds (#1316 )

2017-02-26 08:15:44 -05:00

SubstructLibrary

First entry of the SubstructLibrary module (#1493 )

2017-07-19 10:39:42 +02:00

test_data

Fixes #607 (#1075 )

2016-09-23 04:57:07 +02:00

testExecs

initial import

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

Trajectory

Fix trajectory tests

2016-11-15 13:47:52 +00:00

Wrap

assorted fixes to get the current master branch to build on Windows (#1495 )

2017-07-18 08:04:23 +02:00

AddHs.cpp

Merge fix/github908 branch

2016-07-27 04:49:55 +02:00

AdjustQuery.cpp

Dev/add update props api (#1479 )

2017-07-10 04:36:12 +02:00

Aromaticity.cpp

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

Atom.cpp

Fixes #1387 (#1392 )

2017-04-07 11:57:43 -04:00

Atom.h

Fixes #1041 (#1070 )

2016-09-22 14:38:13 +02:00

atomic_data.cpp

Fixes #1204 (#1212 )

2016-12-19 12:50:28 -05:00

atomic_data.h

Fixes #694

2016-02-16 15:38:02 +01:00

AtomIterators.cpp

Fix/github1366 (#1382 )

2017-03-28 16:01:36 -04:00

AtomIterators.h

Fix/github1366 (#1382 )

2017-03-28 16:01:36 -04:00

Bond.cpp

Add cis/trans tags to double bonds (#1316 )

2017-02-26 08:15:44 -05:00

Bond.h

Add cis/trans tags to double bonds (#1316 )

2017-02-26 08:15:44 -05:00

BondIterators.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

BondIterators.h

first pass, using google style

2015-11-14 14:58:11 +01:00

bulktest.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

Canon.cpp

Add cis/trans tags to double bonds (#1316 )

2017-02-26 08:15:44 -05:00

Canon.h

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

Chirality.cpp

Fixes #1423 (#1424 )

2017-06-03 09:32:07 -04:00

Chirality.h

first pass, using google style

2015-11-14 14:58:11 +01:00

CMakeLists.txt

First entry of the SubstructLibrary module (#1493 )

2017-07-19 10:39:42 +02:00

Conformer.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

Conformer.h

Fixes missing rdcast (caused infinite recursion)

2015-11-29 20:33:09 -05:00

ConjugHybrid.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

cptest.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

details.h

first pass, using google style

2015-11-14 14:58:11 +01:00

FindRings.cpp

SSSR performance improvements to support larger systems (#1131 )

2016-10-29 04:38:14 +02:00

GraphMol.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

GraphMol.h

first pass, using google style

2015-11-14 14:58:11 +01:00

hanoitest.cpp

Fixes #1423 (#1424 )

2017-06-03 09:32:07 -04:00

itertest.cpp

Fix/github1366 (#1382 )

2017-03-28 16:01:36 -04:00

Kekulize.cpp

Fix for #1478 (#1486 )

2017-07-01 09:03:26 -04:00

Matrices.cpp

Addressed code review suggestions

2016-02-09 09:21:48 +02:00

memtest1.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

MolDiscriminators.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896 )

2016-05-29 17:04:21 +01:00

MolOps.cpp

make the perchlorate cleanup pattern more generic to cover all halogenates;

2016-04-01 07:54:32 +02:00

MolOps.h

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

molopstest.cpp

Dev/add update props api (#1479 )

2017-07-10 04:36:12 +02:00

MolPickler.cpp

Dev/pickle properties (#1277 )

2017-02-09 16:06:01 +01:00

MolPickler.h

Fixes #1388 (#1389 )

2017-04-01 08:13:52 -04:00

MonomerInfo.h

first pass, using google style

2015-11-14 14:58:11 +01:00

new_canon.cpp

Add cis/trans tags to double bonds (#1316 )

2017-02-26 08:15:44 -05:00

new_canon.h

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

PeriodicTable.cpp

Fixes #381 (#924 )

2016-05-30 19:58:39 -04:00

PeriodicTable.h

Fixes #381 (#924 )

2016-05-30 19:58:39 -04:00

QueryAtom.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

QueryAtom.h

first pass, using google style

2015-11-14 14:58:11 +01:00

QueryBond.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896 )

2016-05-29 17:04:21 +01:00

QueryBond.h

first pass, using google style

2015-11-14 14:58:11 +01:00

QueryOps.cpp

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

QueryOps.h

Partial support for reading CXSMILES (#1237 )

2017-01-31 13:50:36 -05:00

querytest.cpp

Adds some additional canned atom and bond query definitions (#1047 )

2016-09-09 10:31:02 -04:00

RDKitBase.h

update copyright statements

2010-09-26 17:04:37 +00:00

RDKitQueries.h

first pass, using google style

2015-11-14 14:58:11 +01:00

regress.txt

initial import

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

Renumber.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

resMolSupplierTest.cpp

Fixes #1162 (resMolSupplierTest failing with boost 1.62) (#1166 )

2016-11-30 14:15:22 +01:00

Resonance.cpp

Fixes #1162 (resMolSupplierTest failing with boost 1.62) (#1166 )

2016-11-30 14:15:22 +01:00

Resonance.h

- fixed a couple of compilation warnings in Resonance.cpp/Resonance.h

2015-12-16 17:33:22 +00:00

RingInfo.cpp

Adds rdcasts where appropriate

2015-11-29 17:52:27 -05:00

RingInfo.h

first pass, using google style

2015-11-14 14:58:11 +01:00

Rings.h

first pass, using google style

2015-11-14 14:58:11 +01:00

ROMol.cpp

Removes exponetial numBonds behavior (#1154 )

2016-11-12 16:05:06 +01:00

ROMol.h

Removes exponetial numBonds behavior (#1154 )

2016-11-12 16:05:06 +01:00

RWMol.cpp

Dev/add update props api (#1479 )

2017-07-10 04:36:12 +02:00

RWMol.h

Dev/add update props api (#1479 )

2017-07-10 04:36:12 +02:00

SanitException.h

first pass, using google style

2015-11-14 14:58:11 +01:00

sanitTest.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

test1.cpp

Fix/github1453 (#1463 )

2017-06-28 09:31:58 -04:00

test_list.py

Issue1071/yapf (#1078 )

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

testCanon.cpp

first pass, using google style

2015-11-14 14:58:11 +01:00

testChirality.cpp

Fixes #1423 (#1424 )

2017-06-03 09:32:07 -04:00

testPickler.cpp

Dev/pickle properties (#1277 )

2017-02-09 16:06:01 +01:00

testPicklerGlobalSettings.cpp

Dev/pickle properties (#1277 )

2017-02-09 16:06:01 +01:00

UnitTestQueryMol.py

Issue1071/yapf (#1078 )

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