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) – Input system in any supported form.

  • element ({'group'}, default 'group') – Hierarchical element for which buried area is returned. Currently only 'group' (i.e. residue) is supported.

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

  • definition ({'rose'}, default 'rose') – Buried-area scale to use. Currently the only supported scale is 'rose', taken from Rose et al. (1985).

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

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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