Greg Landrum 4f2ec84e7b Add some 3D molecular descriptors (#1084) ...

* update .gitignore

* foundation for 3D descriptors
move PBF into core

* cleanup work

* a bit more cleanup

* move the principal moments calc to MolTransforms

* cleanup

* cleanups

* add caching of the principal moments and values

* do not include the 3D descriptors in MolDescriptors.h

* the properties are computed

* add PMI descriptors and tests

* add tests for NPR descriptors

* return 0 when the largest PMI is zero

* PMI edge case tests

* NPR edge case tests

* PBF edge case tests

* PBF edge case tests

* more edge cases

* add a few more 3d descriptors

* add defns to docs

* tests for the new descriptors

* add versions to new descriptors

* add 3d descriptors to python wrapper

* add eigen support to the travis build

* try to get non-windows builds working

* remove computeCovarianceMatrix() from java wrapper

* make pmi property names "private"

2016-10-10 08:34:08 -04:00

..

Basement/FeatTrees

first pass, using google style

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

ChemReactions

Issue1071/yapf (#1078)

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

ChemTransforms

Issue1071/yapf (#1078)

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

Depictor

Issue1071/yapf (#1078)

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

Descriptors

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

DistGeomHelpers

Issue1071/yapf (#1078)

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

FileParsers

clear up a bunch of windows warnings (#1086)

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

FilterCatalog

clear up a bunch of windows warnings (#1086)

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

Fingerprints

clear up a bunch of windows warnings (#1086)

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

FMCS

Issue1071/yapf (#1078)

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

ForceFieldHelpers

Issue1071/yapf (#1078)

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

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

Issue1071/yapf (#1078)

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

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

Issue1071/yapf (#1078)

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

MolDrawing

first pass, using google style

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

MolHash

Issue1071/yapf (#1078)

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

MolTransforms

Add some 3D molecular descriptors (#1084)

2016-10-10 08:34:08 -04:00

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

Issue1071/yapf (#1078)

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

SmilesParse

Issue1071/yapf (#1078)

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

Subgraphs

Issue1071/yapf (#1078)

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

Substruct

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +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

Java wrappers for Trajectory/Snapshot objects (#977)

2016-07-20 22:51:01 -04:00

Wrap

Issue1071/yapf (#1078)

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

AddHs.cpp

Merge fix/github908 branch

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

AdjustQuery.cpp

Adds aromatization and reaction options to AdjustQuery (#965)

2016-06-29 05:09:30 +02:00

Aromaticity.cpp

Add support for a simplified aromaticity model. (#942)

2016-06-17 17:48:20 -04:00

Atom.cpp

Adds Atom atom map and rlabel apis (#1004)

2016-08-11 04:46:41 +02:00

Atom.h

Fixes #1041 (#1070)

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

atomic_data.cpp

Fixes #694

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

atomic_data.h

Fixes #694

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

AtomIterators.cpp

first pass, using google style

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

AtomIterators.h

first pass, using google style

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

Bond.cpp

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

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

Bond.h

Fixes #1041 (#1070)

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

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

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

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

Canon.h

first pass, using google style

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

Chirality.cpp

Fixes #607 (#1075)

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

Chirality.h

first pass, using google style

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

CMakeLists.txt

- removed the dependency on Trajectory from ROMol and ForceField

2016-05-11 19:37:09 +01:00

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

fixes #1023 (#1027)

2016-08-18 16:29:29 -04:00

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

first pass, using google style

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

itertest.cpp

first pass, using google style

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

Kekulize.cpp

Fixes #962 (#1003)

2016-08-05 07:57:20 -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

Adds aromatization and reaction options to AdjustQuery (#965)

2016-06-29 05:09:30 +02:00

molopstest.cpp

Fixes #607 (#1075)

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

MolPickler.cpp

Fixes #713

2015-12-22 07:18:35 +01:00

MolPickler.h

first pass, using google style

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

MonomerInfo.h

first pass, using google style

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

new_canon.cpp

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

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

new_canon.h

remove wave of warnings

2016-03-30 13:09:59 +02:00

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

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

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

QueryOps.h

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

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

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

first pass, using google style

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

Resonance.cpp

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

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

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

Adds Atom atom map and rlabel apis (#1004)

2016-08-11 04:46:41 +02:00

ROMol.h

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

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

RWMol.cpp

Bug when removing stereo info?

2016-06-20 16:40:33 +01:00

RWMol.h

Adds Atom atom map and rlabel apis (#1004)

2016-08-11 04:46:41 +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

Fixes #1041 (#1070)

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

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 #803

2016-03-09 05:05:33 +01:00

testPickler.cpp

add a test for #713

2015-12-23 05:31:37 +01:00

UnitTestQueryMol.py

Issue1071/yapf (#1078)

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