molsysmt.physchem.get_hydrophobicity#

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

Hydrophobicity index per residue group from a reference scale.

Returns a dimensionless hydrophobicity value for each selected residue group, looked up from one of several published hydrophobicity scales. Values are normalized or consensus-derived depending on the chosen scale.

Parameters:

  • molecular_system (molecular system) – Input system in any supported form.

  • element ({'group'}, default 'group') – Hierarchical element for which hydrophobicity is returned. Only 'group' (residue level) is currently supported.

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

  • definition ({'eisenberg', 'rao', 'sweet', 'kyte', 'abraham', 'bull', 'guy', 'miyazawa', 'roseman', 'wolfenden', 'chothia', 'hopp', 'manavalan', 'black', 'fauchere'}, default 'eisenberg') – Hydrophobicity scale to use. All scales are taken from the ExPASy ProtScale resource. The default 'eisenberg' is the normalized consensus scale (Eisenberg et al., 1984).

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

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

Returns:

1-D array of shape (n_groups,) with dimensionless hydrophobicity values for the selected residues.

Return type:

numpy.ndarray

Raises:

NotImplementedMethodError – If an unsupported definition is requested.

Notes

Supported scales and their primary references:

  • 'eisenberg': Eisenberg D. et al. J. Mol. Biol. 179:125–142 (1984).

  • 'rao': Rao M.J.K., Argos P. Biochim. Biophys. Acta 869:197–214 (1986).

  • 'kyte': Kyte J., Doolittle R.F. J. Mol. Biol. 157:105–132 (1982).

  • 'hopp': Hopp T.P., Woods K.R. Proc. Natl. Acad. Sci. 78:3824–3828 (1981).

  • 'chothia': Chothia C. J. Mol. Biol. 105:1–14 (1976).

  • 'wolfenden': Wolfenden R. et al. Science 206:575–577 (1979).

  • Other scales follow their respective original publications as indexed in ExPASy ProtScale.

Added in version 1.0.0.

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