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105 Commits

Author SHA1 Message Date
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
ae3aebeb32 Get queries from the new cactvs SMARTS extensions to pickle correctly (#1712) 
* not yet working

* update smarts testing so that it verifies that the parsed patterns can also be pickled/unpickled

* fix pickling/unpickling of range queries;
add unpickling of new cactvs queries and range_ queries

* force CI to re-run

* cleanup in response to review
 2018-01-09 12:23:36 -05:00
Greg Landrum
1efa8e696e another clang-format run 2017-10-12 06:42:15 +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
Brian Kelley
3d75f5c78f Fixes blanking of non-query atom data when QueryAtomData was being pi… (#1541) 
* Fixes blanking of non-query atom data when QueryAtomData was being pickled

* Adds old version pickle test for properties

* Makes pickle py2 and py3 compatible
 2017-09-07 20:43:08 +02:00
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
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
c8862fb111 Fixes #713 2015-12-22 07:18:35 +01:00
kelley
5dbec2fe85 Adds rdcasts where appropriate 2015-11-29 17:52:27 -05:00
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
Greg Landrum
797db2fa82 remove Atom::setMass() 2015-03-22 17:57:04 +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
2d8500b407 Fixes #314 2014-08-21 07:29:09 +02:00
Greg Landrum
8959e07798 Fixes #313 
NOTE: this still needs testing on machines with older versions of flex/bison
 2014-08-19 07:20:04 +02:00
Greg Landrum
d8c523352c fix a profoundly stupid mistake from an earlier commit 2014-05-10 07:43:30 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +02:00
Greg Landrum
7eca2ead35 Fixes #149 2014-01-01 09:24:06 +01:00
Greg Landrum
60a68669da remove more clang warnings 2013-12-02 04:46:46 +01:00
Greg Landrum
0726c3ea9d changes suggested by Roger S: 
add residueNumber
serialNumber -> int
add segmentNumber
 2013-10-08 05:49:54 +02:00
Greg Landrum
866e43ec2b add data fields for heteroatom and secondary structure 2013-08-21 04:56:40 +02:00
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
a4734bbd43 start using the alternate getProp form 2013-07-20 07:26:06 -04:00
Greg Landrum
97dd2d1f44 Fixes #60 2013-07-04 06:47:03 +02:00
Greg Landrum
8adebd6321 Fixes #52 2013-06-19 05:48:30 -04:00
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
162662186d not working yet 2012-04-19 06:15:40 +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
a99ad44859 clean up some compiler warnings 2011-12-31 15:58:57 +00:00
Greg Landrum
a7a145f3d9 modifications to the pickle binary format to make serialized molecules smaller 2011-03-29 04:35:43 +00:00
Greg Landrum
c3c929f02d fix and test sf.net issue 3202580 2011-03-08 05:00:01 +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
9edbb9909a more extensive testing of pickler 2010-06-17 05:53:37 +00:00
Greg Landrum
96adbc11ea remove the deprecated assign{Atom,Bond}ChiralCodes functions 2009-08-02 15:33:08 +00:00
Greg Landrum
c425bc8c03 fix and test sf.net Issue2788233 2009-06-01 13:04:33 +00:00
Greg Landrum
fc6c2b2f9a fixes to issues 2196817 and 2208994 2008-10-30 06:56:39 +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
029e08d6b4 merge in the changes from the 64 bit port branch r703:717 2008-06-11 05:01:17 +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
c86ee3fcf6 implement and test feature request 1906758 : 
support dimensionality flag on conformations
https://sourceforge.net/tracker/index.php?func=detail&aid=1906758&group_id=160139&atid=814653
 2008-03-04 07:06:26 +00:00