Commit Graph

4 Commits

Author SHA1 Message Date
Greg Landrum
5a79190261 rename SGroup -> SubstanceGroup (#2375)
We leave the names of the bit connected with Mol files as SGroups, since that is
appropriate there, but the more generic pieces are renamed
2019-03-30 14:53:24 -04:00
Greg Landrum
b739a2c208 Add a read-only Python wrapper for SGroups (#2343)
* added a set of test files for SGroups.
Many thanks to Gerd Blanke for providing these

* Partial version of the wrapper
Definitely needs more work

* add some properties

* basic SGroup property change test

* not working; backup commit

* disable writing for now

* add ClearMolSGroups() function

* review response: add a couple missing methods

* remove spaces from filenames

* update filename in test

* changes in response to review

* add operator== to SGroups

* solve lifetime problems with a vector_indexing_suite
2019-03-15 08:50:32 -04:00
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
Ric
d26d4b076e Support for parsing/writing SGroups in SD Mol files. (#2138)
* Implementation of SGroups

* remove sample files test

* update gitignore with test outputs

* fix RevisionModifier

* re-enable tests

* backup commit; things seem to work so far

* some refactoring; obvious s group tests pass now

* more refactoring

* everything now out of the public API

* not sure why this was still in there

* rename functions; all tests now pass

* remove getNextFreeSGroupId; readd comment in copy SGroups

* clang-format

* squash-merge current master

* squash merge master

* Address comments on PR

- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
2019-01-22 15:42:27 +01:00