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
c0bf384832
Fixes #290
2014-07-12 08:20:31 +02:00
Greg Landrum
a310f3bff5
Fixes #249
2014-04-16 08:58:03 +02:00
Greg Landrum
5586330f16
Fixes #243
2014-04-13 07:15:35 +02:00
Greg Landrum
ddc66b90a9
initial verison of allowing rxns to be built from smiles
2014-04-11 04:41:48 +02:00
Greg Landrum
254cb7a405
Fixes #233
2014-03-14 18:40:10 +01:00
Greg Landrum
296bbfb65b
Fixes #228
2014-03-05 05:48:17 +01:00
Greg Landrum
8db139da5e
steps towards #222
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at least now agents no longer generate parse errors
2014-02-23 09:55:30 +01:00
Greg Landrum
4ace62f019
remove more clang warnings
2013-12-02 05:10:23 +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
60956a59b3
get component level SMARTS grouping working in reaction smarts;
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this probably needs some more work
2012-10-10 10:17:52 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
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there are still some problems with double bonds
2012-06-11 03:21:30 +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
de2126b641
optimization work
2012-04-15 06:19:22 +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
a99ad44859
clean up some compiler warnings
2011-12-31 15:58:57 +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
faab610321
add string replacements to smiles and smarts parsers
2011-05-22 10:45:14 +00:00
Greg Landrum
2ffaa92cf7
fix and test issue3228150;
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note that as part of these changes MolToSmiles and MolToSmarts no longer have
side effects on the original molecule.
2011-03-26 06:51:50 +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
5ef1a2c6eb
improve depiction quality by (optionally) doing a bit of chemistry perception
2010-06-23 04:07:23 +00:00
Greg Landrum
46bfbba903
make sure to convert atoms from rxn files into queries;
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add reaction depiction;
add ChemicalReactionToRxnBlock();
This stuff needs more testing and so far has only been built on linux.
2010-06-17 05:57:18 +00:00
Greg Landrum
fbf3e51f07
add ability to write reactions as SMARTS; RXN files still need to be done
2010-06-07 04:26:19 +00:00
Greg Landrum
a09fd9f63a
cleanup work on file parsers code; add v3K rxn support
2010-06-03 06:59:48 +00:00
Greg Landrum
bf4e28e67c
Change handling of atom-map numbers in SMARTS parsing.
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this fixes sf.net bug 1804420
2010-01-15 06:41:16 +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
cefd866c37
the implicit property stuff should be "private";
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allow extraction of the reaction/product template molecules
2009-06-02 06:47:52 +00:00
Greg Landrum
7fdece9cd7
initial pass at supporting reaction pickles
2009-06-02 05:06:06 +00:00
Greg Landrum
527a3ccc6a
handle dots in reactions correctly; this needs a bug entered against it.
2009-03-17 16:40:22 +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
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
335d379d35
fix and test issue 2050085
2008-08-14 11:49:19 +00:00
Greg Landrum
7b1d76a295
Should have been part of previous commit.
2008-08-13 04:57:32 +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
e28938475f
a couple more chirality tests for reactions
2008-04-08 10:22:19 +00:00
Greg Landrum
31d03cc949
further progress towards fixing bug 1920627
2008-04-01 19:34:27 +00:00
Greg Landrum
45ad82f715
further tests of sf.net Issue 1920627
2008-03-26 05:20:01 +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
