Greg Landrum
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6e2508972c
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all tests passing
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2012-04-21 05:37:34 +00:00 |
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Greg Landrum
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e7d25d7973
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tests passing except reactions
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2012-04-21 04:40:55 +00:00 |
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Greg Landrum
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de2126b641
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optimization work
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2012-04-15 06:19:22 +00:00 |
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Greg Landrum
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dd609388e4
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further improvements to getReactingAtoms()
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2012-01-19 08:43:57 +00:00 |
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Greg Landrum
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e8cb290f18
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add an initial pass at getReactingAtoms() for reactions
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2012-01-18 05:52:38 +00:00 |
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Greg Landrum
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a99ad44859
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clean up some compiler warnings
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2011-12-31 15:58:57 +00:00 |
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Greg Landrum
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5e49aacd06
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fix and test issue 3434271
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2011-11-07 05:08:35 +00:00 |
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Greg Landrum
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2bc9481be8
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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
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2011-10-29 05:51:05 +00:00 |
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Greg Landrum
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faab610321
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add string replacements to smiles and smarts parsers
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2011-05-22 10:45:14 +00:00 |
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Greg Landrum
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2ffaa92cf7
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fix and test issue3228150;
note that as part of these changes MolToSmiles and MolToSmarts no longer have
side effects on the original molecule.
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2011-03-26 06:51:50 +00:00 |
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Greg Landrum
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2cea8b58b4
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fix for issue 3140490
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2010-12-20 05:00:23 +00:00 |
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Greg Landrum
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18a8be8538
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add isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() convenience functions
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2010-08-21 00:16:02 +00:00 |
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Greg Landrum
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5ef1a2c6eb
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improve depiction quality by (optionally) doing a bit of chemistry perception
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2010-06-23 04:07:23 +00:00 |
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Greg Landrum
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46bfbba903
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make sure to convert atoms from rxn files into queries;
add reaction depiction;
add ChemicalReactionToRxnBlock();
This stuff needs more testing and so far has only been built on linux.
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2010-06-17 05:57:18 +00:00 |
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Greg Landrum
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fbf3e51f07
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add ability to write reactions as SMARTS; RXN files still need to be done
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2010-06-07 04:26:19 +00:00 |
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Greg Landrum
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a09fd9f63a
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cleanup work on file parsers code; add v3K rxn support
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2010-06-03 06:59:48 +00:00 |
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Greg Landrum
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bf4e28e67c
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Change handling of atom-map numbers in SMARTS parsing.
this fixes sf.net bug 1804420
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2010-01-15 06:41:16 +00:00 |
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Greg Landrum
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1896aac566
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transfer conformer data to products in reactions; sf.net issue 2832951
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2009-08-06 04:39:04 +00:00 |
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Greg Landrum
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cefd866c37
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the implicit property stuff should be "private";
allow extraction of the reaction/product template molecules
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2009-06-02 06:47:52 +00:00 |
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Greg Landrum
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7fdece9cd7
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initial pass at supporting reaction pickles
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2009-06-02 05:06:06 +00:00 |
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Greg Landrum
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527a3ccc6a
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handle dots in reactions correctly; this needs a bug entered against it.
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2009-03-17 16:40:22 +00:00 |
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Greg Landrum
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82661fb59b
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partial fix for sf.net issue 2540021;
valence changes caused by modifying bond orders still not handled
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2009-02-02 05:30:26 +00:00 |
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Greg Landrum
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e1a4c98503
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enforce reaction initialization requirement
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2008-11-26 10:44:56 +00:00 |
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Greg Landrum
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1e5f0afcf6
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fix handling of properties in the products
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2008-11-26 07:41:33 +00:00 |
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Greg Landrum
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de86e06e10
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make sure aromaticity flags get copied onto dummy atoms too
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2008-11-17 14:33:52 +00:00 |
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Greg Landrum
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110e67c1a0
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support query bonds in the products
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2008-11-17 14:00:27 +00:00 |
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Greg Landrum
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023f7b4f0f
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Merge changes from the iterative chirality branch:
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.
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2008-09-19 09:40:15 +00:00 |
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Greg Landrum
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335d379d35
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fix and test issue 2050085
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2008-08-14 11:49:19 +00:00 |
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Greg Landrum
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7b1d76a295
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Should have been part of previous commit.
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2008-08-13 04:57:32 +00:00 |
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Greg Landrum
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f5b0d637aa
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don't update implicit props when the atomic number changes
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2008-04-25 05:04:05 +00:00 |
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Greg Landrum
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b1aac14542
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progress towards fixing and testing issue 1934052
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2008-04-24 05:41:03 +00:00 |
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Greg Landrum
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e28938475f
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a couple more chirality tests for reactions
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2008-04-08 10:22:19 +00:00 |
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Greg Landrum
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31d03cc949
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further progress towards fixing bug 1920627
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2008-04-01 19:34:27 +00:00 |
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Greg Landrum
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45ad82f715
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further tests of sf.net Issue 1920627
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2008-03-26 05:20:01 +00:00 |
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Greg Landrum
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84a48a03c7
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preliminary fix for sf.net issue 1920627
more testing is required, but this should have it mostly solved
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2008-03-25 06:36:59 +00:00 |
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Greg Landrum
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eebff68d3c
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test commit
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2008-02-13 11:03:31 +00:00 |
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Greg Landrum
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e21af3db7b
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update chirality handling in reactions;
fix and test issue 1882479
make sure reaction tests get run when the GraphMol tests go;
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2008-01-31 06:47:53 +00:00 |
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Greg Landrum
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38e5d9d030
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fix stupid typo in the copyright
add test for sf.net bug 1804420
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2007-09-29 06:34:30 +00:00 |
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Greg Landrum
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ebb196b8f8
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Major thing here: fix and test Issue 1748846 (https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1748846&group_id=160139)
Others:
SmilesParse: clean up some of the smiles generation code
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2007-07-06 17:31:58 +00:00 |
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Greg Landrum
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80c76c59ac
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merge in chemical reactions branch (r173:183)
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2007-02-23 18:05:50 +00:00 |
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