Greg Landrum
297f5d7877
minor optimization of chirality determination
2013-12-14 08:30:57 +01:00
Greg Landrum
c82e1151b3
Fixes #90
2013-08-23 12:58:41 +02:00
Greg Landrum
40ab2c06e3
Fixes #87
2013-08-21 08:20:19 +02:00
Greg Landrum
a4734bbd43
start using the alternate getProp form
2013-07-20 07:26:06 -04:00
Greg Landrum
f467bdad9a
fix problem caused by github-8 fix
2013-03-14 06:23:13 +00:00
Greg Landrum
0b446d696e
minor efficiency tweak
2013-02-25 05:41:50 +00:00
Greg Landrum
7610e1e6f5
additional help for sf.net issue 275
2013-01-10 05:10:40 +00:00
Greg Landrum
24e269f8ac
I *think* that this fixes sf.net issue 40:
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the long-standing problem with ring stereochemistry and canonicalization
2012-11-02 06:33:11 +00:00
Greg Landrum
b96cff10e8
fix and test sf.net issue 254
2012-09-23 10:13:46 +00:00
Greg Landrum
103c427f3f
fix and test issue 3524984
2012-05-09 04:20:24 +00:00
Greg Landrum
5d48f52545
a quick optimization of the stereochemistry code
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(thanks to Roger Sayle for the suggestion
2012-03-27 10:27:18 +00:00
Greg Landrum
acb61df900
update/reformat
2012-01-17 03:25:58 +00:00
Greg Landrum
5eadc06bf6
fix and test for issue 3453172
2011-12-30 07:13:33 +00:00
Greg Landrum
d512e49fff
partial solution to the chiral phosphorus problem
2011-07-28 05:22:55 +00:00
Eddie Cao
adbd5c7b18
Several InChI generation fixes, including perchloric acid, isotopic property, chirality loss, stereoany
2011-07-25 06:41:47 +00:00
Greg Landrum
d6741adc22
make some types more explicit in MolOps.h (easier SWIG wrapping)
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support finding non-specfied chiral centers
remove vestigial GetFragmentSmiles() function
additional flexibility in AllChem.TransformMol()
2011-02-24 08:00:39 +00:00
Greg Landrum
28747ea745
checkin some fragment and fingerprint changes. these are not yet well tested
2011-01-14 06:24:03 +00:00
Greg Landrum
006c696067
an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534);
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this needs a ton more testing, but it is worth getting a "working" version in
2010-12-28 10:38:14 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
052ec66542
cleanups:
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remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
2010-09-08 04:25:57 +00:00
Greg Landrum
80c0a8825e
fix issue 3009836; partial fix for issue 3009911
2010-06-01 17:54:49 +00:00
Greg Landrum
2805355f34
First pass at the rewrite:
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this gets rid of all the "preceding atom" code and passes all tests on linux
builds on other OS's and more extensive regression testing is required
2010-05-31 14:08:11 +00:00
Greg Landrum
6b9943e5bd
minor cleanup
2010-05-31 04:51:47 +00:00
Greg Landrum
268b08ec17
fix and test sf.net issue 2804599
2009-06-11 04:55:44 +00:00
Greg Landrum
09455ef42e
resolves issue 2705543
2009-03-28 06:43:04 +00:00
Greg Landrum
a412664c65
just for backup
2009-03-27 16:12:54 +00:00
Greg Landrum
6042af28b9
add removeStereochemistry function to MolOps
2009-03-06 09:55:53 +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
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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
ac4eee9115
continuing refinement of issue 1896935
2008-12-03 19:53:51 +00:00
Greg Landrum
a61cc8a07b
fix a ring-stereochem edge case
2008-12-03 17:04:01 +00:00
Greg Landrum
023f7b4f0f
Merge changes from the iterative chirality branch:
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https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/IterativeChirality_20Aug2008
into the trunk.
This covers revs 798-828.
Dependent chirality should now be correctly handled, but the
handling of ring stereochemistry, i.e. things like:
C[C@H]1CC[C@H](C)CC1
is still not 100% correct.
2008-09-19 09:40:15 +00:00
Greg Landrum
40e7700307
optimization of the chiral atom ranking code: decrease the max number of cycles
2008-07-23 04:33:21 +00:00
Greg Landrum
6e05e3c7c2
update the chirality from 3d stuff a bit and expose it to python; fix a reporting error in SDMolSupplier
2008-07-09 15:43:04 +00:00
Greg Landrum
76f32244aa
- support splitting a molecule into fragments (in MolOps)
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- expose the calculation of atom CIP ranks
2008-06-27 03:43:42 +00:00
Greg Landrum
148a3a87c4
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
Greg Landrum
2547ddf5de
minor code cleanups
2008-05-06 12:41:07 +00:00
Greg Landrum
a6c1a64d1a
remove some compiler warnings
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rearrange the argument ordering for the Dice similarity stuff so
that it can be invoked the same as the other similarity metrics.
2008-04-24 19:03:34 +00:00
Greg Landrum
d8151e7856
Fixes for sf.net bug 1942656: five-coordinate carbon left with stereochem
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http://sourceforge.net/tracker/index.php?func=detail&aid=1942656&group_id=160139&atid=814650
minor optimization
2008-04-17 04:49:14 +00:00
Greg Landrum
3228f9926f
doc update
2008-04-10 04:26:21 +00:00
Greg Landrum
3c57caabfb
partially tested fix for sf.net bug 1894348
2008-02-15 16:13:12 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
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The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
66ec16dedf
Fix and test sf.net bug 1725068:
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http://sourceforge.net/tracker/index.php?func=detail&aid=1725068&group_id=160139&atid=814650
2007-06-06 17:25:08 +00:00
Greg Landrum
c6ad039a2f
fix for sf.net issue 1719053: ring stereochemistry incorrectly removed:
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http://sourceforge.net/tracker/index.php?func=detail&aid=1719053&group_id=160139&atid=814650
This will need more torture testing, but the unit tests here do cover the edge cases I can think of.
2007-05-23 05:17:07 +00:00
Greg Landrum
ee60199400
continue fix and test for sf.net issue 1718794
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http://sourceforge.net/tracker/index.php?func=detail&aid=1718794&group_id=160139&atid=814650
2007-05-14 17:41:17 +00:00
Greg Landrum
db1b02febf
fix and test for sf.net issue 1718794
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http://sourceforge.net/tracker/index.php?func=detail&aid=1718794&group_id=160139&atid=814650
2007-05-14 17:27:59 +00:00
Greg Landrum
9bd4c59606
substantial optimization of SD/mol file parsing;some reformattig
2007-03-20 21:06:37 +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
