Commit Graph

6 Commits

Author SHA1 Message Date
Greg Landrum
e0b7fc298a Support SubstanceGroups and StereoGroups in JSON (#5909)
* write stereogroups

* Parse stereogroups

* add parameters to python wrappers

* more tests

* write substancegroups

* parse SubstanceGroups

* Fix a crashing bug with null molecules

* more testing

* add some docs

* update expected cffi results

* oh, this is delightful syntax

* adapt minimallib and the cartridge tests
some small cleanups

* stupid padding

* update expected

* changes in response to review
2023-01-04 16:29:36 +01:00
Greg Landrum
b55514806d bonds with "either' stereo cannot be read from JSON (#3290)
* do not require stereoAtoms for "either" stereochemistry

* add one more test
2020-07-14 10:06:12 -04:00
Paolo Tosco
f7c888844d moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074) 2018-10-11 17:35:23 -04:00
Greg Landrum
60b052fb73 fixes #2046 (#2047)
also fixes a problem with retrieving version info
2018-09-18 04:48:43 +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
5cf8a6a9b7 Support for a JSON-based molecule interchange format (#1798)
* expose addRing to python

* backup commit

* basics of atom and bond loading

* basics of atom and bond loading

* do bond stereo too

* Loads of cleanups
Read conformers and molecule properties
Better tests
update one of the test values so that we aren't always testing ccw

* enable auto-download of rapidjson distrib

* reader now mostly done (still missing atomic/bond properties)

* a bit of optimization

* a bit of cleanup

* a bit more optimization

* backup

* test zero-order bonds

* prep work for writer (not done)

* add isotope support

* backup

* getting there with the writing

* progress on writing; still need to do the RDKit part though

* can now roundtrip, including chirality.
double bond stereo needs to wait for backend fixes

* add a timing test for benchmarking

* add a timing test for benchmarking

* add another template

* add parse params; optionally set bond types to aromatic; add python wrapper

* disable benchmark run by default

* write conformers

* refactoring

* docs

* port to commonchem

* switch representation

* start reading and writing properties

* fix a memory problem

* set a common_property for gasteiger charges

* parse partial charges

* add partial charge writing

* reformatting

* add support for disabling parts of the parsing

* remove the "name" property from files

* editing

* more post-review changes

* make the molinterchange build optional

* make them really optional
2018-04-02 05:12:03 +02:00