molsysmt.physchem.get_transmembrane_tendency#

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

Transmembrane tendency index per residue group.

Returns a dimensionless score representing the propensity of each selected residue to reside within a lipid bilayer. Values are looked up from a static scale indexed by residue name. Positive values indicate hydrophobic (membrane-favouring) character; negative values indicate preference for aqueous environments.

Parameters:

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

  • element ({'group'}, default 'group') – Hierarchical element for which transmembrane tendency 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 ({'zhao', 'senes'}, default 'zhao') –

    Transmembrane tendency scale to use.

    • 'zhao': free-energy-based scale from Zhao & London (2006).

    • 'senes': pseudo-potential scale from Senes et al. (2007).

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

Returns:

Transmembrane tendency 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:

  • 'zhao': Zhao G., London E. Protein Sci. 15:1987–2001 (2006).

  • 'senes': Senes A. et al. J. Mol. Biol. 366:436–448 (2007).

Added in version 1.0.0.