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
