molsysmt.physchem.get_buried_fraction#

molsysmt.physchem.get_buried_fraction(molecular_system, element='group', selection='all', definition='janin', syntax='MolSysMT', skip_digestion=False)[source]#

Fraction of residues observed in a buried environment.

Returns a tabulated molar fraction value representing how frequently each residue type is found in a buried (solvent-inaccessible) environment in a reference dataset of folded proteins. Values are looked up from a static scale indexed by residue name.

Parameters:

molecular_system (molecular system) – Molecular system in any supported MolSysMT format.
element (str, default='group') – Structural element level to query (‘atom’, ‘group’, ‘component’, ‘molecule’, ‘chain’, ‘entity’).
selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.
definition (object, default='janin') – Argument definition.
syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).
skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

Buried fraction values (in %) for each selected group, in the same order as the selection. Length n_groups.

Return type:

list of float

Raises:

NotImplementedMethodError – If an unsupported definition is requested.

Notes

The 'janin' scale reports the molar fraction (%) of each amino acid among 2001 buried residues from a structural database, as described in:

Janin J. Nature 277:491–492 (1979).

Added in version 1.0.0.