Schneider
8aac978f1b
ChemReactions: Extented functionality of chemical reactions
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- Module to generate reaction fingerprints: structural FP for screening,
difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now
2014-08-19 13:08:11 +02:00
Greg Landrum
5586330f16
Fixes #243
2014-04-13 07:15:35 +02:00
Greg Landrum
296bbfb65b
Fixes #228
2014-03-05 05:48:17 +01:00
Greg Landrum
5904be011d
update reaction stereochem handling (needs more work)
2013-04-06 06:39:22 +00:00
Greg Landrum
0a1621e97d
fix and initial tests for github issue 4
2013-02-09 07:26:49 +00:00
Greg Landrum
03ef0e6f1b
Add support for merging recursive queries on the C++ side
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(contribution from Sereina Riniker)
A pure Python version of this was in the tutorial material from the RDKit UGM.
2013-01-08 15:13:01 +00:00
Greg Landrum
009f7259a2
support _protected flags in reactions
2012-12-01 06:26:50 +00:00
Greg Landrum
6e2508972c
all tests passing
2012-04-21 05:37:34 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
6229f639a5
clean up some debugging printing; get the handling of the sanitization options more robust on windows; this needs testing back on mac and linux
2012-04-12 04:23:41 +00:00
Greg Landrum
dd609388e4
further improvements to getReactingAtoms()
2012-01-19 08:43:57 +00:00
Greg Landrum
e8cb290f18
add an initial pass at getReactingAtoms() for reactions
2012-01-18 05:52:38 +00:00
Greg Landrum
5e49aacd06
fix and test issue 3434271
2011-11-07 05:08:35 +00:00
Greg Landrum
2bc9481be8
further work on the SMARTS parser: support [13] as a free-standing query and update the reaction code so that the resulting queries work correctly in reactions
2011-10-29 05:51:05 +00:00
Greg Landrum
2cea8b58b4
fix for issue 3140490
2010-12-20 05:00:23 +00:00
Greg Landrum
18a8be8538
add isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() convenience functions
2010-08-21 00:16:02 +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
1896aac566
transfer conformer data to products in reactions; sf.net issue 2832951
2009-08-06 04:39:04 +00:00
Greg Landrum
7fdece9cd7
initial pass at supporting reaction pickles
2009-06-02 05:06:06 +00:00
Greg Landrum
73784d8f6f
fix a problem with transfer of aromatic bond info to products
2009-03-04 16:14:56 +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
82661fb59b
partial fix for sf.net issue 2540021;
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valence changes caused by modifying bond orders still not handled
2009-02-02 05:30:26 +00:00
Greg Landrum
e1a4c98503
enforce reaction initialization requirement
2008-11-26 10:44:56 +00:00
Greg Landrum
1e5f0afcf6
fix handling of properties in the products
2008-11-26 07:41:33 +00:00
Greg Landrum
de86e06e10
make sure aromaticity flags get copied onto dummy atoms too
2008-11-17 14:33:52 +00:00
Greg Landrum
110e67c1a0
support query bonds in the products
2008-11-17 14:00:27 +00:00
Greg Landrum
335d379d35
fix and test issue 2050085
2008-08-14 11:49:19 +00:00
Greg Landrum
57be4a92ef
This is a fix for sf.net issue 1968930:
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http://sourceforge.net/tracker/index.php?func=detail&aid=1968930&group_id=160139&atid=814650
In order to fix the problem, the value of the query function for atomMass queries
is being multiplied by a constant factor (currently 1000) before converting
to an int. This allows distinguishing between things like [CH4] (where the
C has mass 12.011) and [12CH4] (where the C has mass 12.000).
2008-08-13 04:56:48 +00:00
Greg Landrum
4d49b70c4a
code cleanups
2008-08-09 07:58:50 +00:00
Greg Landrum
f5b0d637aa
don't update implicit props when the atomic number changes
2008-04-25 05:04:05 +00:00
Greg Landrum
b1aac14542
progress towards fixing and testing issue 1934052
2008-04-24 05:41:03 +00:00
Greg Landrum
31d03cc949
further progress towards fixing bug 1920627
2008-04-01 19:34:27 +00:00
Greg Landrum
84a48a03c7
preliminary fix for sf.net issue 1920627
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more testing is required, but this should have it mostly solved
2008-03-25 06:36:59 +00:00
Greg Landrum
e21af3db7b
update chirality handling in reactions;
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fix and test issue 1882479
make sure reaction tests get run when the GraphMol tests go;
2008-01-31 06:47:53 +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
6aeeca797d
fix a small memory leak
2008-01-26 04:34:45 +00:00
Greg Landrum
38e5d9d030
fix stupid typo in the copyright
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add test for sf.net bug 1804420
2007-09-29 06:34:30 +00:00
Greg Landrum
ebb196b8f8
Major thing here: fix and test Issue 1748846 ( https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1748846&group_id=160139 )
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Others:
SmilesParse: clean up some of the smiles generation code
2007-07-06 17:31:58 +00:00
Greg Landrum
80c76c59ac
merge in chemical reactions branch (r173:183)
2007-02-23 18:05:50 +00:00
