Brian Kelley
fb84c9f0b7
Switches to URANGE_CHECK when appropriate
2015-10-18 21:14:02 -04:00
Brian Kelley
5f59333a56
Silences unused parameters
2015-10-18 14:02:29 -04:00
Brian Kelley
6ebbeb3bd3
Major conversion of std::string API to const std::string &
2015-09-25 15:15:59 -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
cd03d877fb
Fixes #337
2014-10-04 14:44:42 +02:00
Greg Landrum
c0bf384832
Fixes #290
2014-07-12 08:20:31 +02:00
Greg Landrum
6b26036f6a
Fixes #269
2014-05-23 08:26:26 +02:00
Greg Landrum
f5cf3322fe
code cleanup: removing compiler warnings
2014-05-08 06:06:07 +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
0839cf41ad
Fixes #210
2014-02-03 05:25:27 +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
aab11535e8
Fixes #196
2014-01-16 02:07:03 -05:00
Greg Landrum
f653e9e961
more isotope fixing
2014-01-08 06:51:48 +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
3fe2e13afd
support forcing V3000 writing and kekulization in the SDWriter
...
Fixes #174
2013-12-30 06:58:48 +01:00
Greg Landrum
0b8bd3079d
fix isotope handling in V3K
2013-12-28 07:37:52 +01:00
Greg Landrum
9e91538d64
get rgroups working
2013-12-25 08:18:44 +01:00
Greg Landrum
b45423be3e
rename makeAtomNumEqualsQuery() to makeAtomNumQuery()
2013-12-14 09:14:57 +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
12ecae962e
merge
2013-12-07 10:51:19 +01:00
Greg Landrum
60a68669da
remove more clang warnings
2013-12-02 04:46:46 +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
1acae67cba
Merge branch 'master' into PDB_29September2013
2013-10-08 05:51:57 +02:00
Greg Landrum
e51d2c1020
Fixes #118
2013-10-05 16:19:02 +02:00
Greg Landrum
937ee9f60a
add in-place form of removeHs()
2013-10-04 07:19:01 +02:00
Greg Landrum
2546ea0d7a
Fixes #82
2013-08-23 09:18:04 +02:00
Greg Landrum
8c70417690
Fixes #88
2013-08-21 20:45:54 +02:00
Greg Landrum
d80ab78f70
initial pass at this
2013-07-15 17:04:15 +02:00
Greg Landrum
c36547010a
Fix #64
2013-07-09 05:40:55 +02:00
Greg Landrum
581695da0f
support R values greater than 9 in ctabs
2013-07-04 08:21:13 +02:00
Greg Landrum
8ac59a261a
continuation of cleanup from issue 279 [follow up from rev2355]
2013-01-09 04:11:15 +00:00
Greg Landrum
b82a6b29a6
another swing at sf.net issue 279. This one is somewhat more efficient
2013-01-08 05:35:03 +00:00
Greg Landrum
b6a26aca44
fix and test sf.net issue273
2012-12-12 09:10:05 +00:00
Greg Landrum
a5baf0239b
more on the locale problem; this still needs testing on non-linux
2012-12-12 04:20:14 +00:00
Greg Landrum
33d571850d
support skip lines in ctabs;
...
get sdf property lines that contain only white space working
2012-10-10 10:16:13 +00:00
Greg Landrum
4a3933ed00
fix and test Issue 3557675
2012-08-15 04:21:33 +00:00
Greg Landrum
e16b345d8b
fix and test issue 3525673
2012-05-12 05:31:54 +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
207b1c181b
fix and test issue 3482695
2012-02-02 03:28:48 +00:00
Greg Landrum
51991c7619
add line numbers to all error messages/warnings from ctab parsing
2012-01-29 08:41:30 +00:00
Greg Landrum
dbd78604c8
fix and test issue 3477283
...
add a new option for ctab parsing to cause the parser to be less strict about
errors in the file syntax.
2012-01-22 09:40:54 +00:00
Greg Landrum
510f68b102
initial pass at fixing issue 3432136
2011-11-03 04:13:02 +00:00
Greg Landrum
82129c3e13
fix and test Issue3399798
2011-08-30 09:13:07 +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
Eddie Cao
adbd5c7b18
Several InChI generation fixes, including perchloric acid, isotopic property, chirality loss, stereoany
2011-07-25 06:41:47 +00:00
Greg Landrum
d34f3dd6b2
do isotope work relative to the most common isotope
2011-07-01 04:34:14 +00:00
Greg Landrum
9316758cec
improved handling of isotope specifications (still definitely not optimal)
2011-07-01 03:42:35 +00:00
