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_proxy_periodic_table()¶
Get proxy periodic table.
- Return type
list[str]
- Returns
Cached list of elements, do not modify!!
- schrodinger.rdkit.coarsegrain.get_cgparticle_to_element_mapper(cg_particle_names)¶
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.prepare_cg_for_rdkit(struct)¶
Create fake AA from a CG structure that can be converted to RDKIT mol.
- Parameters
struct (schrodinger.structure.Structure) – Input CG structure
- Return type
- Returns
Fake AA structure and internal mapping dict between schrodinger particle name and rdkit proxy element name
- schrodinger.rdkit.coarsegrain.get_coarsegrain_smiles(st, atom_ids=None)¶
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