Commit Graph

44 Commits

Author SHA1 Message Date
Brian Kelley
bae005bd75 Dev/expose setquery to python (#2088)
* Expose SetQuery to python

* Add a default for maximum products generated by a reaction (maxProducts=1000)

* Add better documentation for test that used to raise exception

* properly import rdqueries
2018-10-08 22:26:52 +02:00
Greg Landrum
9277c1f578 Allow Atom.GetAtomSmarts() to return isomeric SMILES (#1902)
* Add more options to GetAtomSmiles() to control output.

The most important one here is that you can now directly control whether or not isomeric SMILES is generated.

Expand the python interface so that we have more control over Atom.GetSmarts()

* make the use of isomeric atomic smiles explicit (since we can)

* start release notes for 2018.09.1

* python formatting
2018-06-19 17:23:02 -04:00
Greg Landrum
ba12d98ad0 Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713)
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers

* Actually delete atoms and bonds...

* RWMol::clear now calls destroy to handle atom/bond deletion

* Changes broken Atom lookup for windows/gcc

* Adds tests for running with valgrind

* Adds test designed for valgrind and molecule deletions

* Removes RNG, actually tests bond deletions

* update swig wrappers

* deal with most recent changes on the main branch
2018-01-07 14:19:47 -05:00
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
769e6648e4 Fixes #1489 (#1556)
* move the describeQuery functions to the RDKit namespace.
They are generally useful

* Fixes #1489
2017-09-11 08:34:25 -04:00
Greg Landrum
915cf08faa run clang-format with c++-11 style over that 2017-04-22 17:19:10 +02:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
Greg Landrum
fbeb88e341 Fixes #1352 (#1353) 2017-03-06 11:22:54 -05:00
Greg Landrum
278efc427c Fixes #1088 (#1096)
merging this myself because it's trivial
2016-10-12 08:20:43 +02:00
Greg Landrum
99efdd2bd3 Fixes #1041 (#1070) 2016-09-22 14:38:13 +02:00
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
Greg Landrum
d2d0071373 Fixes #955 (#956) 2016-06-24 07:42:46 -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
Brian Kelley
1b69b940a8 Converts RuntimeError to better described ValueError 2016-01-17 16:33:34 -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
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
Greg Landrum
a743cff4d7 Fixes #573 2015-09-20 04:44:39 +02:00
Greg Landrum
797db2fa82 remove Atom::setMass() 2015-03-22 17:57:04 +01:00
Brian Kelley
93f31d07cd RDKit python API learns Atom/Bond Queries on properties
BondQuery was exposed to python
Atoms and Bonds can now set and Query String/Int/Bool
 and Double properties through python.
2015-03-11 23:22:35 -04:00
Nadine Schneider
0bbf3ec79b Add function to test if UpdatePropertyCache is necessary 2014-12-19 13:59:42 +01:00
Greg Landrum
1567ec4462 add getFullDescription() to Query;
Fixes #287
2014-05-22 15:18:07 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +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
c1836ae28a modify the monomer info interface so that it works with older boost versions 2013-10-17 23:00:26 -07:00
Greg Landrum
dcbceede73 initial python wrapper support (no tests yet) 2013-08-22 05:57:18 +02:00
Greg Landrum
b4f2ec374e Fixes: #61 2013-07-04 18:00:09 +02:00
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
6e2508972c all tests passing 2012-04-21 05:37:34 +00:00
Greg Landrum
617151e8c5 fix sf.net issue 3495619 2012-02-29 11:27:22 +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
7065810cfd - add describeQuery() method to atoms (this is primarily for debugging)
- add SetConjugation() and SetHybridization() methods for molecules.
2010-06-23 04:14:25 +00:00
Greg Landrum
f5a26c72b8 expose Atom.GetTotalDegree() 2010-05-11 15:07:24 +00:00
Greg Landrum
a5c010c91e add GetPropNames methods to Atoms and Bonds 2009-04-05 13:15:22 +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
6d3a9f6fb3 Check in a bunch of changes to fix radical handling.
These are connected to issues 2093420, 2091890, and 2091839
this still needs more testing.
2008-09-23 06:02:02 +00:00
Greg Landrum
ca857c820c a bit of refactoring. 2008-07-11 11:14:40 +00:00
Greg Landrum
41fa5fa7b0 The force argument to getExplicitValence and getImplicitValence wasn't doing anything 2008-06-12 05:44:57 +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
15a3b9b4c6 add HasQuery and GetSmarts methods 2007-08-03 16:48:45 +00:00
Greg Landrum
5d03333c22 setup svn keywords (should have done this before import... grn) 2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00