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67 Commits

Author SHA1 Message Date
Greg Landrum
3077ea75dc an optimization for when molecules have no stereochemistry indicated 2015-04-12 06:44:45 +02:00
Greg Landrum
97d70dd306 add compile-time option to use new sterochem 2015-04-10 09:47:17 +02:00
Greg Landrum
a66662b2a2 switch back to using the previous stereochemistry code for now 2015-04-10 09:47:17 +02:00
Nadine Schneider
7ddff9c71c Some performance fixes 2015-03-20 18:19:08 +01:00
Greg Landrum
6d7b2b0914 merge with master 2015-01-22 06:30:51 -05:00
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
Greg Landrum
52d44a1e47 At this point all C++ tests pass except the two postponed smiles tests dealing with fragment-smiles creation and the smiles test for issue 1844617 (this still needs to be tracked down and fixed). 
The commit is just from an untabify run
 2014-12-31 07:12:33 +00:00
Greg Landrum
ab0f1dcf60 rename to new_canon (probably should come up with a better name, but this will do for now) 2014-12-22 07:56:26 +00:00
Greg Landrum
cad05ca184 get rid of RankAtoms.cpp and 
move the remaining functionality from RankAtoms.h into the new file
RDGeneral/Ranking.h
 2014-12-22 07:35:58 +00:00
Greg Landrum
0d21cdc7c9 backup commit 2014-08-24 16:24:31 +02:00
Greg Landrum
6f909ed449 switch chirality to using unsigned ints 2014-07-27 08:09:00 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +02:00
Greg Landrum
0839cf41ad Fixes #210 2014-02-03 05:25:27 +01:00
Greg Landrum
deed4a9acf Merge branch 'Issue194_V3000MolWriter' 
Conflicts:
	Code/GraphMol/Chirality.cpp
	Code/GraphMol/FileParsers/test1.cpp
 2014-01-22 07:07:27 +01:00
Greg Landrum
c13a643e06 Fixes #191 2014-01-12 05:42:50 +01:00
Greg Landrum
11af614ebc more cleanups of this stuff 2014-01-01 17:35:35 +01:00
Greg Landrum
64366007e1 more C++ style cleanups 2014-01-01 17:16:25 +01:00
Greg Landrum
d779c850c9 further stereochemistry speedupb 2013-12-18 05:12:32 +01:00
Greg Landrum
4d47482f0f speed-up the stereochemistry cleanup 2013-12-18 04:59:30 +01:00
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: 
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 
(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) 
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); 
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: 
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: 
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 
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: 
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