Get surface area#

Retrieving reference surface areas for amino acid residues.

The function molsysmt.physchem.get_surface_area() queries tabulated reference surface areas for standard amino acids using established biochemical scales (e.g. Collantes et al.).

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.physchem.get_surface_area().

Basic usage#

Let’s extract reference residue surface areas from a molecular structure:

import molsysmt as msm

molsys = msm.convert(msm.systems['Met-enkephalin']['met_enkephalin.h5msm'])

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We query reference surface areas using the Collantes scale:

sa = msm.physchem.get_surface_area(molsys, element='group', definition='collantes')
print('Residue surface areas (Collantes):', sa)

Residue surface areas (Collantes): [132.16, 19.93, 19.93, 189.42, 132.22]