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57 Commits

Author SHA1 Message Date
Jeff van Santen
e593d13f6f Fix typo in GetBoolProp documentation (#1770) 
@jvansan Thanks!
 2018-03-23 12:25:36 +01:00
Greg Landrum
1efa8e696e another clang-format run 2017-10-12 06:42:15 +02:00
Greg Landrum
87786c08b5 Merge branch 'master' into modern_cxx 
# Conflicts:
#	.travis.yml
#	Code/GraphMol/FileParsers/MolFileParser.cpp
#	Code/GraphMol/FileParsers/MolFileStereochem.cpp
#	Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
#	Code/GraphMol/MolAlign/testMolAlign.cpp
#	Code/GraphMol/MolDraw2D/MolDraw2D.cpp
#	Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
#	Code/GraphMol/QueryOps.cpp
#	Code/GraphMol/ROMol.cpp
#	Code/GraphMol/SmilesParse/test.cpp
#	Code/GraphMol/Trajectory/Trajectory.cpp
#	Code/GraphMol/Wrap/Atom.cpp
#	Code/GraphMol/Wrap/Bond.cpp
#	Code/GraphMol/new_canon.cpp
#	Code/RDGeneral/testDict.cpp
#	Code/SimDivPickers/Wrap/MaxMinPicker.cpp
 2017-10-05 05:58:38 +02:00
Greg Landrum
0775cf0da5 add substructure searches of Mols using MolBundles from Python (#1603) 2017-10-03 17:46:44 -04:00
Greg Landrum
6ed76d9fff Expose the MolBundle to python (#1583) 
* backup

* initial mol bundle wrapper

* Move the substructure matching wrapper code to a template header file to clean stuff up.

* update python docs
 2017-09-26 13:00:53 -04:00
Brian Kelley
6a76fc9381 Dev/add update props api (#1479) 
* Adds RDProps updateProps API point

* AdjustQuery now copies over original atom data to the query ato

* Preserves existing data on the replacing atom

* Exposes preserveProps to Python replaceAtom/Bond
 2017-07-10 04:38:59 +02:00
Brian Kelley
b76af93513 Dev/add update props api (#1479) 
* Adds RDProps updateProps API point

* AdjustQuery now copies over original atom data to the query ato

* Preserves existing data on the replacing atom

* Exposes preserveProps to Python replaceAtom/Bond
 2017-07-10 04:36:12 +02:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
Greg Landrum
283332e4de Fix/github1366 (#1382) 
* add test

* update that test

* add python version of a test

* add some preconditions before dereferencing pointers

* make data members of AtomIterators private (not sure why these were ever made public)

* Fixes #1366

* switch to using std::runtime_error

* switch python tests too

* move the tests from the C++ side to be on the python side.
 2017-03-28 16:01:36 -04:00
Brian Kelley
e70599a12e Dev/pickle properties (#1277) 
* Adds pickling of properties (optional)

* Ignores RDKit::Dict::Pairs - previously private

* Fixes AllProps definition

* Fixes BondProps seperation

* Fixes reaction pickling - Adds ability to pickle atom + QueryAtom

* Bumps pickle version

* Removes fugly post-increments

* Changes Default to NoProps

* Tests more options for pickling

* Runs clang format

* Adds get/setDefaultPropertyPickleOptions, exposes to python

* turns tests back on.

* Fixes enum (clang was allowing c++11 semantics)

* Adds global settings test

* Code/GraphMol/testPicklerGlobalSettings.cpp
 2017-02-09 16:06:01 +01:00
Brian Cole
a4054c0657 Expose RWMol.ReplaceBond to Python (#1174) 
This will be more useful in a later pull request I'm working on that
exposes QueryBonds to Python. Though it is usable without QueryBonds
as well, so submitting this for now.
 2016-11-21 09:41:53 -05:00
Greg Landrum
3b41772851 add support for a default constructor to the python-exposed RWMol class (#1129) 2016-10-29 02:17:12 +02:00
Greg Landrum
2644a7af02 Allow the output of ROMol::debugMol() to show up in jupyter (#1110) 
* allow Mol::debug output to show up in jupyter notebooks

* use rdInfoLog instead of rdWarningLog

* fix a typo
 2016-10-17 13:03:15 -04:00
Brian Kelley
2debdfde0d Adds RDAny (smaller generic holder) Updates all used dictionaries (#896) 
* Adds RDAny (smaller generic holder) Updates all used dictionaries

This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.

