Greg Landrum 29c10590b4 change the ring-invariant computation scheme: ...

The original version using products of primes broke down for proteins (or things with
  large numbers of atoms) since collisions were quite possible.
  Switched to using a hashing scheme; collisions are also possible here, but are even
  less likely.

2010-08-14 06:21:47 +00:00

..

Basement/FeatTrees

this is a mass of cleanup stuff; mostly line endings

2008-07-07 13:21:24 +00:00

ChemReactions

improve depiction quality by (optionally) doing a bit of chemistry perception

2010-06-23 04:07:23 +00:00

ChemTransforms

First pass at the rewrite:

2010-05-31 14:08:11 +00:00

Depictor

cleanup

2010-06-06 03:56:02 +00:00

Descriptors

add additional forms of the morgan, atom-pair, and topological torsion fps

2010-07-02 04:17:21 +00:00

DistGeomHelpers

fix and test sf.net issue 3019283

2010-06-22 05:08:00 +00:00

FileParsers

add close() method to writers

2010-07-28 04:29:58 +00:00

Fingerprints

fix an SSS fingerprint bug

2010-08-09 06:40:17 +00:00

ForceFieldHelpers

sync in trunc changes in preparation for merge-back

2010-06-02 07:08:53 +00:00

FragCatalog

refactoring of the BitVect interface to make capitalization consistent

2010-05-30 15:15:46 +00:00

libs

initial import

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

MolAlign

make python wrappers and tests optional

2010-01-22 11:22:58 +00:00

MolCatalog

make python wrappers and tests optional

2010-01-22 11:22:58 +00:00

MolChemicalFeatures

add GetFeatureDefs() method

2010-06-04 06:00:56 +00:00

MolTransforms

improvements to query writing to mol files

2010-06-05 13:44:08 +00:00

PartialCharges

make python wrappers and tests optional

2010-01-22 11:22:58 +00:00

ShapeHelpers

make python wrappers and tests optional

2010-01-22 11:22:58 +00:00

SLNParse

make sure we use the dynamic version of regex on windows

2010-07-30 17:03:41 +00:00

SmilesParse

minor updates

2010-06-23 04:15:38 +00:00

Subgraphs

add some comments

2009-11-04 04:41:09 +00:00

Substruct

enabling infrastructure for making repeated recursive

2010-06-03 10:02:15 +00:00

test_data

chirality support in the fix for issue 2951221

2010-02-14 06:39:51 +00:00

testExecs

initial import

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

Wrap

add close() method to writers

2010-07-28 04:29:58 +00:00

AddHs.cpp

fix a leak when removeHs fails

2010-06-08 13:49:00 +00:00

Aromaticity.cpp

fix and test sf.net issue 2787221

2009-05-05 12:54:41 +00:00

Atom.cpp

cleanup

2010-06-03 15:49:32 +00:00

Atom.h

First pass at the rewrite:

2010-05-31 14:08:11 +00:00

atomic_data.cpp

since there's not really a right answer about default valence for transition metals, we might as well be consistent

2009-03-30 07:15:46 +00:00

atomic_data.h

Fixes for sf.net bugs 1942657 : square brackets in smiles allow invalid valences

2008-04-17 05:09:02 +00:00

AtomIterators.cpp

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

AtomIterators.h

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

AtomProps.h

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

Bond.cpp

some speedups

2010-02-15 19:20:24 +00:00

Bond.h

Bond::expandQuery() should have been virtual all along

2009-06-05 04:52:48 +00:00

BondIterators.cpp

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

BondIterators.h

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

BondProps.h

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

bulktest.cpp

setup svn keywords (should have done this before import... grn)

2006-05-06 22:54:39 +00:00

Canon.cpp

fix and test sf.net issue 3018558

2010-06-20 03:46:58 +00:00

Canon.h

merge the changes from the CanonicalizerRework30Nov branch in.

2008-01-30 14:53:04 +00:00

Chirality.cpp

fix issue 3009836; partial fix for issue 3009911

2010-06-01 17:54:49 +00:00

Chirality.h

Merge changes from the iterative chirality branch:

2008-09-19 09:40:15 +00:00

CMakeLists.txt

moving towards a release candidate.

