Commit Graph

11 Commits

Author SHA1 Message Date
Greg Landrum
84c1ea5e7a some much-needed optimization work on the new property lists (#2317) 2019-03-06 16:06:32 -05:00
Greg Landrum
180c15fe0e support reading/writing atom props from SD files (#2297)
* first crude pass

* fix a deprecation

* change naming scheme, support bools

* add standalone function

* add a default value for missings

* support long lines

* stupid typo

* make operator[] work

* revisit missing value handling

* modify missing value handling

* switch to an alternate scheme for specifying missing values

* clang-format

* First pass at property list parser
still needs more tests

* add test for processMolPropertyLists

* get this working as part of the ForwardSDMolSupplier

* first pass at python wrappers and tests

* clang-format run

* add creation of property lists at the mol level

* wrap long lines on output

* remove PoC implementation

* fix python wrappers

* remove out-of-date reference to the Python PoC

* changes in response to review
2019-03-03 13:17:13 -05:00
Greg Landrum
2738c35178 Fixes #1903 (#1971)
* Fixes #1903

* update SWIG bindings too
2018-07-25 09:14:17 +02:00
Paolo Tosco
c08ea49bda - enable building DLLs on Windows (#1861)
* - enable building DLLs on Windows

* - export.h and test.h are now auto-generated by CMake
2018-05-16 08:42:41 +02:00
Greg Landrum
270f7b76e5 Partial support for reading CXSMILES (#1237)
* add a SmilesParserParams object to prepare for this

* add a SmilesParserParams object to prepare for this

* add tests for the SmilesParseParmas

* support name parsing, should it be the default?

* rename CXNSmiles to CXSmiles;
add a spirit parser for CXSmiles coordinate that is at least syntax correct

* abandon boost::spirit for now; crude atom token parser

* support params in smiles parser (not tested, may not build)

* can read coords and atom labels along with mol names; crude, but works

* read coordinate bonds

* remove some compiler warnings with VS2015

* remove a bunch of compiler warnings on windows

* remove more warnings on windows

* remove more warnings on windows

* backup commit: first pass at parsing query features

* radical spec parsing

* handle attachment points using atom mapping

* switch to a named property for atom labels

* fix handling of the "A" atom query

* add functions to construct A and Q queries (needs more work)

* fix a problem created while cleaning up warnings earlier

* add some additional convenience functions for making generic atoms.
Still need M and to recognize these while writing CXSMILES

* add M queries; update some tests

* fix a linux compile problem

* get the cxsmiles stuff working in python; basic testing

* support "M" in CXSMILES
2017-01-31 13:50:36 -05:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
8c70417690 Fixes #88 2013-08-21 20:45:54 +02:00
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
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
4d168b2637 further leak stoppage 2010-06-09 18:30:22 +00:00
Greg Landrum
a09fd9f63a cleanup work on file parsers code; add v3K rxn support 2010-06-03 06:59:48 +00:00