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13 Commits

Author SHA1 Message Date
Ric
880a8e5725 Reformat Python code for 2023.03 release (#6294) 
* run yapf

* run isort

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2023-04-28 06:53:56 +02:00
Greg Landrum
99aa358fe0 make it easy to create DAT SGroups from Python (#5544) 2022-09-09 15:20:11 +02:00
Ric
0e6d73b8ef expose clearprop (#4515) 2021-09-15 14:31:44 +02:00
Greg Landrum
58e6743df0 Fixes #4468 and #4476 (#4482) 
* stop removing substance groups with replaceAtom()
change default for keepSGroups argument to replaceBond()

* enable logging output for the fileparserscatch

* basics of parsing SMARTSQ SubstanceGroups

* Fixes #4476
test coming in the next commit

* handle multi-atom SMARTS as recursive
more testing
Test #4476

* a bit of cleanup

* get the tests working

* additional testing

* Update Code/GraphMol/FileParsers/MolFileParser.cpp

Co-authored-by: Ric <ricrogz@users.noreply.github.com>

Co-authored-by: Ric <ricrogz@users.noreply.github.com>
 2021-09-05 05:43:13 +02:00
Ric
5d2f167bfe Addresses #4434 (#4435) 
* add index property to v2000 sgroups

* add a simple test

* update old test
 2021-08-24 05:10:06 +02:00
Greg Landrum
ab2fc55292 add methods to allow the following properties from SubstanceGroups to be cleared: (#3547) 
- Brackets
- CStates
- AttachPoints
 2020-11-03 12:02:25 -05:00
Greg Landrum
ff50f176c2 expose additional SubstanceGroup data members to Python (#3375) 
* support read-only access to cstates from python

* expose GetBrackets

* expose getAttachPoints too

remove vestigial SubstanceGroupCState_VECT
 2020-09-04 12:37:40 -04:00
Greg Landrum
c7e7614568 Fix #3312 (#3313) 
* additional testing: ensure we can delete SubstanceGroups

* fixes #3312

* stupid test mistake

* Fixes #3315
 2020-08-01 04:36:34 +02:00
Greg Landrum
98add2cec8 add GetStringVectProp() to SubstanceGroup class so that DATAFIELDS can be used (#3251) 2020-06-25 04:51:57 +02:00
Greg Landrum
83a1e75597 basic handling of XBCORR and XBHEAD (#3242) 2020-06-22 16:54:57 +02:00
Greg Landrum
e5620e0c57 [WIP] Make StructureGroups editable from Python (#2692) 
* first steps towards StructureGroups being editable in Python

* typo fix

* Add initial features to allow editing SGroups from Python.

* update test

* typo
 2019-10-15 22:32:26 -04:00
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