Welcome to besmarts’s documentation!¶
Description¶
This package was written to handle binary-encoded SMARTS (BESMARTS) with an emphasis on handling aspects which are needed for molecular mechanics (MM) force field (FF) parameterization. Standard MM force fields apply forces to atoms, bonds, angles, and dihedrals (both “torsions” and “out-of-planes”), termed structures. BESMARTS considers all SMARTS, SMILES, and everywhere in between as graphs, and structures are subgraphs of some underlying graph. Much effort has gone into manipulating SMARTS patterns which describe structures. The SMIRNOFF force field specification uses SMARTS structures to assign parameters to molecules, and a major difficulty using this specification is how to programmatically create new parameters. This work stemmed from the need to manipulate SMARTS patterns in fine detail, primitive at a time. We hope that you find this work useful!
Getting Started¶
Important considerations¶
This package only implements and processes a subset of SMARTS for encoding.
Recursive SMARTS are not handled, and all SMARTS primitives are assumed to be
independent. This means that it is not possible to encode something like
[#6H3,#7H2], but it is possible to encode [#6,#7;H2,H3].
The former case is harder to reason with using functionality such as taking the
union and other mapping tasks, and has been put to the side for now.