Compounds filtering

[rubbs14]

It would be great to add some custom substructure filters to eliminate some undesired chemistry. NIBR filters built-in in the contrib dir is a good starting point, but it's single-threaded so it needs a bit of a speedup. Custom FilterCatalog modules can be also added

[rubbs14]

NIBR implementation:
Contrib/NIBRSubstructureFilters

[DrrDom]

I looked through these patterns. If molecules containing these patterns will be removed before CReM fragment database creation, the vast majority of these patterns will not appear in output molecules if a user will choose radius 3 or greater. With radius 2 some of these patterns can be re-created.

This is an important feature of CReM, because there is possible to avoid generation of molecules with undesired patterns and it is better than remove them later. The rule is that patterns of the size (graph diameter) equal or smaller than a chosen radius should not be recreated by design.

It might be reasonable to implement some common filtering strategies to suggest users post-processing of generated structures, but maybe not within this repository to keep flexibility and the less number of inter connections within the repository.

[DrrDom]

One more note. CReM cannot create new rings absent in a fragment database, so any cycles in molecules removed before fragmentation will never appear in output. This is irrespective to the chosen radius.