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
Riccardo Vianello
78d7f6c1d9
Fix regressions occurring when building with msvc9
2015-10-14 09:43:16 +02:00
Brian Kelley
6ebbeb3bd3
Major conversion of std::string API to const std::string &
2015-09-25 15:15:59 -04:00
Nadine Schneider
0132cc72e9
Merge branch 'newCanon' into master3
...
Conflicts:
Code/GraphMol/SmilesParse/test.cpp
2015-04-10 10:25:47 +02:00
Brian Kelley
85e2e94d20
Fix MolFile Atom Line List Writer
...
Only the first element in the atom one was being
written correctly, the remainder were not being
padded correctly and could not be round tripped.
2015-04-05 20:47:02 -04:00
Greg Landrum
a0a02b4a99
merge on master
2015-02-03 16:41:46 +01:00
Brian Kelley
ff0548a871
RDKit learns how to round grip MOLFile values.
...
This is CTAB form:
“V XXX YYYYYY”
where (XXX is atom index, Y is the value)
2015-01-29 15:44:32 -05:00
Greg Landrum
6d7b2b0914
merge with master
2015-01-22 06:30:51 -05:00
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
cad05ca184
get rid of RankAtoms.cpp and
...
move the remaining functionality from RankAtoms.h into the new file
RDGeneral/Ranking.h
2014-12-22 07:35:58 +00:00
Nadine Schneider
53cd0666eb
Introduce UpdatePropertyCache to MolWriter
2014-12-19 13:59:56 +01:00
Greg Landrum
114ff2fe8d
Fixes #357
2014-10-23 06:04:48 +02:00
Greg Landrum
cd03d877fb
Fixes #337
2014-10-04 14:44:42 +02:00
Greg Landrum
f94ed4a1f5
get queries from SMARTS into CTABs more reasonably
2014-05-26 09:02:08 +02:00
Greg Landrum
665872cb39
Fixes #268
2014-05-25 06:55:30 +02:00
Greg Landrum
684f451352
Fixes #266
2014-05-22 17:34:06 +02:00
Greg Landrum
601c21f19d
Fixes #189
2014-03-13 05:23:56 +01:00
Greg Landrum
75be63fd6b
merge with trunk
2014-02-09 05:00:18 +01:00
Greg Landrum
deed4a9acf
Merge branch 'Issue194_V3000MolWriter'
...
Conflicts:
Code/GraphMol/Chirality.cpp
Code/GraphMol/FileParsers/test1.cpp
2014-01-22 07:07:27 +01:00
Greg Landrum
5dca39e2f7
Fixes #187
2014-01-11 05:38:11 +01:00
Greg Landrum
0ce8f23c6e
further R group handling
2014-01-10 04:24:22 +01:00
Greg Landrum
4b72d1b153
add (non-standard) handling of R groups to v3k mol parser
2014-01-08 05:22:15 +01:00
Greg Landrum
763543ef70
a couple more tweaks from Jan
2014-01-07 05:55:54 +01:00
Greg Landrum
11af614ebc
more cleanups of this stuff
2014-01-01 17:35:35 +01:00
Greg Landrum
64366007e1
more C++ style cleanups
2014-01-01 17:16:25 +01:00
Greg Landrum
355556b7de
get atom lists working
2013-12-29 07:05:25 +01:00
Greg Landrum
0b8bd3079d
fix isotope handling in V3K
2013-12-28 07:37:52 +01:00
Greg Landrum
d280c90117
a few more tests and a fix to not print empty bond blocks
2013-12-26 07:40:16 +01:00
Greg Landrum
9e91538d64
get rgroups working
2013-12-25 08:18:44 +01:00
Greg Landrum
329841d9ba
add some tests; add radicals to output
2013-12-24 06:56:12 +01:00
Greg Landrum
2ee9f1c02a
add to python wrapper
2013-12-23 06:43:12 +01:00
Greg Landrum
7e5222a369
minor updates
2013-12-23 06:35:09 +01:00
Greg Landrum
73b9cabcbc
initial version from Jan Holst Jensen
2013-12-23 06:32:46 +01:00
Greg Landrum
ae14fa3bd9
add support for the ZCH and HYD elements in mol files
2013-12-07 17:40:04 +01:00
Greg Landrum
3b0c72c4bf
initial pass at ZBO support.
...
does not yet handle the HYD and ZCH lines
2013-11-30 06:58:03 +01:00
Greg Landrum
e51d2c1020
Fixes #118
2013-10-05 16:19:02 +02:00
Greg Landrum
d80ab78f70
initial pass at this
2013-07-15 17:04:15 +02:00
Greg Landrum
f592d40997
apply Roger's patch
2013-07-15 16:03:10 +02:00
Greg Landrum
c36547010a
Fix #64
2013-07-09 05:40:55 +02:00
Greg Landrum
e8624ca6c4
patch from Roger S to include CTAB aliases
2013-03-17 15:24:58 +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
ee95f8ba65
fix and test issue 3484552
2012-02-05 07:27:01 +00:00
Greg Landrum
59c05266b7
fix and test issue 3392107. Add first pass at being able to write atom list queries to mol files
2011-08-16 06:03:27 +00:00
Greg Landrum
c7a9903e41
fix and test issue 3359739
2011-07-09 04:46:55 +00:00
Greg Landrum
739a989617
improve error message
2011-07-09 03:22:24 +00:00
Greg Landrum
f0c0a060a2
fix and test Issue 3313540
2011-06-10 03:27:46 +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
