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) – Input system in any supported form.

  • element ({'group'}, default 'group') – Hierarchical element for which the buried fraction is returned. Currently only 'group' (i.e. residue) is supported.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Selection of groups to include in the output.

  • definition ({'janin'}, default 'janin') – Buried-fraction scale to use. Currently the only supported scale is 'janin', which reports the molar fraction (%) of each residue type among 2001 buried residues.

  • syntax (str, default 'MolSysMT') – Selection syntax.

  • skip_digestion (bool, default False) – If True, bypass argument validation (for internal use only).

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.

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