Nadine Schneider
0b8b6a3690
Some performance fixes for the new canonicalization
...
- handling molecules/proteins with multiple fragments
- add criteria for using special symmetry invariant
2015-04-15 18:42:29 +02:00
Nadine Schneider
ca4bcca6ae
Include atom-mapping numbers if present in the canonicalization
2015-04-10 09:47:16 +02:00
Nadine Schneider
33f9906572
Chemical reactions: allow canonical order in reaction smiles
2015-04-10 09:47:15 +02:00
Nadine Schneider
465c7cb4c6
new_canon: Delete numRingMember invariant
2015-02-12 18:06:27 +01:00
Greg Landrum
a0a02b4a99
merge on master
2015-02-03 16:41:46 +01:00
Greg Landrum
ac5756310a
a bit of test cleanup
2015-01-30 04:20:42 +01:00
Brian Kelley
ff0548a871
RDKit learns how to round grip MOLFile values.
...
This is CTAB form:
“V XXX YYYYYY”
where (XXX is atom index, Y is the value)
2015-01-29 15:44:32 -05:00
Greg Landrum
2d9f809770
fix some broken tests; pyDistGeom is still failing
2015-01-23 06:43:12 -05:00
Greg Landrum
6d7b2b0914
merge with master
2015-01-22 06:30:51 -05:00
Greg Landrum
53bf6a4609
merge master
2015-01-16 05:49:11 +01:00
Brian Kelley
95a92282d1
Dictionary access is saniztized and optimized.
...
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
2015-01-15 12:23:29 -05:00
Nadine Schneider
d8ee04b5b7
Bugfix in the chirality handling of chemical reactions
2015-01-09 10:34:28 +01:00
Greg Landrum
775369bbf1
update to new canonicalization
2014-12-31 06:36:40 +00:00
Greg Landrum
e6826d335a
remove some compile warnings
2014-11-03 13:30:00 +01:00
Schneider
2b05873136
ChemReactionUtils: remove unused/specialized functions from interface
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- specialized utils functions only used in the pgsql cartridge were removed
from the interface
2014-08-25 16:30:09 +02:00
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
...
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
...
(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;
...
this probably needs some more work
2012-10-10 10:17:52 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
...
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;
...
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;
...
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.
...
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";
...
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
