Commit Graph

8 Commits

Author SHA1 Message Date
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
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
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
b36e6a911f fix a drawing bug
update release notes and docs
implement the new dummy atom stuff in ChemTransforms
expose lists of atom rings and bond rings from RingInfo
2008-05-14 20:20:52 +00:00
Greg Landrum
37d96faca8 expose RingInfo structure 2007-08-03 04:49:52 +00:00