Commit Graph

16 Commits

Author SHA1 Message Date
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