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) – Input system in any supported form.
selection (str, list, tuple or numpy.ndarray, default 'all') – Selection of groups to include in the output.
syntax (str, default 'MolSysMT') – Selection syntax.
definition ({'grantham'}, default 'grantham') – Volume scale to use. Currently the only supported scale is 'grantham', which tabulates side-chain volumes (in arbitrary units) for the 20 standard amino acids.

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.