Greg Landrum
c0811e3261
get the excludes right
2007-11-06 17:50:07 +00:00
Greg Landrum
13e6b91601
sync with changes rev401:404 in the PyCleaning_4Nov2007 branch
2007-11-06 05:04:47 +00:00
Greg Landrum
445393837b
rename arg
2007-11-06 05:01:40 +00:00
Greg Landrum
483d1261e3
still testing this
2007-11-04 08:14:41 +00:00
Greg Landrum
09c67ab78f
Switch the crippen stuff to c++
2007-10-20 06:26:50 +00:00
Greg Landrum
98598680be
these are hanging on linux at the moment and the code isn't being used anyway
2007-10-12 03:52:28 +00:00
Greg Landrum
17678e1f17
add skipProps options
2007-10-10 05:50:50 +00:00
Greg Landrum
50130f9597
better error support using the new GetItemText() method of suppliers
2007-10-09 05:32:41 +00:00
Greg Landrum
e1d73ab18e
backwards compatibility
2007-10-08 17:51:36 +00:00
Greg Landrum
1a9bbfae0f
move torsions into C++ too
...
this still has not been tested on windows
NOTE: there is a known bug in the size of the topological torsion
fingerprints (they are 1 bit too small), this is to maintain
backwards compatibility with the python code, which also had this
bug.
2007-10-08 06:16:50 +00:00
Greg Landrum
6a1637c053
A good start on getting the atom-pair stuff into C++;
...
This has been tested on Linux only, Windows is not going to work until
(at least) the workspace has been updated.
2007-10-07 15:40:32 +00:00
Greg Landrum
faa2bc3f8a
start to transition out the python code for similarity
2007-10-04 05:37:14 +00:00
Greg Landrum
87426eee15
add a bit more flexibility
2007-10-04 03:35:34 +00:00
Greg Landrum
a753202a87
these should have been added a long time ago
...
but somehow escaped my notice
2007-10-02 16:50:46 +00:00
Greg Landrum
41ab585a93
fix another amide bug in Recap and add some more testing
2007-10-01 19:45:00 +00:00
Greg Landrum
542159a36c
fix some broken definitions,
...
move ureas over amides (duh)
much, much more extensive testing
2007-09-30 13:34:22 +00:00
Greg Landrum
3023fb9be3
really fix issue 1804418 ( http://sourceforge.net/tracker/index.php?func=detail&aid=1804418&group_id=160139&atid=814650 )
2007-09-29 06:48:49 +00:00
Greg Landrum
4eb26b8b5e
fix issue 1804418 ( http://sourceforge.net/tracker/index.php?func=detail&aid=1804418&group_id=160139&atid=814650 )
...
workaround issue 1804420 (http://sourceforge.net/tracker/index.php?func=detail&aid=1804420&group_id=160139&atid=814650 )
2007-09-29 06:38:07 +00:00
Greg Landrum
560239d7c0
move fingerprint folding stuff into C++. This implementation should break no existing code
2007-09-27 05:27:16 +00:00
Greg Landrum
c74c8ed1f8
further motion towards resolving sf.net issue 1757265
...
http://sourceforge.net/tracker/index.php?func=detail&aid=1757265&group_id=160139&atid=814650
still needs testing on linux
2007-09-25 16:56:19 +00:00
Greg Landrum
d0ab41d4a0
fix sf.net issue1801871
...
https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1801871&group_id=160139
RECAP implementation ignores "forbidden" fragments
2007-09-25 16:09:15 +00:00
Greg Landrum
de0657caaa
SparseIntVect now in c++
2007-09-23 06:53:43 +00:00
Greg Landrum
4d45a45301
sf.net issue 17557265 "too difficult to set up testing on a new machine"
2007-09-18 05:13:20 +00:00
Greg Landrum
7e6441e73d
sf.net issue 17557265 "too difficult to set up testing on a new machine"
2007-09-18 05:12:24 +00:00
Greg Landrum
eb5b0fa967
sf.net issue 17557265 "too difficult to set up testing on a new machine"
2007-09-18 05:12:00 +00:00
Greg Landrum
04824a26a5
cleanup and renaming
2007-09-16 05:27:43 +00:00
Greg Landrum
40621682aa
1) remove some extraneous numeric imports
...
