Commit Graph

6 Commits

Author SHA1 Message Date
Greg Landrum
606dbd9cdd bonds with "either' stereo cannot be read from JSON (#3290)
* do not require stereoAtoms for "either" stereochemistry

* add one more test
2020-08-12 09:46:31 +02:00
Greg Landrum
d41752d558 run clang-tidy with readability-braces-around-statements (#2899)
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke

* fix problem on windows
2020-01-25 14:19:32 +01:00
Greg Landrum
ec366c1ab7 Dev/pvs studio cleanups2 (#2877)
* a round of cleanups courtesy of PVS studio

* add a test to make sure that a warning is a false alarm

* bug fix

* Fix a UFF bug

* more PVS studio cleanups

* next round of PVS studio cleanups

* completely remove the chances for that bug

* changes in response to review

* add an additional test
+ a bit of reformatting that snuck in
2020-01-22 15:10:58 +01:00
Ric
91008ff11d Address compile warnings & trivial improvements (#2097)
* Address compile warnings & trivial improvements

* revert unwanted initializers; use RDUNUSED_PARAM for unused params

* revert fix in testRDFcustom; marked with 'TO DO' comment
2018-10-12 06:39:32 -04:00
Greg Landrum
60b052fb73 fixes #2046 (#2047)
also fixes a problem with retrieving version info
2018-09-18 04:48:43 +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