molsysmt.physchem.get_area_buried#

molsysmt.physchem.get_area_buried(molecular_system, element='group', selection='all', definition='rose', skip_digestion=False)[source]#

Average area buried per residue group upon protein folding.

Returns a tabulated value (in Ų) representing the average surface area buried when each residue transfers from a standard (extended chain) state to the folded protein interior. Values are looked up from a static scale indexed by residue name.

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.

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

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

Returns:

1-D array of shape (n_groups,) with buried area values in Ų.

Return type:

numpy.ndarray

Raises:

NotImplementedMethodError – If an unsupported definition is requested.

Notes

The 'rose' scale reports the average area buried on transfer from a standard state to the folded protein, as tabulated for the 20 standard amino acids in:

Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Science 229:834–838 (1985).

Added in version 1.0.0.

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