schrodinger.rdkit.coarsegrain module¶
Conversions between Coarse-grained Schrodinger structure objects (mmct) and RDKit mol objects.
Please see schrodinger.rdkit_adapter for structural/philosophic differences between these two formats
- schrodinger.rdkit.coarsegrain.get_cgparticle_to_element_mapper(cg_particle_names)[source]¶
Create a mapper between coarse-grain particle name and an element.
- Parameters
cg_particle_names (list) – list of CG particle names
- Return type
dict
- Returns
dict with CG particle name as key and element name as value
- schrodinger.rdkit.coarsegrain.get_map_sdgr_to_rdk(mol)[source]¶
Get a dict mapping schrodinger atoms index to rdkit atom index
- Parameters
mol (
rdkit.Mol) – rdkit molecule for which mapping is desired- Return type
dict
- Returns
dict with key as schrodinger atom index and rdkit atoms index as value
- schrodinger.rdkit.coarsegrain.get_coarsegrain_smiles(st, atom_ids=None)[source]¶
Get smiles for coarse-grained structure
- Parameters
st (
schrodinger.structure.Structure) – structureatom_ids (list) – list of substructure atom id
- Returns
str
- Return type
smiles for coarse grain substructure