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Release_2016_09
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52 Commits

Author SHA1 Message Date
Greg Landrum
406c222b13 Fixes #1251 (#1252) 2017-02-05 08:34:27 +01:00
Greg Landrum
f0bb85dfdb Fixes #1049 (#1050) 
* fixes #1049
That was almost too easy

* elaborate the test a bit
 2016-09-01 09:22:17 +02:00
Greg Landrum
8009b867b5 Fixes #1034: squiggle bonds are now preserved if no sanitization is done (#1043) 
* backup commit

* typo

* forgot the test file

* also test that atom chirality is handled properly
 2016-08-30 16:02:31 +02:00
Greg Landrum
91212a4eb3 A variety of drawing-related changes (#986) 
* Fixes #982
also changes bond-wedging algorithm to favor lighter non-ring bonds

* prefer wedging bonds to lower-degree atoms

* Fixes #983

* small fixes
- Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom
- Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom.

* Fixes #985

This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
 2016-07-25 17:28:41 -04:00
Greg Landrum
53b6e52765 ok, this time it is a proper fix 2016-03-29 13:09:22 +02:00
Greg Landrum
9a13afba24 Fixes #188 2016-03-29 10:58:56 +02:00
Greg Landrum
55e2f7c821 document a magic constant 2016-02-15 15:02:54 +01:00
Greg Landrum
added01998 Prefer wedging bonds to Hs when possible 
Fixes #772
 2016-02-15 14:32:30 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
136de13e8d Fixes #611 (testing still required) 2015-09-10 15:52:20 +02:00
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
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
c6dd83a47c Fixes #360 2014-10-25 12:13:01 +02:00
Greg Landrum
cd03d877fb Fixes #337 2014-10-04 14:44:42 +02:00
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
e38e60d283 Fixes #186 2014-01-11 06:01:30 +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
03b333734e some C++ style cleanups 2014-01-01 16:50:09 +01:00
ptosco
ec8eb5a1bf - Changed all occurrences of RDKit::PI into M_PI 
- added #ifdef M_PI (...) #endif in all relevant places
- made length() and sqLength() method consistent
  with respect to usage of pow(x, 2) vs x*x in
  Code/Geometry/point.h
- removed gzip-related boost.iostreams dependency and
  replaced with portable "cmake -E tar xzf" command
  in Code/ForceField/MMFF/CMakeLists.txt
 2013-09-20 17:45:41 +02:00
Greg Landrum
cc154d03ee handle isotopic H better from ctabs 2013-08-23 12:59:09 +02:00
Greg Landrum
8efd65111a allow molblock generation to work even if rings have not be found 2012-05-24 15:02:31 +00:00
Greg Landrum
43dc95bfea fix issue 3528136 2012-05-20 08:54:08 +00:00
Greg Landrum
4536db1630 document the known remaining failure point 2012-05-09 14:54:27 +00:00
Greg Landrum
4b40a7d3f4 a bit more robustification around issue 3525000b 2012-05-09 13:41:22 +00:00
Greg Landrum
03ecdbc1cc fix and test issue 3525000 2012-05-09 13:13:46 +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
f6ff447b0b fix and test issue 3376319 
NOTE: the R/S labels that one gets for phosphates do not match those from chemdraw/marvin
 2011-07-23 16:53:04 +00:00
Greg Landrum
8b077509e9 another piece of Issue3375684 2011-07-23 04:47:17 +00:00
Greg Landrum
67eccc1620 fix and tests Issue3375684 2011-07-23 03:49:36 +00:00
Greg Landrum
951f4b7fd3 fix and tests sf.net issue3375647 2011-07-22 15:53:05 +00:00
Greg Landrum
f61d48cadf add some of the inchi rules for ignoring mol file stereochemistry 2011-07-22 14:21:39 +00:00
Greg Landrum
10cb677b33 fix and test Issue3374639 2011-07-22 10:55:40 +00:00
Greg Landrum
8734dc86c8 cleanup 2011-03-30 03:28:35 +00:00
Greg Landrum
5c14f36de7 partial fix for Issue3228150 2011-03-25 03:26:03 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
80c0a8825e fix issue 3009836; partial fix for issue 3009911 2010-06-01 17:54:49 +00:00
Greg Landrum
c235b26126 fix and test issues 3009756 and 3009836 2010-06-01 09:39:42 +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
268b08ec17 fix and test sf.net issue 2804599 2009-06-11 04:55:44 +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
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
Greg Landrum
5e9d1e8307 fix and test issue 1965035 2008-05-16 05:35:50 +00:00
Greg Landrum
65d1d8d63b we should be able to generate mol files even without reasonable conformers 2008-02-29 07:47:16 +00:00
Greg Landrum
a788e29511 merge the changes from the CanonicalizerRework30Nov branch in. 
The changes are revs 451:498.
 2008-01-30 14:53:04 +00:00
Greg Landrum
66ec16dedf Fix and test sf.net bug 1725068: 
http://sourceforge.net/tracker/index.php?func=detail&aid=1725068&group_id=160139&atid=814650
 2007-06-06 17:25:08 +00:00
Greg Landrum
db1b02febf fix and test for sf.net issue 1718794 
http://sourceforge.net/tracker/index.php?func=detail&aid=1718794&group_id=160139&atid=814650
 2007-05-14 17:27:59 +00:00
Greg Landrum
9bd4c59606 substantial optimization of SD/mol file parsing;some reformattig 2007-03-20 21:06:37 +00:00