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1978 Commits

Author SHA1 Message Date
Greg Landrum
e37296d7c7 post review 2015-11-14 08:08:14 +01:00
Greg Landrum
5618819c64 merge #641 2015-11-14 05:03:24 +01:00
Paolo Tosco
95fcfe5cc4 - Fixed a post-decrement which causes a crash when compiling under Windows 
with MSVC 9
 2015-11-12 13:43:30 +00:00
Paolo Tosco
8b500a922a Merge remote-tracking branch 'upstream/master' 2015-11-11 18:45:33 +00:00
Brian Kelley
39b69b3600 Adds maxCutBonds to MMPA interface to limit combinitorial explosion 2015-11-11 08:02:11 -05:00
Brian Kelley
fe42eb87ef Fixes a memory leak in fragmentMol 2015-11-11 07:23:40 -05:00
Paolo Tosco
74f6f0ccec - added forward declaration of MMFFMolProperties to 
Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h
- added an include directive to Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h
 2015-11-10 17:39:22 +00:00
Nadine Schneider
624dd72ad6 new canon: fix in special symmetry invariant 2015-11-06 18:05:04 +01:00
Brian Kelley
56f74e2831 Fix unordered_map header 2015-11-04 18:09:53 -05:00
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
Greg Landrum
07dc85c384 cleanup 2015-11-04 05:29:41 +01:00
Greg Landrum
81719862d8 Merge branch 'master' of https://github.com/rdkit/rdkit 2015-11-02 08:11:50 +01:00
Greg Landrum
5af44952f2 make tests work with python3.4 2015-11-02 08:05:59 +01:00
Greg Landrum
11f5df5746 Fixes #655 2015-11-02 04:36:50 +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
Greg Landrum
cdedcc1d64 get the mmpa code working on windows 2015-10-31 05:53:37 +01:00
Greg Landrum
88183fcbd5 disable one failing test 2015-10-30 04:59:02 +01:00
Greg Landrum
2513e73465 merge mmpa branch 2015-10-30 04:45:58 +01:00
Greg Landrum
1cde397acb merge commit 2015-10-30 02:58:46 +01:00
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
076831aa31 - removed d_ceMapTmp and d_ceMap from ResonanceMolSupplier 
(they both were temporary data structures and there was
  no real reason for them to be there, especially in view
  of a possible code parallelization)
- converted most uint64_t to unsigned int since they weren't
  really necessary
- fixed a couple of compilation warnings
 2015-10-25 21:50:20 +00:00
Paolo Tosco
04c28693d8 - fixed a compilation warning 2015-10-24 01:29:57 +01:00
Paolo Tosco
517de5b5d8 - Fixed a few glitches which caused the build to fail on Windows 
- added a few tests for ResonanceMolSupplier
 2015-10-24 01:18:10 +01:00
Paolo Tosco
72de596280 - implemented correct resonance structure sorting for degenerate cases 
- moved classes that do not need being exposed in Resonance.h to Resonance.cpp
- added the ALLOW_CHARGE_SEPARATION flag: now by default charge
  separation structures are not displayed if there's at least one
  structure with no charge separation
- TODO
  * add SWIG wrappers
  * add a few test tp resMolSupplierTest.cpp
 2015-10-23 18:41:53 +01:00
Paolo Tosco
30df45bb29 Merge remote-tracking branch 'upstream/master' 2015-10-23 18:27:13 +01:00
Brian Kelley
f1e6a16e73 Added more C++ tests include setProp(const char*) 2015-10-22 17:50:02 -04:00
Brian Kelley
c2f52ede77 Fixes bug in precondition & -> && 2015-10-22 16:15:27 -04:00
Brian Kelley
b94aeced30 Calls parents constructor 2015-10-22 16:15:18 -04:00
Brian Kelley
058263585d Fixes bug — setProp(const char *) did nothing 2015-10-22 16:15:00 -04:00
Paolo Tosco
6ccda75d77 - fixed a problem when selecting maxStructs = 0 2015-10-21 20:27:02 +01:00
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
1aa8e474fd Merge remote-tracking branch 'upstream/master' 2015-10-21 20:06:15 +01:00
Sereina
26ab552232 fixes based on code review 2015-10-21 14:51:53 +02:00
Sereina
239527f8a6 small fix 2015-10-21 07:21:03 +02:00
Sereina
687b464e91 small fixes 2015-10-20 17:04:54 +02:00
Sereina
9cf706b581 enforceChirality flag added back 2015-10-20 15:04:13 +02:00
Sereina
ac7ef34f05 ETKDG implementation 2015-10-20 13:51:43 +02:00
Greg Landrum
c6b3d5d4a0 sync 2015-10-19 17:47:52 -04:00
Greg Landrum
91fc0de1ed include cleanup 2015-10-19 16:06:48 +02:00
Greg Landrum
442e842c58 remove vestigial svn tags 2015-10-19 16:04:42 +02:00
Greg Landrum
214254060b export the enum values for the ResonanceFlags to simplify using them 2015-10-19 15:33:01 +02:00
Brian Kelley
e1b92efeee Adds more boost header file ignores 2015-10-18 22:23:58 -04:00
Brian Kelley
742c6c3b4d Fixes bug in precondition & -> && 2015-10-18 21:20:33 -04:00
Brian Kelley
210f2951e0 Silences warnings in tests 2015-10-18 21:20:11 -04:00
Brian Kelley
b93bf6a3cd Calls parents constructor 2015-10-18 21:18:24 -04:00
Brian Kelley
ba00c48932 Switches char_widths from static storage to const 2015-10-18 21:17:44 -04:00
Brian Kelley
26b3dfd160 Removes unused variable 2015-10-18 21:17:20 -04:00
Brian Kelley
a81b7b4dae Removes always true invariants 2015-10-18 21:16:51 -04:00