2010-04-13 04:51:54 +00:00

Conformer.cpp

implement and test feature request 1906758 :

2008-03-04 07:06:26 +00:00

Conformer.h

implement and test feature request 1906758 :

2008-03-04 07:06:26 +00:00

ConjugHybrid.cpp

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

cptest.cpp

setup svn keywords (should have done this before import... grn)

2006-05-06 22:54:39 +00:00

FindRings.cpp

change the ring-invariant computation scheme:

2010-08-14 06:21:47 +00:00

GraphMol.cpp

initial import

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

GraphMol.h

initial import

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

itertest.cpp

remove a bunch of compiler warnings

2008-05-26 20:05:57 +00:00

Jamfile

remove vflib from Jamfiles

2009-06-29 11:47:38 +00:00

Kekulize.cpp

fix and test sf.net issue2830244

2009-07-31 10:25:31 +00:00

Matrices.cpp

obsolete include removed

2009-08-01 10:33:06 +00:00

MolDiscriminators.cpp

move the MolDiscriminators calculations into Subgraphs in order to remove the lapack dependency from the core molecule code;

2009-04-10 04:09:49 +00:00

MolOps.cpp

primarily minor code cleanups.

2010-05-26 18:27:40 +00:00

MolOps.h

remove the deprecated assign{Atom,Bond}ChiralCodes functions

2009-08-02 15:33:08 +00:00

molopstest.cpp

First pass at the rewrite:

2010-05-31 14:08:11 +00:00

MolPickler.cpp

more extensive testing of pickler

2010-06-17 05:53:37 +00:00

MolPickler.h

merge in the changes from the 64 bit port branch r703:717

2008-06-11 05:01:17 +00:00

PeriodicTable.cpp

setup svn keywords (should have done this before import... grn)

2006-05-06 22:54:39 +00:00

PeriodicTable.h

Fixes for sf.net bugs 1942657 : square brackets in smiles allow invalid valences

2008-04-17 05:09:02 +00:00

QueryAtom.cpp

remove vflib from Jamfiles

2009-06-29 11:47:38 +00:00

QueryAtom.h

Major thing here: fix and test Issue 1748846 (https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1748846&group_id=160139)

2007-07-06 17:31:58 +00:00

QueryBond.cpp

remove vflib from Jamfiles

2009-06-29 11:47:38 +00:00

QueryBond.h

Major thing here: fix and test Issue 1748846 (https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1748846&group_id=160139)

2007-07-06 17:31:58 +00:00

QueryOps.cpp

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

QueryOps.h

enabling infrastructure for making repeated recursive

2010-06-03 10:02:15 +00:00

querytest.cpp

test issue2892580

2010-01-14 16:08:21 +00:00

RankAtoms.cpp

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

RankAtoms.h

Merge changes from the iterative chirality branch:

2008-09-19 09:40:15 +00:00

RDKitBase.h

merge changes from QuerySerialization_6March2008 branch, revs 555:563, into the trunk;

2008-03-12 06:11:39 +00:00

RDKitQueries.h

initial import

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

regress.txt

initial import

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

RingInfo.cpp

Merge changes from the iterative chirality branch:

2008-09-19 09:40:15 +00:00

RingInfo.h

(re)organize some of the documentation

2008-07-14 03:53:20 +00:00

Rings.h

not done, this is a backup commit

2008-12-02 07:01:46 +00:00

ROMol.cpp

primarily minor code cleanups.

2010-05-26 18:27:40 +00:00

ROMol.h

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

RWMol.cpp

primarily minor code cleanups.

2010-05-26 18:27:40 +00:00

RWMol.h

This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties

2009-02-11 20:19:25 +00:00

SanitException.h

initial import

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

sanitTest.cpp

setup svn keywords (should have done this before import... grn)

2006-05-06 22:54:39 +00:00

test1.cpp

primarily minor code cleanups.

2010-05-26 18:27:40 +00:00

test_list.py

get the new lapack-free version working on windows

2009-10-31 05:24:15 +00:00

testCanon.cpp

setup svn keywords (should have done this before import... grn)

2006-05-06 22:54:39 +00:00

testChirality.cpp

fix issue 3009836; partial fix for issue 3009911

2010-06-01 17:54:49 +00:00

testPickler.cpp

more extensive testing of pickler

2010-06-17 05:53:37 +00:00

UnitTestQueryMol.py

now all tests pass here as well

2009-02-03 05:26:10 +00:00