pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-06 22:39:55 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
acdfe26dea13a592b804fabb2cd6859e759cf79a
rdkit/Code/GraphMol
History
hjuinj acdfe26dea Improve Conformational Sampling of Small and Large Ring Molecules (#2999) 
* improvements for smal anr large ring conformer generation

* add documentation and reorder parameters in EmbedParam

* resolve merge conflict due to coordMap null pointer

* minor changes to address merge comments

* reorder variables in EmbedParameters

* add regression test for small ring and macrocycle torsion preferences

* not apply small ring torsions to bridged ring systems

* fix and test for bridged small rings torsion pattern exclusion

* add ETKDGv3 and srETKDGv3 option to keep compatiblity for original ETKDG

* EKTDG version 3 related minor fix

* add reference to doc string

* Java wrapper for ETKDGv3

* fix doc

* change CPCI to shared_ptr, but it seems to be much slower

* minor modifications to small bridged ring systems, and share_ptr from previous commit is fine

* rollback from shared_ptr(map) to just map

* run clang-format

Co-authored-by: Shuzhe Wang <shuwang@eu-login-10.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-14.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-17.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-45.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-05.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-15.euler.ethz.ch>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
2020-03-23 14:57:46 +01:00
..
Basement/FeatTrees
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
ChemReactions
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
ChemTransforms
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Depictor
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
Descriptors
Remove unnecessary files (#3012)
2020-03-17 13:51:46 +01:00
DistGeomHelpers
Improve Conformational Sampling of Small and Large Ring Molecules (#2999)
2020-03-23 14:57:46 +01:00
FileParsers
remove accidental commits
2020-03-21 14:12:12 +01:00
FilterCatalog
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Fingerprints
Merge branch 'master' of https://github.com/daenuprobst/rdkit into daenuprobst-master
2020-03-21 14:11:22 +01:00
FMCS
Added support for Python FMCS functors (#3023)
2020-03-23 11:20:57 +01:00
ForceFieldHelpers
Improve Conformational Sampling of Small and Large Ring Molecules (#2999)
2020-03-23 14:57:46 +01:00
FragCatalog
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolAlign
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
MolCatalog
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolChemicalFeatures
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
MolDraw2D
fixes DLL build failure (#3025)
2020-03-23 10:03:36 +01:00
MolHash
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolInterchange
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolStandardize
Fixes #2990 (#3016)
2020-03-22 04:58:01 +01:00
MolTransforms
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
PartialCharges
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
ReducedGraphs
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
RGroupDecomposition
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
ScaffoldNetwork
ScaffoldNetwork rearrangements (#2985)
2020-03-06 13:51:38 +01:00
ShapeHelpers
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
SLNParse
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
SmilesParse
adds a one-liner for getting a vector of random smiles for a molecule (#3002)
2020-03-12 13:10:29 -04:00
StructChecker
Remove unnecessary files (#3012)
2020-03-17 13:51:46 +01:00
Subgraphs
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Substruct
Allow enhanced stereo to be used in substructure search (#3003)
2020-03-21 05:12:40 +01:00
SubstructLibrary
Add multithreaded pattern/fp generator (#2973)
2020-03-04 09:41:03 -05:00
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
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
Wrap
Added support for Python FMCS functors (#3023)
2020-03-23 11:20:57 +01:00
AddHs.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
AdjustQuery.cpp
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
Aromaticity.cpp
Fixes #2895 (#2906)
2020-01-26 07:41:51 -05:00
Atom.cpp
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
Atom.h
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Bond.h
Fixes #2450 (#2457)
2019-05-22 09:23:44 -04:00
BondIterators.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
adds a one-liner for getting a vector of random smiles for a molecule (#3002)
2020-03-12 13:10:29 -04:00
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_graphmol.cpp
Address issue #2890 (#3015)
2020-03-21 14:01:54 +01:00
catch_main.cpp
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
catch_sgroups.cpp
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
Chirality.cpp
Address issue #2890 (#3015)
2020-03-21 14:01:54 +01:00
Chirality.h
Assign stereo bond labels in molecules read from SMARTS (#2623)
2019-08-23 14:07:46 -07:00
CMakeLists.txt
Add a scaffold network implementation (#2911)
2020-02-11 08:21:01 -05:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
ConjugHybrid.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
cptest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
Remove bogus URFLib library (#2900)
2020-01-28 08:52:58 -05:00
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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
itertest.cpp
Fix (most of) mem problems (#2123)
2018-10-29 14:33:26 +00:00
Kekulize.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Matrices.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolOps.h
Parse and handle the stereoCare or STBOX flags in CTABs (#2917)
2020-02-03 15:55:57 -05:00
molopstest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
MolPickler.cpp
Fixes #2510 (#2907)
2020-01-28 05:07:31 +01:00
MolPickler.h
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
MonomerInfo.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
new_canon.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
new_canon.h
Code cleanups from PVS/Studio (#2531)
2019-07-13 07:25:37 +02:00
PeriodicTable.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
PeriodicTable.h
clang-tidy-7 pass (#2408)
2019-04-16 12:05:47 -04:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryBond.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryBond.h
Removal of redundant wildcards in SMARTS (Null Atom/Bond Query combination) (#2595)
2019-08-15 14:37:17 +02:00
QueryOps.cpp
Enable larger ring matches in SMARTS expressions (#2981)
2020-03-07 15:09:38 +01:00
QueryOps.h
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
querytest.cpp
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
2020-01-29 15:13:39 +01:00
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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Resonance.cpp
Fix a couple residual problems created by #2899 (#2935)
2020-02-05 16:32:08 +01:00
Resonance.h
Fix typo [ci skip]
2019-10-17 17:45:50 +09:00
RingInfo.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
ROMol.h
Fix typo [ci skip]
2019-10-17 17:45:50 +09:00
RWMol.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
RWMol.h
Fixes #2144 (#2147)
2018-11-18 10:41:33 -05:00
SanitException.h
Override what() in exceptions (Addresses #2920) (#2928)
2020-02-05 08:20:17 +01:00
sanitTest.cpp
Do not catch exceptions by value
2019-10-10 20:22:17 +09:00
StereoGroup.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
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
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +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 #2510 (#2907)
2020-01-28 05:07:31 +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
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