25 Commits

Author SHA1 Message Date
Greg Landrum
e35f7db009 Cleanup/get atoms and bonds (#9243) 2026-04-18 05:22:09 +02:00
Greg Landrum
fa048eacc5 Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926) 2025-01-28 21:09:03 +01:00
Greg Landrum
69b143edd0 Swap from RDUNUSED_PARAM to unnamed parameters (#4433)
* cleanup

* more cleanup
2021-08-24 17:19:46 -04:00
Greg Landrum
5712176605 Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)
* Deprecation: planned removal of .message() and .getMessage() methods

* Deprecation: planned removal of old MolHash code

* document deprecations

* output the diffs when the psql tests fail

* remove .message() from SWIG wrappers

note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway

* typo
2020-04-01 14:30:07 +02:00
Greg Landrum
d41752d558 run clang-tidy with readability-braces-around-statements (#2899)
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke

* fix problem on windows
2020-01-25 14:19:32 +01:00
Eisuke Kawashima
5cd27a242f Fix typo (#2862)
* Fix typo

* Reflect the comments

* Fix more typos
2019-12-31 06:43:27 +01:00
Ric
be3170d0d5 Mem errors clean up (#2305)
* fix test leaks

* fix "invalid read" when casting Query to EqualityQuery

* fix error cleanup in SMILES/SMARTS parsers

* SMILES/SMARTS parser fix updated *.cmake

* fix error cleanup in SLN parser

* SLN parser updated *.cmake

* updated suppressions

* update loop in sln bison
2019-03-08 05:39:59 +01:00
Greg Landrum
b0f44cac0c switch to using std::regex in the SLN parser (#1746)
* switch to using std::regex in the SLN parser;
removes the boost regex dependency

* cleanup
2018-02-14 20:54:55 -05:00
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
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Brian Kelley
66b1c81a61 Fixes more unused parameters 2015-10-18 16:38:50 -04:00
Brian Kelley
c4c46e8bca Fixes trailing whitespace parsing issues. 2015-09-26 10:40:43 -04:00
Brian Kelley
d50fd264f6 Change to const std::string & API 2015-09-25 15:15:21 -04:00
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
937ee9f60a add in-place form of removeHs() 2013-10-04 07:19:01 +02:00
Greg Landrum
fccbe02ce4 fix sf.net issue282 2013-01-11 03:39:33 +00:00
Greg Landrum
cbd8928642 improve error reporting for smiles, smarts, and sln parsers
(sf.net issue 3302363)
2011-05-15 10:10:56 +00:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
be56337e6a this much is working on the mac. 2010-05-22 14:05:28 +00:00
Greg Landrum
d33ce4884d make the sln, smiles, and smarts parsers multi-threadable (theoretically).
This has been tested on linux, still needs windows and mac compiles
2010-05-22 13:13:05 +00:00
Greg Landrum
49ef84ed45 a bunch of fixes to SLN handling 2010-04-11 09:06:52 +00:00
Greg Landrum
cb8732c004 further "refinements" of the SLN parser 2008-12-04 14:12:40 +00:00
Greg Landrum
3c13cbfc6f property update 2008-12-04 06:09:54 +00:00
Greg Landrum
cfc3fcbd08 merge sybyl file parsers into trunk. These are revs831:895 from the branch 2008-11-25 06:04:17 +00:00