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
Greg Landrum
7c1aa77c2e
remove a compiler warning in smiles.ll;
...
initial version of implementation of feature request 2047386; This all still needs some more testing
2008-08-12 05:52:25 +00:00
Greg Landrum
9c7f33a5c8
merge changes from QuerySerialization_6March2008 branch, revs 555:563, into the trunk;
2008-03-12 06:11:39 +00:00
Greg Landrum
4e7d182fcc
Support editable molecules in Python.
...
This is Feature Request #1764162
http://sourceforge.net/tracker/index.php?func=detail&aid=1764162&group_id=160139&atid=814653
This implementation has been tested on Windows
2007-07-31 05:30:11 +00:00
Greg Landrum
d5ffea669d
add support for chirality in substructure searches;
...
this only is going to work in cases where CIP codes have been (i.e. can be)
assigned to atoms.
2006-11-03 06:35:14 +00:00
Greg Landrum
81f341882e
try to get ChemTransforms checked in
2006-07-18 05:33:58 +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
