Get mass#

Evaluating atomic, residue, and total molecular system masses.

The function molsysmt.physchem.get_mass() computes masses in unified atomic mass units (Daltons) aggregated at atom, residue group, chain, molecule, or whole system levels.

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_mass().

Basic usage#

Let’s compute the molecular weight of a protein system:

import molsysmt as msm
import pyunitwizard as puw

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 calculate the total mass of the system:

mass_total = msm.physchem.get_mass(molsys, element='system')
print('Total molecular mass:', mass_total)

Total molecular mass: 2170.438 dalton

Hierarchical mass aggregation#

Masses can also be extracted at individual residue or atom levels:

mass_groups = msm.physchem.get_mass(molsys, element='group')
print('Residue masses (Da):\n', mass_groups)

Residue masses (Da):
 [116.12 113.15999999999998 163.17600000000004 113.15999999999998 128.131 186.214 113.15999999999998 129.183 114.07999999999998 57.05200000000001 57.05200000000001 97.11699999999996 87.07799999999999 87.07799999999999 57.05200000000001 157.19699999999997 97.11699999999996 97.11699999999996 97.11699999999996 103.07699999999997] dalton