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181 Commits

Author SHA1 Message Date
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
7a49dd3bb9 fixes #1023 (#1027) 2016-08-18 16:29:29 -04:00
Brian Kelley
ddf7c73b50 Adds Atom atom map and rlabel apis (#1004) 
* Adds Atom atom map and rlabel apis

* Moves RLabels to their own namespace, adds other properties.

* Removes namespaces, liberally adds Atom to function names.

* move detail::computedPropName to RDKit::detail::computedPropName
 2016-08-11 04:46:41 +02:00
Brian Kelley
900fc391aa Fixes middle-justified symbols in sd files, adds M_CHG tests (#1002) 
* Adds boost::trim, M  CHG tests

* stoi is a c++11 feature

* Actually test charges
 2016-08-02 14:41:08 +02:00
Paolo Tosco
63b6bdef46 - RCSB SDF files which feature right-justified element names can now be parsed (#994) 
- added a relevant test
 2016-07-27 14:49:52 +02:00
Greg Landrum
339fa081e5 Merge fix/github908 branch 2016-07-27 04:49:55 +02:00
Greg Landrum
d30bf4a6df the fix for #188 also 
fixes #192
 2016-03-29 13:19:10 +02:00
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
added01998 Prefer wedging bonds to Hs when possible 
Fixes #772
 2016-02-15 14:32:30 +01:00
Greg Landrum
2ca85c775f Fixes #741 2016-02-13 05:38:03 +01:00
Brian Kelley
6d5b7a0305 Adds more extensive tests (recursion, multithreading) 2016-01-20 17:09:58 -05:00
Brian Kelley
ae13f0a93a Adds tests for locale switching 2016-01-20 17:09:58 -05:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Brian Kelley
210f2951e0 Silences warnings in tests 2015-10-18 21:20:11 -04:00
Brian Kelley
54311dff9c Suppresses warnings in tests 2015-10-18 16:09:58 -04:00
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
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
2d8500b407 Fixes #314 2014-08-21 07:29:09 +02:00
Greg Landrum
6b26036f6a Fixes #269 2014-05-23 08:26:26 +02:00
Greg Landrum
e4cfc340a4 support white and black lists for getMolFragsWithQuery 2014-03-25 08:18:30 -04:00
Greg Landrum
fe07610683 copy over conformers too. Part of #234 2014-03-18 06:06:24 +01:00
Greg Landrum
196c2278fb Fixes #234 2014-03-17 08:33:07 +01:00
Greg Landrum
601c21f19d Fixes #189 2014-03-13 05:23:56 +01:00
Greg Landrum
75be63fd6b merge with trunk 2014-02-09 05:00:18 +01:00
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
aab11535e8 Fixes #196 2014-01-16 02:07:03 -05:00
Greg Landrum
53a2937eb6 Fixes #194 2014-01-15 03:19:26 -05:00
Greg Landrum
c13a643e06 Fixes #191 2014-01-12 05:42:50 +01:00
Greg Landrum
0ce8f23c6e further R group handling 2014-01-10 04:24:22 +01:00
Greg Landrum
f653e9e961 more isotope fixing 2014-01-08 06:51:48 +01:00
Greg Landrum
4b72d1b153 add (non-standard) handling of R groups to v3k mol parser 2014-01-08 05:22:15 +01:00
Greg Landrum
3f90cecd9c Fixes #164 2013-12-31 08:27:09 +01:00
Greg Landrum
355556b7de get atom lists working 2013-12-29 07:05:25 +01:00
Greg Landrum
0b8bd3079d fix isotope handling in V3K 2013-12-28 07:37:52 +01:00
Greg Landrum
d280c90117 a few more tests and a fix to not print empty bond blocks 2013-12-26 07:40:16 +01:00
Greg Landrum
9e91538d64 get rgroups working 2013-12-25 08:18:44 +01:00
Greg Landrum
329841d9ba add some tests; add radicals to output 2013-12-24 06:56:12 +01:00
Greg Landrum
ae14fa3bd9 add support for the ZCH and HYD elements in mol files 2013-12-07 17:40:04 +01:00
Greg Landrum
0f92877061 stop messing up aromaticity and hybridization; 
all tests pass, but this is definitely not the most efficient thing.
 2013-11-30 08:07:09 +01:00
Greg Landrum
3b0c72c4bf initial pass at ZBO support. 
does not yet handle the HYD and ZCH lines
 2013-11-30 06:58:03 +01:00
Greg Landrum
f6517b572e Fixes #166 2013-11-25 05:36:45 +01:00
Greg Landrum
1501af51a5 PDB reader/writer fixes; 
add MolToMolFile() to python API
 2013-10-25 05:02:09 +02:00
Greg Landrum
e0e741bd49 very minimal testing of pdb reading/writing 2013-10-11 16:58:20 +02:00
Greg Landrum
e51d2c1020 Fixes #118 2013-10-05 16:19:02 +02:00
Greg Landrum
cc154d03ee handle isotopic H better from ctabs 2013-08-23 12:59:09 +02:00
Greg Landrum
2546ea0d7a Fixes #82 2013-08-23 09:18:04 +02:00