besmarts.core.hierarchies module¶

besmarts.core.hierarchies

Hierarchies are SMARTS trees.

class besmarts.core.hierarchies.smarts_hierarchy(index, smarts)[source]¶

Bases: object

A hierarchy that has a mapping of nodes to SMARTS

copy()[source]¶

index: tree_index¶

smarts: Dict[int, str]¶

besmarts.core.hierarchies.smarts_hierarchy_copy(smahi: smarts_hierarchy) → smarts_hierarchy[source]¶

besmarts.core.hierarchies.smarts_hierarchy_print(smahi: smarts_hierarchy)[source]¶

besmarts.core.hierarchies.smarts_hierarchy_rename(A: smarts_hierarchy, prefix='p')[source]¶

besmarts.core.hierarchies.smarts_hierarchy_to_structure_hierarchy(shier: smarts_hierarchy, gcd: graph_codec, topo: structure_topology)[source]¶

besmarts.core.hierarchies.smarts_hierarchy_to_structure_hierarchy_angles(shier: smarts_hierarchy, gcd: graph_codec)[source]¶

besmarts.core.hierarchies.smarts_hierarchy_to_structure_hierarchy_atoms(shier: smarts_hierarchy, gcd: graph_codec)[source]¶

besmarts.core.hierarchies.smarts_hierarchy_to_structure_hierarchy_bonds(shier: smarts_hierarchy, gcd: graph_codec)[source]¶

besmarts.core.hierarchies.smarts_hierarchy_to_structure_hierarchy_outofplanes(shier: smarts_hierarchy, gcd: graph_codec)[source]¶

besmarts.core.hierarchies.smarts_hierarchy_to_structure_hierarchy_torsions(shier: smarts_hierarchy, gcd: graph_codec)[source]¶

class besmarts.core.hierarchies.structure_hierarchy(index, smarts, subgraphs, topo)[source]¶

Bases: smarts_hierarchy

copy()[source]¶

index: tree_index¶

smarts: Dict[int, str]¶

subgraphs: Dict[int, subgraph]¶

topology: structure_topology¶

besmarts.core.hierarchies.structure_hierarchy_copy(th: structure_hierarchy) → structure_hierarchy[source]¶

besmarts.core.hierarchies.structure_hierarchy_to_smarts_hierarchy(shier: structure_hierarchy, gcd: graph_codec)[source]¶