Get polarity#

Querying amino acid polarity indices from reference scales.

The function molsysmt.physchem.get_polarity() determines residue polarity scores representing sidechain electrostatic and hydrogen-bonding propensities using two reference scales:

'grantham': Classic side-chain polarity scale from Grantham (1974).
'zimmerman': Polarity index from Zimmerman et al. (1968).

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_polarity().

Basic usage#

By default (definition='grantham'), Grantham polarity values are returned for each residue:

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 Grantham polarity values for all residues:

pol_grantham = msm.physchem.get_polarity(molsys, element='group', definition='grantham')
print('Grantham polarity scores:\n', pol_grantham)

Grantham polarity scores:
 [11.6, 4.9, 6.2, 5.2, 10.5, 5.4, 4.9, 11.3, 13.0, 9.0, 9.0, 8.0, 9.2, 9.2, 9.0, 10.5, 8.0, 8.0, 8.0, 9.2]

Alternative polarity scales#

Setting definition='zimmerman' evaluates polarity based on electric dipole and dielectric properties:

pol_zimmerman = msm.physchem.get_polarity(molsys, element='group', definition='zimmerman')
print('Zimmerman polarity scores:\n', pol_zimmerman)

Zimmerman polarity scores:
 [3.38, 0.13, 1.61, 0.13, 3.53, 2.1, 0.13, 49.5, 49.7, 0.0, 0.0, 1.58, 1.67, 1.67, 0.0, 52.0, 1.58, 1.58, 1.58, 1.67]