Commit Graph

4 Commits

Author SHA1 Message Date
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
Riccardo Vianello
51bd3f51f2 Fix the compressed sd mol supplier and cleanup the python iterators (#3202)
* fix the CompressedSDMolSupplier python iterator interface

* cleanup the python iterators code (remove support for python2)
2020-07-03 13:15:07 +02:00
Greg Landrum
a102eaf932 Add options for substructure searching (#2254)
* first pass at adding a SubstructMatchParameter struct

* start moving the rest of the backend to use the parameters

* backend at least mostly moved over

* add aromaticMatchesConjugated
add tests

* switch over the MolBundle too
Add templates to reduce duplicated code

* support older compilers

let's see if it works...

* add SubstructMatchParameters to Python wrapper

* remove some deprecations and warnings

* damn compilers

* parameter support for bundles in python wrapper

* add the parameters to the java wrappers

* response to review
2019-02-08 09:10:10 -05:00
Greg Landrum
6ed76d9fff Expose the MolBundle to python (#1583)
* backup

* initial mol bundle wrapper

* Move the substructure matching wrapper code to a template header file to clean stuff up.

* update python docs
2017-09-26 13:00:53 -04:00