molsysmt.physchem.get_polarity#

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

Polarity index per residue group from a reference scale.

Returns a dimensionless polarity value for each selected residue group, looked up from one of the published amino-acid polarity scales. Polarity quantifies the tendency of the side chain to participate in electrostatic interactions and hydrogen bonding.

Parameters:

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

  • element ({'group'}, default 'group') – Hierarchical element for which polarity 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.

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

  • definition ({'grantham', 'zimmerman'}, default 'grantham') –

    Polarity scale to use.

    • 'grantham': side-chain polarity from Grantham (1974), used in the original amino acid distance metric.

    • 'zimmerman': polarity scale from Zimmerman et al. (1968).

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

Returns:

Polarity values 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

Supported scales and their primary references:

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

  • 'zimmerman': Zimmerman J.M., Eliezer N., Simha R. J. Theor. Biol. 21:170–201 (1968).

Added in version 1.0.0.

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