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64 Commits

Author SHA1 Message Date
Greg Landrum
5992c6fd23 - made the ResonanceMolSupplier really lazy, i.e. resonance structure enumeration is only carried out when the user asks for a structure or when the user explicitly request that calling the enumerate() member function. This makes object creation fast and enables calling getNumConjGrps(), getBondConjGrpIdx() and getAtomConjGrpIdx() member function without incurring in the cost of necessarily enumerating resonance structures 
- now bonds and atoms with do not belong to conjugated groups get a -1 index
- added a few Python wrappers
- added a few tests
 2015-11-04 05:39:46 +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
380badc12f Removes IFDEF internal API points, uses BOOST_FOREACH 2015-10-29 13:49:35 -04:00
Brian Kelley
bf99daea04 Merge branch 'master' into fix/fix-unlocking-mutexes-that-arent-locked 
Merged with ResonanceSupplier based changes
 2015-10-28 18:10:47 -04:00
Brian Kelley
340d4274cc Fixes trying to unlock mutexes that aren't locked 2015-10-28 16:42:36 -04:00
Paolo Tosco
f43677b978 - fixed a problem with thiocarboxylates/thiolates not being perceived 
as conjugated like their oxygen analogs
- fixed an issue with large numbers of resonance structures exceeding
  the unsigned int allowance
- implemented the uniquify feature properly
- uniquify now defaults to false when using the ResonanceMolSupplier-
  enabled SubstructMatch() version
- the concept of 'laziness' is now clearer
- TODO:
  * remove some debugging info
  * move classes from .h to .cpp
  * SWIG wrappers
  * improve resonance structure sorting for degenerate resonance
    structures
  I will do all of the above ASAP
 2015-10-21 20:06:53 +01:00
Paolo Tosco
eaa187b03d - added ResonanceMolSupplier 
- added overloaded SubstructMatch() version supporting ResonanceMolSupplier
- added relevant Python wrappers
- added C++/Python tests
 2015-10-04 23:21:28 +01:00
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
4b8caf2ceb Fixes #409 2015-01-10 07:21:55 +01:00
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; 
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
126e75a8b3 comment out the new substruct atom-match caching code; it does not seem to actually make things faster 2013-04-27 03:04:12 +00:00
Greg Landrum
d07a674fa4 fix and test GitHub issue 15 2013-03-28 12:51:05 +00:00
Greg Landrum
c00d323eee set props 2013-03-28 10:30:40 +00:00
Greg Landrum
d79491aaf9 use caching of vertex matches to speed up the VF2 searches 2013-03-28 10:28:13 +00:00
Greg Landrum
24764635d8 initial support for double bond stereochem in substructure searching 2013-03-11 05:36:00 +00:00
Greg Landrum
414b579b1c first pass at support for supporting atomic stereochemistry in substructure matches 2013-03-10 07:33:00 +00:00
Greg Landrum
14314b01ad add cmake configure variable to make multi-threaded stuff optional 2012-12-17 04:07:20 +00:00
Greg Landrum
f8c1999207 update build system to work with boost v1.51 2012-10-26 03:48:04 +00:00
Greg Landrum
bcf6310f11 an attempt to make handling of recursive SMARTS threadsafe. 
This passes the tests here and in knime on linux64. Other OSs still need testing
 2012-09-29 09:01:43 +00:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
b993f89afe remove the bjam-based build system 2010-09-27 03:54:07 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
4db8233db6 sync with trunk 2010-09-10 05:12:41 +00:00
Greg Landrum
052ec66542 cleanups: 
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
 2010-09-08 04:25:57 +00:00
Greg Landrum
cb6cdb99b3 merge in a set of changes from Riccardo V. to install .h files as well; 
this needs more testing.
 2010-09-04 14:07:22 +00:00
Greg Landrum
0ce95829a5 cleanup deprecated args 2010-08-21 00:16:55 +00:00
Greg Landrum
f42f479d28 enabling infrastructure for making repeated recursive 
smarts queries run faster (like vector bindings). Though there is an addition to the smarts parser
exposed here, I do not recommend using it in client code.
 2010-06-03 10:02:15 +00:00
Greg Landrum
ec2c2042e8 remove the vflib usage code from Substruct area 2010-04-19 07:45:22 +00:00
Greg Landrum
49ef84ed45 a bunch of fixes to SLN handling 2010-04-11 09:06:52 +00:00
Greg Landrum
803b459289 merge in changes from trunk in preparation for moving this stuff onto the trunk 2009-10-25 05:51:56 +00:00
Greg Landrum
44b5041ef2 fix and test sf.net bug 2884178 2009-10-24 06:01:32 +00:00
Greg Landrum
53485592ca builds on windows with visual studio; need to pass back to linux now 2009-10-01 13:35:48 +00:00
Greg Landrum
76297b0fff builds and passes tests on linux 2009-09-28 11:02:18 +00:00
Greg Landrum
96adbc11ea remove the deprecated assign{Atom,Bond}ChiralCodes functions 2009-08-02 15:33:08 +00:00
Greg Landrum
9cabf87374 remove vflib from Jamfiles 
remove const specifiers from return values in DataStructs
add initial pass at query-query matching for Atoms and Bonds
fix and test for sf.net issu 2738320
add Mol.AddRecursiveQuery() method to Mol
 2009-06-29 11:47:38 +00:00
Greg Landrum
b418472bd5 cleanup 2009-04-20 08:14:52 +00:00
Greg Landrum
17fa9210e6 merge revs1065:1087 from vf2 branch into trunk 2009-04-18 18:25:27 +00:00
Greg Landrum
8e731f9e70 move the MolDiscriminators calculations into Subgraphs in order to remove the lapack dependency from the core molecule code; 
At some point the BalabanJ calculation, still in MolDiscriminators.cpp, should be 
moved to MolDescriptors.
 2009-04-10 04:09:49 +00:00
Greg Landrum
f3dc387bc4 merge changes from revs991:996 on Ullmann_9Feb2009 branch; 
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 
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
4056ad7e6c use vertex degree to prune matches 2009-02-09 16:49:26 +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
8bf7a4c187 now all tests pass here as well 2009-02-03 05:26:10 +00:00
Greg Landrum
2580fbaaa2 this is probably a ways from done, but now at least we can run bjam under mingw without it immediately erroring out 2008-11-15 17:14:13 +00:00
Greg Landrum
21bb475b61 further jamfile mods for macosx 2008-10-19 05:36:09 +00:00
Greg Landrum
89a34d1a39 get this building on Darwin; NOTE: this may not work on win or linux yet 2008-09-03 19:24:35 +00:00
Greg Landrum
e8f3536845 remove a bunch of compiler warnings 2008-05-26 20:05:57 +00:00
Greg Landrum
8424d36830 get things building on windows. 2008-04-08 18:24:56 +00:00