Shift dihedral angles#

Shifting dihedral angles by incremental angular amounts.

The function molsysmt.structure.shift_dihedral_angles() rotates dihedral angles incrementally relative to their existing values, applying an angular displacement \(\Delta \theta\) while preserving connected covalent blocks.

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.structure.shift_dihedral_angles().

Basic usage#

Let’s show how to shift a specific backbone \(\phi\) dihedral angle by \(+90.0^\circ\) in Met-enkephalin:

import molsysmt as msm
import pyunitwizard as puw

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 the backbone \(\phi\) quartets and measure the current value of the second \(\phi\) angle:

phi_quartets = msm.topology.get_dihedral_quartets(molsys, phi=True)
initial_angle = msm.structure.get_dihedral_angles(molsys, dihedral_quartets=phi_quartets[1])
print('Initial phi angle:', puw.convert(initial_angle, to_unit='degrees'))

Initial phi angle: [[-179.9997685580422]] degree

We inspect the initial 3D conformation of the peptide:

msm.view(molsys)

We shift the dihedral angle by \(+90.0^\circ\) using molsysmt.structure.shift_dihedral_angles():

molsys_shifted = msm.structure.shift_dihedral_angles(molsys, dihedral_quartets=phi_quartets[1], shifts='90.0 degrees')

We verify that the new angle reflects exactly the \(+90.0^\circ\) angular increment:

new_angle = msm.structure.get_dihedral_angles(molsys_shifted, dihedral_quartets=phi_quartets[1])
print('Shifted phi angle:', puw.convert(new_angle, to_unit='degrees'))

Shifted phi angle: [[-89.99976855823314]] degree

Visualizing the shifted system in 3D confirms the updated peptide backbone geometry:

msm.view(molsys_shifted)

Shifting multiple dihedral angles simultaneously#

Multiple dihedral angles can be shifted concurrently by providing a list or array of angular shifts:

shifts = puw.quantity([30.0, 30.0, 30.0, 30.0], 'degrees')
molsys_multi_shift = msm.structure.shift_dihedral_angles(molsys, dihedral_quartets=phi_quartets, shifts=shifts)
all_shifted = msm.structure.get_dihedral_angles(molsys_multi_shift, dihedral_quartets=phi_quartets)
print('All phi angles after multi-shift:', puw.convert(all_shifted, to_unit='degrees'))

All phi angles after multi-shift: [[-149.9997705129718 -149.99976855823317 -149.99976916209638  -149.99977065270835]] degree