molsysmt.physchem.get_volume#

molsysmt.physchem.get_volume(molecular_system, selection='all', syntax='MolSysMT', definition='grantham')[source]#

Side-chain volume per residue group from a reference scale.

Returns a tabulated volume value for each selected residue group, looked up from one of the published amino-acid volume scales. Volume provides a measure of steric bulk of the amino acid side chain and is used in evolutionary distance metrics.

Parameters:

molecular_system (molecular system) – Molecular system in any supported MolSysMT format.
selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.
syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).
definition (object, default='grantham') – Argument definition.

Returns:

1-D array of shape (n_groups,) with volume values for the selected residues (dimensionless relative units as defined by the scale).

Return type:

numpy.ndarray

Raises:

NotImplementedMethodError – If an unsupported definition is requested.

Notes

The 'grantham' scale reports side-chain volumes as part of the composite physicochemical distance between amino acids defined in:

Grantham R. Science 185:862–864 (1974).

Added in version 1.0.0.