Greg Landrum
87786c08b5
Merge branch 'master' into modern_cxx
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# 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 )
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* 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
0eb715ed5e
initial pass at dative directions ( #1254 )
2017-01-27 17:25:58 -05:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Brian Kelley
95a92282d1
Dictionary access is saniztized and optimized.
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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
c26cbc26cb
switch to using references to smart pointers for the Match functions;
...
really ought to re-examine when/how we are passing smart pointers
around in general, but that is a bigger job.
Ref: http://herbsutter.com/2013/06/05/gotw-91-solution-smart-pointer-parameters/
2014-05-10 06:21:27 +02:00
Greg Landrum
34ab68ca2a
introduce QueryBond::QueryMatch, as with QueryAtoms;
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all tests passing;
performance tests still needed
2014-05-07 05:29:25 +02:00
Greg Landrum
4a14a52674
Fixes #153
2013-11-15 06:47:18 +01:00
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
ec2c2042e8
remove the vflib usage code from Substruct area
2010-04-19 07:45:22 +00:00
Greg Landrum
44b5041ef2
fix and test sf.net bug 2884178
2009-10-24 06:01:32 +00:00
Greg Landrum
f3dc387bc4
merge changes from revs991:996 on Ullmann_9Feb2009 branch;
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get USE_VFLIB fulling working and make it the default
2009-02-28 16:52:06 +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
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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
30fe77b609
initial commit: passes all tests and seems to be faster than the original code
2009-02-09 16:19:31 +00:00
Greg Landrum
d5ffea669d
add support for chirality in substructure searches;
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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
88d596abca
get the AR_MOLGRAPH caching write with substructs; the current implementation introduces a core leak, so it is disabled by default
2006-10-19 05:24:05 +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
