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49 Commits

Author SHA1 Message Date
Greg Landrum
5618819c64 merge #641 2015-11-14 05:03:24 +01:00
Sereina
26ab552232 fixes based on code review 2015-10-21 14:51:53 +02:00
Sereina
687b464e91 small fixes 2015-10-20 17:04:54 +02:00
Sereina
9cf706b581 enforceChirality flag added back 2015-10-20 15:04:13 +02:00
Sereina
ac7ef34f05 ETKDG implementation 2015-10-20 13:51:43 +02:00
Brian Kelley
633ac22b51 Silences unused params and casting issues 2015-10-18 21:16:17 -04:00
Brian Kelley
daa7e62258 Fixes signed conversion issues (use rdcast) 2015-10-18 15:16:38 -04:00
Brian Kelley
5f59333a56 Silences unused parameters 2015-10-18 14:02:29 -04:00
Brian Kelley
a146c3826a Remove unused variables/functions and register keyword 2015-10-18 10:01:00 -04:00
Sereina
f28ebaf448 chirality test added and flag for them introduced 2015-09-29 11:30:54 +02:00
Greg Landrum
87bfa334d6 add a central method for calculating the number of threads that supports negative numbers 2015-09-04 13:48:52 +02:00
Greg Landrum
49cada6e46 First pass at #586 2015-09-04 11:09:57 +02:00
Greg Landrum
79518c9a6f Fixes #568 2015-08-17 04:24:58 +02:00
Greg Landrum
ed9c96f544 still not really working 2015-08-15 14:26:52 +02:00
Greg Landrum
33306bc2bb fix the chiral volume flag 2015-08-14 16:07:21 +02:00
Greg Landrum
ee850b232f progress on #563 2015-08-14 07:23:18 +02:00
Greg Landrum
55f6fed10d progress on #563 2015-08-14 07:19:52 +02:00
Greg Landrum
80f7ac4515 Merge branch 'master' of github.com:rdkit/rdkit 2015-04-11 03:06:13 +02:00
Greg Landrum
0e56ca1dc0 default to 400 iterations for the dgeom force field 2015-04-11 03:06:08 +02:00
Nadine Schneider
5d963846b8 merge 2015-04-10 09:44:18 +02:00
Riccardo Vianello
7c346d7c2e Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 22:31:48 +01:00
Greg Landrum
250c621310 add multi-threaded support for multi-conf embedding 
part of #445
 2015-03-13 06:03:08 +01:00
Greg Landrum
d5e1f0a7f6 now all tests pass 2015-01-23 06:50:17 -05:00
Greg Landrum
2d9f809770 fix some broken tests; pyDistGeom is still failing 2015-01-23 06:43:12 -05:00
Brian Kelley
95a92282d1 Dictionary access is saniztized and optimized. 
o rdkit gains a RDKit::common_properties namespace that contains common string value properties

 o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
  true/false on success or failure.  This is used to optimize access.

 o rdkit learns how to pass property keys by reference, not value.

A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties.  This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values.  All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.

Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
 2015-01-15 12:23:29 -05:00
Greg Landrum
ab1f936425 Fixes #256 2014-05-05 05:44:36 +02:00
Greg Landrum
e71c0a2d2d Fixes #167 
I am not completely comfortable with the fact that one reference energy in testDistGeom.py
  had to be changed. This is worth looking into some more
 2013-11-27 07:26:05 +01:00
Greg Landrum
4adb4d9889 Fixes #55 2013-07-02 05:23:56 +02:00
Greg Landrum
3afbb41cfb fix and test issue 3483968 2012-02-05 07:27:40 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
ec192d981e changes to robustify (and somewhat speed up) the optimizer. These will change results 2010-02-28 13:11:34 +00:00
Greg Landrum
74d4dba964 fix and test sf.net issue 2835784; 
this should make embedded geometries of fused rings (and around rings)
much better
 2009-10-02 04:58:50 +00:00
Greg Landrum
96adbc11ea remove the deprecated assign{Atom,Bond}ChiralCodes functions 2009-08-02 15:33:08 +00:00
Greg Landrum
9cabf87374 remove vflib from Jamfiles 
remove const specifiers from return values in DataStructs
add initial pass at query-query matching for Atoms and Bonds
fix and test for sf.net issu 2738320
add Mol.AddRecursiveQuery() method to Mol
 2009-06-29 11:47:38 +00:00
Greg Landrum
1449a7657c get the embedding more robust in crowded chiral molecules 2009-04-20 16:37:59 +00:00
Greg Landrum
e05580e495 This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties 
instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
 2009-02-11 20:19:25 +00:00
Greg Landrum
507d7e84e7 fix and test sf.net issue2378119 2008-12-03 19:34:55 +00:00
Greg Landrum
03c17bbcb7 fix and test sf.net issue 2091974; switch test5 back on 2008-09-26 10:27:06 +00:00
Greg Landrum
2620dcba2f first pass at constrained conformation generation 2008-07-15 05:31:45 +00:00
Greg Landrum
a75e666f0d check a provisional fix in for bug 1989539. 2008-06-25 15:18:21 +00:00
Greg Landrum
05f390fe6d rename EmbedObject.h -> ChiralSet.h and clean it up a bit 2008-05-18 05:14:40 +00:00
Greg Landrum
026078a64e minimize away 4th coordinate when doing random coords 2008-01-04 07:20:51 +00:00
Greg Landrum
0e456c8afa DistGeom/ and 
GraphMol/DistGeomHelpers/: 
  Support generating random initial coordinates of atoms as an alternative to embedding. This has so far only been tested on windows (all tests pass) and it needs to be optimized (particularly force field parameters). 
  Other changes here are primarily cosmetic code cleanups.
 2007-12-29 06:16:39 +00:00
Greg Landrum
08a7315c4e Embedder: reformatting 
Geometry: fixes to PointND and its python wrapper.
 2007-07-09 05:31:32 +00:00
Santosh Putta
218032f32b letting hydrogens in the graph be part of chiral volume calculation atoms 2006-11-30 00:24:34 +00:00
Santosh Putta
086faee1a9 changes related to chirality addition 2006-11-22 00:53:26 +00:00
Santosh Putta
2d1f48cc2a All typedefs based on points move to point.h - dependancies updated here 2006-10-19 23:29:58 +00:00
Santosh Putta
9af1c6259b adding option argument pruneRmsThresh to EmbedMultipleConfs to prune away similar conformations 2006-10-02 23:17:04 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00