Greg Landrum
b6645fab90
Allows CIS/TRANS double bonds to be de-pickled ( #1710 ) ( #1711 )
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* Fixes #1710
* add an additional test for #1563 while we're here
2018-01-07 14:54:01 -05:00
Greg Landrum
db89172bf8
handle the heavy-atom degree queries differently ( #1560 )
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* 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 )
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* 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
Brian Kelley
e70599a12e
Dev/pickle properties ( #1277 )
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* 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.
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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
2d8500b407
Fixes #314
2014-08-21 07:29:09 +02:00
Greg Landrum
8959e07798
Fixes #313
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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:
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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;
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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.
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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 :
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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
Greg Landrum
26c28976c9
some regression objects were not being removed; minor cleanups to molpickler code(e.g. typo fixes)
2007-09-23 06:57:11 +00:00
Greg Landrum
e35d093dc3
modify the depickler so that it no longer has to seek within the stream;
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this increases our flexibility a LOT
2006-11-21 17:48:48 +00:00
Santosh Putta
3061511f68
All typedefs based on points move to point.h - dependancies updated here
2006-10-19 23:37:59 +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