* Removes code duplication

* Converts CHECK_INVARIANT to TEST_ASSERT

* Fixes DoubleTag issue

* Adds Bool to DoubleMagic implementation

* Removes reference to property pickler
 2016-05-29 17:04:21 +01:00
Paolo Tosco
2b3a818f84 - removed the dependency on Trajectory from ROMol and ForceField 2016-05-11 19:37:09 +01:00
Paolo Tosco
d16b312ee6 - Completely revised coordinate ownership 
- Implemented Python wrappers
- prepared relevant test cases
 2016-04-24 23:30:25 +01:00
Brian Kelley
d5299d8ad6 Use GetProp (as opposed to MolGetProp) 2016-01-19 07:45:43 -05:00
Brian Kelley
1b69b940a8 Converts RuntimeError to better described ValueError 2016-01-17 16:33:34 -05:00
Brian Kelley
5c3f864980 Fixes GetPropsAsDict to return non-string values 2016-01-17 11:20:30 -05:00
Brian Kelley
5c398036da Adds GetPropsAsDict to Mol/Atom/Bond 2015-12-21 08:44:59 -05:00
Brian Kelley
ae49289a62 Changes GetUInt to GetUnsigned 2015-12-21 08:44:33 -05:00
Brian Kelley
bd7782465f Exposes Get/Set Double, Int, Uint and bool props to molecules 2015-12-20 09:49:29 -05:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
5618819c64 merge #641 2015-11-14 05:03:24 +01:00
Paolo Tosco
3d48ba72e1 - added threading support to ResonanceMolSupplier and relevant tests 
- added threading support to the ResonanceMolSupplier-enabled
  SubstructMatch() and relevant tests
- modified/removed some code in O3AAlignMolecules.cpp which doesn't
  seem necessary anymore
- modified Code/GraphMol/CMakeLists.txt to allow building
  on Windows
 2015-11-01 23:01:34 +00:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Brian Kelley
52732df2f0 Fixes #629 - python GetSubstructureMatch thread safety 2015-10-13 15:36:11 -04:00
Greg Landrum
a3414b2d6d Fixes #572 2015-08-24 10:46:42 +02:00
Greg Landrum
2b107bd886 Fixes #467 2015-04-01 02:37:02 +02:00
Greg Landrum
b78bb40ca5 Fixes #384 2015-03-30 07:20:24 +02:00
Brian Kelley
d61c78581d RDKit learns how to release the GIL in python 2015-03-11 20:08:09 -04:00
Brian Kelley
f0bc4d0817 rdkit learns how to wrap a proper RWMol (kinda) 
RWMol becomes a replacement for EditableMol.
It has the EditableMol interface in addition
to the ROMol interface.  In the future this
may or may not grow the RWMol C++ interface.

Conflicts:
	Code/GraphMol/Wrap/rough_test.py
 2015-01-30 12:16:23 -05:00
Greg Landrum
4b8caf2ceb Fixes #409 2015-01-10 07:21:55 +01:00
Nadine Schneider
0bbf3ec79b Add function to test if UpdatePropertyCache is necessary 2014-12-19 13:59:42 +01:00
Greg Landrum
50332b599e get some of the pickle problems resolved; this probably only works with python3 and is not yet 100% functional 2014-06-19 06:05:42 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
118306d1f9 expose useQueryQueryMatch info to python; 
Fixes #258
 2014-05-07 06:04:38 +02:00
Greg Landrum
819272f375 initial batch of decent QueryAtom support for python; 
Fixes #181
 2013-12-17 05:55:18 +01:00
Greg Landrum
4520ee1263 more progress towards #181; the problem now is that there is 
not really anyway to build a query atom from python
 2013-12-16 05:24:04 +01:00
Greg Landrum
aef75dced2 Progress towards #181 2013-12-14 15:45:45 +01:00
Greg Landrum
62efc6ab42 Fixes #133 2013-10-17 02:51:39 +02:00
Greg Landrum
d1cae9346f an initial version of the "atomBits" feature for RDKit fingerprints 2013-03-12 04:39:43 +00:00
Greg Landrum
01afbca87b add ClearProp() method to atoms and bonds; modify Mol.ClearProp() so that it no longer raises an exception when the property is not there 2012-12-01 06:28:00 +00:00
Greg Landrum
8d9fd053b2 fix and test issue 256; 
this is a change that affects backwards compatibility.
 2012-10-08 03:18:05 +00:00
Greg Landrum
d380027514 fix and test for issue 3510149 2012-03-23 04:47:22 +00:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
845687f6f3 expose Bond.GetOwningMol(); 
> fix and test issue 3007178
 2010-05-26 16:18:43 +00:00
Greg Landrum
de2286c17c doc update 2010-05-12 09:30:24 +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