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83 Commits

Author SHA1 Message Date
gedeck
e9af48ffd7 Issue1071/yapf (#1078) 
* Issue #1071: add yapf configuration file

* yapf formatting of Code directory

* yapf formatting of Contrib directory

* yapf formatting of Data directory

* yapf formatting of Docs directory

* yapf formatting of External directory

* yapf formatting of Projects directory

* yapf formatting of Regress directory

* yapf formatting of Scripts directory

* yapf formatting of Web directory

* yapf formatting of rdkit directory
 2016-09-23 04:58:46 +02:00
Brian Kelley
71a0ae32b2 Adds replaceCore function that takes a matchVect (#1013) 
* Adds replaceCore function that takes a matchVect

* Fixes error reporting, adds tests

* Switches PRECONDITION to ValueError exceptions

* Fixes MatchVectType annoyance in swig.  Don't know why this is necessary.

* Silences warnings

* Adds working doctests and better explanations.
 2016-08-17 04:40:59 +02:00
Brian Kelley
fe7d4fefb3 Dev/chemtransforms chirality (#1006) 
* Adds useChirality to replaceCore, fixes atom ordering
  n.b. when replaceDummies==False and labelByIndex==True
   the indices used are the indices of the dummy atom,
   previously they were the atoms the dummy was connected
   to.

* Adds useChirality to the remaining functions in ChemTransforms

* Adds a mess o tests

* Fixes labelByIndex=false ordering for dummies

* Removes debugging statements
 2016-08-09 04:41:36 +02:00
Greg Landrum
b0f140a55c Fixes #511 2016-03-29 16:56:15 +02:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Brian Kelley
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -04:00
Greg Landrum
97d8b8a7db this was a similar bug to #584 2015-08-27 10:13:46 +02:00
Nadine Schneider
5d963846b8 merge 2015-04-10 09:44:18 +02:00
Nadine Schneider
7e59908121 SmilesWrite: introduce new function for fragments 2015-03-20 16:38:23 +01:00
Riccardo Vianello
7c346d7c2e Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 22:31:48 +01:00
Greg Landrum
7fa02f748b Fixes #430 2015-02-04 13:45:47 +01:00
Greg Landrum
2fbea33612 Fixes #429 2015-02-04 10:20:13 +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
Greg Landrum
3f23c91eba did not have the version for breakSomeBonds() quite right 2014-11-22 10:42:17 +01:00
Greg Landrum
1725e22cca allow tracking the number of cuts made by the fragmentation code on a per-atom basis 2014-11-22 07:57:39 +01:00
Greg Landrum
2187437649 fix a couple typos 2014-07-07 15:57:27 +02:00
Greg Landrum
288feb7a8a support partial fragmentation on bonds; 
Fixes #288
 2014-07-02 05:47:02 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +02:00
Greg Landrum
302b84960b improve docs; 
cleanup some compiler warnings;
add parseQueryDefText()
 2014-05-03 06:45:35 +02:00
Greg Landrum
d7971cc40c Fixes #171 2013-12-06 06:54:31 +01:00
Greg Landrum
4ace62f019 remove more clang warnings 2013-12-02 05:10:23 +01:00
Greg Landrum
6c354852d1 small cleanups 2013-11-07 10:57:18 +01:00
Greg Landrum
6d936e9d31 Merge branch 'master' of https://github.com/rdkit/rdkit 2013-11-02 07:23:31 +01:00
Greg Landrum
95c6c7f261 fragmentOnBonds() fix 2013-11-02 07:17:42 +01:00
Greg Landrum
afb9f1ddfa add fragmentOnBonds() to python API 
Fixes #142
 2013-10-30 04:59:29 +01:00
Greg Landrum
70f2829524 do not include _static versions for test links. This breaks on windows 2013-03-22 05:18:35 +00:00
Greg Landrum
5a340dd454 Fix a typo 2013-03-01 06:53:17 +00:00
Greg Landrum
c595c29cb2 add missing headers for "make install" 
fixes github issue 2
 2013-02-05 04:57:59 +00:00
Greg Landrum
ea42bf5465 BRICS-related bug fixes 2013-02-05 04:56:10 +00:00
Greg Landrum
89398a10c2 make sure computed props get cleared 2013-01-31 04:54:28 +00:00
Greg Landrum
84d6ddb3f3 add fragmentOnBRICSBonds() 2013-01-30 06:31:06 +00:00
Greg Landrum
fa2b82b606 breaking all BRICS bonds now works 2013-01-29 16:22:27 +00:00
Greg Landrum
00655e7bd6 backup commit; may not build 2013-01-29 06:28:31 +00:00
Greg Landrum
052b87564c add one more test for issue 275 2013-01-09 13:12:27 +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
68e370d581 initial pass at a fix for sf.net issu275 2012-12-18 17:16:06 +00:00
Greg Landrum
bef74c1c81 initial support for reading query files. Python wrapper still needs to be done. 2012-12-17 10:28:35 +00:00
Greg Landrum
57572918de add initial support for addRecursiveQueries to ChemTransforms. 
active and tested in C++ and python, in the SWIG wrapper but untested.
still needs linux and windows builds.
 2012-12-17 09:06:02 +00:00
Greg Landrum
cfaea83d7d optimizations for molecule construction 2012-08-27 04:52:27 +00:00
Greg Landrum
93f6445e01 minor cleanup to RWMol::insertMol; add combineMols to ChemTransforms 2012-07-10 04:00:46 +00:00
Greg Landrum
2e5b33e2fd fix and test issue 3537675 2012-07-02 03:07:02 +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
e7d25d7973 tests passing except reactions 2012-04-21 04:40:55 +00:00
Greg Landrum
a99ad44859 clean up some compiler warnings 2011-12-31 15:58:57 +00:00
Greg Landrum
3b751bad46 fix and test issue 3453144 2011-12-13 04:56:56 +00:00
Greg Landrum
3ba11316b2 initial pass at requiring core-dummy matches in replaceCore; remove an extra header import from MolOps.cpp 2011-03-28 06:13:48 +00:00
Greg Landrum
633be739b0 - fix an edge case with disconnected molecules in the MurckoDecompose code. 
- test that empty results are handled properly in MurckoDecompose.
 2011-03-04 06:37:26 +00:00
Greg Landrum
f3a570fe29 add the test file 2011-03-04 05:23:13 +00:00
Greg Landrum
e1e1e5929d fix assignment of dummy positions in replaceCore 2011-03-03 05:02:13 +00:00