Coarse Graining

mlcg.cg contains useful tools for projecting all-atom systems to a coarser resolution.

mlcg.cg.projection.build_cg_topology(topology, cg_mapping=None, special_terminal=True, bonds=<function add_chain_bonds>, angles=<function add_chain_angles>, dihedrals=<function add_chain_dihedrals>)[source]

Takes an mlcg.geometry.topology.Topology instance and returns another mlcg.geometry.topology.Topology instance conditioned on the supplied CG mapping

Parameters:

  • topology (Topology) – Original MLCG topology before coarse graining

  • cg_mapping (Optional[Dict[Tuple[str, str], Tuple[str, int, int]]]) – A suitable CG mapping. See mclg.cg._mapping.py for examples.

  • special_termini – If True, the first and last CG atoms recieve their own special types

  • bonds (Optional[Callable]) – Function to enumerate and define bonds in the final CG topology

  • angles (Optional[Callable]) – Function to enumerate and define angles in the final CG topology

  • dihedrals (Optional[Callable]) – Function to enumerate and define dihedrals in the final CG topology

Returns:

CG topoology

Return type:

Topology

mlcg.cg.projection.build_cg_matrix(topology, cg_mapping=None, special_terminal=True)[source]

Function for producing coarse grain types, masses, and mapping matrices using a slicing strategy and a predetermined set of atoms to retain at the coarse grain resolution.

Parameters:

  • topology (Topology) – System topology instance

  • cg_mapping (Optional[Dict[Tuple[str, str], Tuple[str, int, int]]]) –

    Mapping dictionary with the following structure:

    {
    (residue name, atom name) : (compound name, type, mass)
    ...
}

    Eg, a row for an alanine carbon alpha atom would be:

    {
    ("ALA", "CA") : ("CA_A", 1, 12)
    ...
}

  • special_termini – If True, special types will be reserved for the first and last CG atoms

Return type:

Tuple[ndarray, ndarray, ndarray, OrderedDict]

Returns:

  • np.ndarray – Array of CG atom types

  • np.ndarray – Array of CG masses

  • np.ndarray – One-hot transformation matrix of shape (n_high_res_atoms, n_cg_atoms) that maps atoms for the high resolution repesentation to the coarse grain representation

  • OrderedDict – Ordered dictionary mapping each CG atom index (with respect to the CG topology) to a list containing the CG atom name, CG atom type and the CG atom mass