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) – 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.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • definition (object, default='zhao') – Argument definition.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

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.