3 Commits

Author SHA1 Message Date
Greg Landrum
22da97b836 Add support for SRUs to MolEnumerator (#4563)
* preliminary first pass at SRU enumeration

* handle HH

* working
plus add a missing file... <doh!>

* passes basic tests for enumeration of multiple non-overlapping SRUs

* more SRU testing

* explore combining the SRU enumeration with enumerate()

* first step towards RepeatUnit in the python interface

* first pass at directly connected SRUs

* Fixes #4561

* make sure we don't try to enumeration SRU + LINKNODE
update python docs

* exception for ladders

* get a bit smarter about rejecting linknode enumerations

* turns out we actually *can* do ladders pretty easily

* update java wrappers

* make sure we can input from CXSMILES too

* some cleanup/documentation

* some refactoring

* response to review
2021-09-28 16:37:39 +02:00
Ric
0022ad34e2 fix build (#3936) 2021-03-16 04:55:14 +01:00
Greg Landrum
73d26036de Support enumerating some mol file features into MolBundles (#3257)
* backup

* compiles

* progress, but not there yet

* basics now working

* start towards adding another test

* test having two variation points

* add actual enumeration and the corresponding tests

* docs and cleanup

* cleanups to get the mac build working

* attempt to get win32 dll builds to work

* dlls are fun

* Add FixedMolSizeMolBundle class

* changes in response to review

Also: add warnings for bad input in ParseV3000Array

* a bit of refactoring

* additional testing

* does not work, backup

* LINKNODES work now

* cleanup

* allow silencing reaction validation warnings during initialization

* docs

* fix (and test) handling of empty enumerations

* silence warnings when doing alchemy

* first pass at a Python wrapper for the enumerator

* Add Java wrappers for MolBundle and the MolEnumerator

* cleanup some comment formatting
2020-07-11 12:54:23 +02:00