Get buried fraction#

Determining statistical buried fractions of residues in folded proteins.

The function molsysmt.physchem.get_buried_fraction() retrieves empirical molar percentage fractions of residues found in buried environments (Janin scale).

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_buried_fraction().

Basic usage#

Let’s extract statistical buried fractions for residues in a protein system:

import molsysmt as msm

molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.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 the Janin buried fraction percentages:

bf = msm.physchem.get_buried_fraction(molsys, element='group', definition='janin')
print('Buried fractions (Janin, %):\n', bf)

Buried fractions (Janin, %):
 [2.9, 11.7, 2.6, 8.6, 1.6, 2.2, 11.7, 0.5, 2.9, 11.8, 11.8, 2.7, 8.0, 8.0, 11.8, 0.5, 2.7, 2.7, 2.7, 8.0]