Commit Graph

6 Commits

Author SHA1 Message Date
Greg Landrum
9fa1df1cf6 Drop usage of CIP information from the canonicalization code (#5385)
* stop using CIP codes in the atomic canonicalization

this will change results in some cases, so lots of tests need to be updated.

* stop breaking string literals... ARGH

* tests now pass

* update double bond canonicalization

* update a python test

* some cleanup

* update expected results for cartridge
2022-07-13 05:40:23 +02:00
Greg Landrum
4bbbc6611d Add a CXSMILES option to the MolHash (#5058)
* Nonchiral atoms should be removed from StereoGroups

This fixes a bug where atoms which have no chirality were left in StereoGroups

In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.

* support CXSmiles extensions in the hashes

* initial tests for that

* some cleanup

* copyright header cleanup

* minor refactoring

* call out the changes in the release notes

* extension and more testing

* add python wrappers
2022-03-03 16:00:38 +01:00
Ric
20e9086af6 fix + test (#4223) 2021-06-09 04:54:42 +02:00
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
Greg Landrum
7a266277fb A few MolHash fixes (#2699)
* do not remove multiple bonds that aren neither conjugated nor to heteroatoms

* unflag aromatic bonds

* remove bond stereo too

* call assignStereochemistry after the tautomer normalizations
2019-10-11 06:26:02 -04:00
Greg Landrum
5dfd67a22a Add new mol hashing code (#2636)
* copy in, get building, add some basic tests

* complete the testing
Except for regiosiomers, which do not work

* regioisomers work now

* backup commit; things work

* remove last of NM macros from hashfunctions.cpp

* remove last of NM macros from hashfunctions.cpp

* remove dependency on the abstraction layer

* typo

* start using namespaces
clang-format

* switch to using enums for the HashFunctions and StripTypes

* Add initial python wrapper (and tests)

* move the new hashing code to the MolHash library

still may want to revise the naming of this

* Setup deprecation of the older hashing code

* better release notes text

* change in response to review
2019-09-24 07:55:21 -04:00