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127 Commits

Author SHA1 Message Date
Matt Swain
e57b7a9bc8 Use numpy not numeric for boost 1.65+ - fixes #1581 (#1664) 
boost python numeric no longer exists in boost 1.65, so check boost version and conditionally use boost python numpy.
 2017-11-20 05:44:19 +01:00
Alain Vaucher
7795a425ff Further cmake improvements (#1515) 
* New syntax to import Qt5 dependency in MolDraw2D

* In QTDemo, not necessary to import Qt explicitly because it is automatically imported through target MolDraw2D

* improve import of Cairo dependency

* Remove explicit linking of Cairo in C++ examples

* Use imported targets for Boost

* Using imported CMake targets for Eigen

* Use imported targets for Threads

* Simplify sample CMakeLists

* Remove duplication

* a couple small changes for travis

* typo

* update toolchain to trusty

* switch to requiring at least boost 1.56

* typo

* update boost dependency to pull in the build that has more libraries

* meaningless commit to trigger travis

* switch to ust libc++

* install libc++

* check abi

* try the other one; disable py27 for the moment to speed things up

* switch to c++11, that seems necessary with the conda boost builds at the moment

* re-enable python2.7
 2017-08-07 15:49:08 +02:00
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
Greg Landrum
79e1f8b1fa compiles without numpy warnings, all tests pass on ubuntu 15.04 with numpy 1.10 2015-11-28 06:49:34 +01:00
Greg Landrum
d07f2ccd05 replace oldnumeric imports 2015-11-28 02:38:58 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
1cde397acb merge commit 2015-10-30 02:58:46 +01:00
Brian Kelley
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -04:00
Andrew Dalke
8747a30ecf removed a bare except from code that is no longer in use 2015-09-07 12:56:07 +02:00
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
Riccardo Vianello
95f60d21bc python3 portability fixes for pandas and the ipython notebook 2014-09-11 23:49:45 +02:00
Greg Landrum
03a5d8ac81 boost_system not required 2014-01-04 16:48:57 +01:00
Greg Landrum
06a11de24c more drawing updates 2013-03-22 04:02:19 +00:00
Greg Landrum
5b97b2ebab working towards a resolutin for github issue 13 2013-03-21 06:21:34 +00:00
Greg Landrum
1b2bcd38dc get draw demo working when cairo is not installed 2013-01-08 20:14:58 +00:00
Greg Landrum
e5640a1079 reflect move of cairo code 2012-12-04 05:16:00 +00:00
Greg Landrum
ee28352889 move the svg drawing code into GraphMol too 2012-12-03 16:03:02 +00:00
Greg Landrum
af4bf0a8c8 get the drawing demos building 2012-12-03 05:12:42 +00:00
Greg Landrum
49c8fdc591 this has been moved to Code/JavaWrappers several releases ago 2012-12-03 04:47:46 +00:00
Greg Landrum
38c5149c3e move c++ drawing code from Demo to GraphMol 2012-12-03 04:40:33 +00:00
Greg Landrum
f8c1999207 update build system to work with boost v1.51 2012-10-26 03:48:04 +00:00
Greg Landrum
4e90f88ab7 get dashes working in the cairo drawing; 
additional improvements to the drawing
 2012-09-20 04:12:24 +00:00
Greg Landrum
00b79222c7 modify drawing code so that it once again handles non-cyclic aromatic bonds (for fragments) 2012-09-19 02:52:37 +00:00
Greg Landrum
b50b4d4a5d add D. Cosgrove's qt demo 2012-08-29 03:33:14 +00:00
Greg Landrum
cb795c7b5d check in a contribution from David Cosgrove to improve drawing 2012-08-14 03:17:16 +00:00
Greg Landrum
ed8dd637e0 added 2011-08-15 03:38:32 +00:00
Greg Landrum
d67d7709a1 add a simple reaction example 2011-08-02 04:17:56 +00:00
Greg Landrum
c552ad6afc add isotope info to depictions 2011-07-01 03:52:01 +00:00
Greg Landrum
f0cd1b076e add a background fill 2011-06-20 04:06:14 +00:00
Greg Landrum
82dac76936 remove extra printing 2011-06-20 04:00:41 +00:00
Greg Landrum
c8995c1f54 experimental cairo support in C++ 2011-06-20 03:00:20 +00:00
Greg Landrum
6fa65fbc68 move the _VSA descriptors into C++ 2011-03-21 05:02:12 +00:00
Greg Landrum
4e27c74652 test TPSA 2011-03-16 06:40:58 +00:00
Greg Landrum
3510396ad0 expose and test descriptor calculators. 2011-03-16 06:33:04 +00:00
Greg Landrum
4325789d25 move lipinski descriptors to C++. 
rename CalcCrippenDescriptors -> calcCrippenDescriptors
 2011-03-14 10:24:42 +00:00
Greg Landrum
80e5f1f38a remove leak 2011-03-09 05:10:14 +00:00
Greg Landrum
9a9ad4a534 expand atom and bond api 2011-03-09 05:07:00 +00:00
Greg Landrum
9fe5a57aec support MolSuppliers and ROMol.{set,get}Prop 2011-02-26 05:53:03 +00:00
Greg Landrum
f7165fac1a minor wrapper cleanups 2011-02-24 07:34:26 +00:00
Greg Landrum
ae19a9d54b add bitvect morgan fps; rename morgan fp functions 2011-02-24 04:23:51 +00:00
Greg Landrum
6191520012 updated std::list and std::vector support for java 2011-02-21 18:31:47 +00:00
Greg Landrum
0bc15ead9d additions to drawing code and SWIG wrappers 2011-02-21 06:45:34 +00:00
Greg Landrum
27f7fa6f6f better handling of uint32, uint64, etc. 2011-02-04 16:38:46 +00:00
Greg Landrum
b685d2917e get this building on windows 2011-01-13 05:37:22 +00:00
Greg Landrum
670d0d84c3 stop taking out the JVM with our exceptions. 
this should be done at a somewhat finer grain, but let's put out the fire first.
 2010-12-27 13:44:22 +00:00
Greg Landrum
5c3cbbd695 add a crude MolToSVG function 2010-12-20 04:31:08 +00:00
Greg Landrum
31e5d6cff6 update the svg generation; improved atomic text 2010-12-20 04:27:50 +00:00
Greg Landrum
ce635c7b45 crude 2010-12-17 05:17:42 +00:00
Greg Landrum
d29e0934b7 initial pass at very crude svg translation 2010-12-17 04:34:16 +00:00
Greg Landrum
4a71e99396 switch reaction pickler over to using int vects (like molecules) 2010-11-19 15:57:41 +00:00