2) start working towards a fix for issue 1757265 (too difficult to set up testing on a new machine):
http://sourceforge.net/tracker/index.php?func=detail&aid=1757265&group_id=160139&atid=814650
2007-07-20 03:39:13 +00:00
Greg Landrum
bf878b7130
update for boost 1.34
2007-07-19 03:50:11 +00:00
Greg Landrum
c653b7a4dc
minor changes
2007-07-16 05:19:53 +00:00
Greg Landrum
e2fb1cd532
merge the changes from the subshape branch (rev284) into the head. The subshape branch is no longer really needed at this point.
2007-07-15 15:00:36 +00:00
Greg Landrum
fe5f29d0e3
Fix and test Issue 1749494 "Descriptor code not properly handling unrecognized atoms"
...
https://sourceforge.net/tracker/index.php?func=detail&aid=1749494&group_id=160139&atid=814650
One of the lipinski regression values has been updated and a comment was added to Lipinski.py dealing with the handling of deuteriums and rotatable bond counts.
2007-07-07 07:50:14 +00:00
Greg Landrum
086c9b6719
optimize the dice metric
2007-07-03 04:23:25 +00:00
Greg Landrum
b5c885ab6a
Fix bug in Pairs.py
...
Optimize things a lot (x2-x3) by pre-computing atom codes
Add some regressions (1000 pubchem molecules)
2007-07-02 17:59:06 +00:00
Greg Landrum
4e15706435
Minor efficiency/clarity change and a test for another edge case.
2007-06-26 04:27:36 +00:00
Greg Landrum
79b316838f
fix a problem with torsions
2007-06-19 16:31:18 +00:00
Greg Landrum
7f540d32c2
linux update
2007-05-14 05:05:06 +00:00
Greg Landrum
4eecdaf3cf
get sqlite working on machines that also have pgsql
2007-05-12 05:36:34 +00:00
Greg Landrum
1f2aff8a3b
fixed a bug in the mathematical operators
...
this was sf.net issue 1716736:
http://sourceforge.net/tracker/index.php?func=detail&aid=1716736&group_id=160139&atid=814650
2007-05-10 19:39:04 +00:00
Greg Landrum
55021c70b7
add functions to get explanations of atom pairs and topological torsions
2007-05-08 04:21:22 +00:00
Greg Landrum
5f371f8c4d
added
2007-05-06 08:10:44 +00:00
Greg Landrum
f9f4fb5e7e
Again, a collection of changes:
...
FingerprintMols.py: set this up so that it can be called without arguments
AlignDepict.py: doc updates
Torsions.py: support the IntVect datastruct used by Pairs.py
Pairs.py: fix a bug with the fpLen, error checking on fp sizes and returning BitVects
AllChem.py: import the reactions code, add convenience wrapper GenerateDepictionMatching3DStructure
2007-04-25 03:29:22 +00:00
Greg Landrum
5817660a9d
added
2007-04-18 19:26:08 +00:00
Greg Landrum
faa97576f8
that stub shouldn't have been in there
2007-04-18 03:57:46 +00:00
Greg Landrum
6cd195ad0b
port over some changes made on Subshape branch (r179:218)
2007-04-18 03:47:40 +00:00
Greg Landrum
80c76c59ac
merge in chemical reactions branch (r173:183)
2007-02-23 18:05:50 +00:00
Greg Landrum
3ec7b1404c
- Partial implementation (due to lack of testing) of a sqlite interface
...
- Fingerprints/FingerprintMols.py: Add FingerprintsFromPickles to complement the other interfaces.
- MoleculeDescriptors.py: a bit of robustification
2007-02-22 04:43:30 +00:00
Greg Landrum
e8161177ba
Robustification
2007-02-21 20:25:46 +00:00
Greg Landrum
17e863b667
Merge in changes from MolCatalog branch (r109:169)
...
This needs some massive testing.
2007-02-13 18:56:04 +00:00
Greg Landrum
c78871c286
minor design change
2006-09-22 03:39:10 +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
