Greg Landrum
ef60d71c6f
Allows CIS/TRANS double bonds to be de-pickled ( #1710 ) ( #1711 )
...
* Fixes #1710
* add an additional test for #1563 while we're here
2018-01-21 07:18:26 +01:00
Greg Landrum
46e494b387
Set atomic properties from SMARTS ( #1716 )
...
* set some chemical properties (charge, isotope) on query atoms when parsing from smiles
* fix an irritating cmake problem
* add explicit Hs too
* I think this is now done
2018-01-12 11:15:05 -05:00
Greg Landrum
f94e277856
another pass of clang modernize
2017-10-12 06:35:51 +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
db89172bf8
handle the heavy-atom degree queries differently ( #1560 )
...
* handle the heavy-atom degree queries differently
* Fixes #1563
* add a test for the heavy atom degree option
* Support (and test) adjustHeavyDegree in the cartridge too.
* test results
2017-09-12 16:10:15 -04:00
Greg Landrum
7c0bb0b743
clang-tidy output
2017-04-22 17:09:24 +02:00
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
Greg Landrum
c53af574e0
add a test for #713
2015-12-23 05:31:37 +01:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Greg Landrum
e37296d7c7
post review
2015-11-14 08:08:14 +01:00
Brian Kelley
5f59333a56
Silences unused parameters
2015-10-18 14:02:29 -04:00
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
7eca2ead35
Fixes #149
2014-01-01 09:24:06 +01:00
Greg Landrum
7b805988f1
rename AtomPeptideMonomerInfo->AtomPDBMonomerInfo;
...
remove element and charge fields
2013-08-20 17:07:37 +02:00
Greg Landrum
7e1843a2c5
initial set of tests in
2013-08-09 14:07:20 +02:00
Greg Landrum
ed84596422
fix and test issue 285
2013-02-01 04:12:41 +00:00
Greg Landrum
e55d73fa57
fix and test sf.net issue 280.
2013-01-08 12:56:24 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
d9949b6765
fixes and tests for sf.net issues 3496759, 3496799, and 3496800
2012-03-04 15:37:50 +00:00
Greg Landrum
33ed58db4d
fix and test issue 3316407
2012-02-16 05:09:21 +00:00
Greg Landrum
c3c929f02d
fix and test sf.net issue 3202580
2011-03-08 05:00:01 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
9edbb9909a
more extensive testing of pickler
2010-06-17 05:53:37 +00:00
Greg Landrum
c425bc8c03
fix and test sf.net Issue2788233
2009-06-01 13:04:33 +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
900a5b4090
further serialization tests
2008-03-14 10:13:51 +00:00
Greg Landrum
4b44b8fde7
mols with queries weren't writeable into smarts; that's fixed now
2008-03-14 06:46:38 +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
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
