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.is_protected_cg_name(name)

Check if a CG particle name is a protected/reserved name.

Protected names are single protected characters optionally followed by digits only. For example: ‘H’, ‘H2’, ‘R1’, ‘D10’ are protected, but ‘HA’, ‘H2O’, ‘RA’ are allowed because they contain letters after the first character.

Parameters:

name (str) – The CG particle name to check

Return type:

bool

Returns:

True if name is protected/forbidden, False if allowed

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 (Structure) – Input CG structure

Return type:

Structure, dict

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:
Returns:

str

Return type:

smiles for coarse grain substructure