Santosh Putta
475bcfa161
Vector now support operator[]
2006-10-19 23:27:37 +00:00
Santosh Putta
9bb9b8fc91
PointPtrVect changed to Point3DPtrVect
2006-10-19 23:26:15 +00:00
Santosh Putta
467b0873d2
Forcefield no longer relies on Point3D - it is assumed to work with the base class Point. A new data member d_dimension keep track of what dimension we live in
2006-10-19 23:25:29 +00:00
Santosh Putta
08f9575e96
Adding a new virtual base class Point. Point2D, POint3D and a new PointND class all inherit from this class
2006-10-19 23:23:16 +00:00
Santosh Putta
3c1591f252
Adding a new virtual base class Point. Point2D, POint3D and a new PointND class all inherit from this class
2006-10-19 23:22:59 +00:00
Santosh Putta
d7213b0730
getting rid of point dependencies here
2006-10-19 23:21:13 +00:00
Greg Landrum
88d596abca
get the AR_MOLGRAPH caching write with substructs; the current implementation introduces a core leak, so it is disabled by default
2006-10-19 05:24:05 +00:00
Greg Landrum
0b4e765f47
test ChemTransforms
2006-10-19 04:22:10 +00:00
Greg Landrum
4b4631d394
support new rdvars format
2006-10-19 04:18:50 +00:00
Greg Landrum
ddb43af7cf
the ongoing quest to get rdvars more flexible continues
2006-10-19 04:17:52 +00:00
Greg Landrum
10d3f616b4
remove curMol_gps; switch to using AtomRingQuery for "is in a ring" queries
2006-10-18 17:09:58 +00:00
Greg Landrum
32c3fbe2cf
reorg the query stuff a bit;
...
add ChemTransforms to the makefile (duh)
2006-10-18 17:08:35 +00:00
Greg Landrum
0c13827abf
doc update
2006-10-18 17:06:54 +00:00
Greg Landrum
33e5d18228
doc update
2006-10-18 17:06:33 +00:00
Greg Landrum
830f05f73f
remove the cache_armolgraphs stuff, it was not being used and probably cannot work anyway as it was being done
2006-10-18 04:09:09 +00:00
Santosh Putta
7bcd8dfb38
adding dependency of wrapDistGeomHelpers on libAlign
2006-10-08 22:12:35 +00:00
Greg Landrum
304cd9a272
add backslashes to extended doc strings
2006-10-03 03:33:23 +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
8b7464646d
er, this should have been added a while ago
2006-09-29 17:49:19 +00:00
Greg Landrum
29da37319d
fixes to get things working on linux using ChemTransforms
2006-09-23 05:32:47 +00:00
Greg Landrum
7041ae233e
handle the NoImplicit flag properly
...
update aromaticity to require unsaturation at single-atom donors
test the above two things
This is not necessarily completely stable, but all current tests pass
(once obvious changes have been made). We will just have to see where
the aromaticity changes cause trouble going forward.
2006-09-19 20:20:09 +00:00
Greg Landrum
034fb70865
handle more permissive mol file parser
2006-09-19 20:17:24 +00:00
Greg Landrum
6615ae5a01
SDMolSupplier: don't throw on errors parsing molecules. This allows the parsing of further mols to continue.
...
Conformer.cpp: make sure we don't ask for space for zero atoms.
Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.
molopstest.cpp: bad smiles corrected in one test.exe
ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)
Wrap/MolOps.cpp: docs for replacesubstructs.
2006-09-18 05:21:39 +00:00
Greg Landrum
a890611a22
merge back in changes from ChemTransforms (r30:51);
...
the makefile for linux is still missing (I have one, I just need to retrieve it)
but otherwise this is in pretty good shape.
err, I think so at least.
2006-09-15 16:44:38 +00:00
Santosh Putta
590c4cea9d
Fix and test for Issue 1526844
2006-07-24 16:54:15 +00:00
Greg Landrum
a5d7fc550a
try to get ChemTransforms checked in
2006-07-18 05:35:12 +00:00
Greg Landrum
81f341882e
try to get ChemTransforms checked in
2006-07-18 05:33:58 +00:00
Greg Landrum
087132797e
rename Clustering.c -> Clustering.cpp
2006-06-16 01:16:28 +00:00
Greg Landrum
3df7c30a9c
if we're going to include RDBuild in setup.py, we need to adjust for the fact that the compiler will be g++, so the external stuff needs to be explicitly marked as being in C
2006-05-11 17:56:20 +00:00
Greg Landrum
8a19c38e21
- Get windows debug builds working
...
- Remove requirement that boost be in $RDBASE/External on windows (the BOOSTHOME environment variable is now required)
- fix dependencies
This builds on windows in debug mode now and most tests pass. There's a problem with PySVD in debug mode and for some reason the rdAlignments wrapper test fails; but these don't seem super important.
https://sourceforge.net/tracker/index.php?func=detail&aid=1485703&group_id=160139&atid=814650
2006-05-11 00:42:39 +00:00
Greg Landrum
62025a1d61
RDBuild really should be imported.
2006-05-11 00:12:55 +00:00
Greg Landrum
39d137575a
fix bug 1485710
...
https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1485710&group_id=160139
2006-05-10 15:59:53 +00:00
Greg Landrum
6f65074376
generate directories with newer doxygen
2006-05-10 13:40:26 +00:00
Greg Landrum
b87de75d56
get g++ out of the makefiles... use CXX instead
2006-05-09 23:20:26 +00:00
Greg Landrum
3c386914bd
clear a typo
2006-05-08 20:23:22 +00:00
Greg Landrum
31b53a96d2
clean up some legacy cruft
2006-05-08 15:21:24 +00:00
Greg Landrum
9467ffbb61
make directory structure of python documentation a bit more rational
2006-05-08 14:27:23 +00:00
Greg Landrum
5d03333c22
setup svn keywords (should have done this before import... grn)
2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
