Get dihedral quartets#

Getting the quartets of atoms defining dihedral angles in a molecular system.

The function molsysmt.topology.get_dihedral_quartets() identifies atom quartets defining standard backbone (\(\\phi, \\psi, \\omega\)) or sidechain (\(\\chi_1, \\chi_2, \\chi_3, \\chi_4, \\chi_5\)) dihedral angles.

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.topology.get_dihedral_quartets().

Basic usage#

Let’s show how to extract backbone and sidechain dihedral quartets using TcTIM (PDB ID: 1TCD):

import molsysmt as msm

molsys = msm.convert(msm.systems['TcTIM']['1tcd.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 extract quartets for all \(\\phi\) backbone angles across the system using molsysmt.topology.get_dihedral_quartets():

phi_quartets = msm.topology.get_dihedral_quartets(molsys, phi=True)

print('Total phi quartets found:', len(phi_quartets))
print('First 5 phi quartets:', phi_quartets[:5])

Total phi quartets found: 495
First 5 phi quartets: [[2, 9, 10, 11], [11, 16, 17, 18], [18, 25, 26, 27], [27, 32, 33, 34], [34, 40, 41, 42]]

We can restrict the search to specific residue selections (e.g. residues 10 to 15):

phi_subset = msm.topology.get_dihedral_quartets(molsys, selection='group_index in [10, 11, 12, 13, 14, 15]', phi=True)
print('Residues 10-15 phi quartets:', phi_subset)

Residues 10-15 phi quartets: [[79, 86, 87, 88], [88, 92, 93, 94], [94, 100, 101, 102], [102, 104, 105, 106], [106, 110, 111, 112]]

Sidechain dihedral angles (such as \(\\chi_5\)) can also be queried:

chi5_quartets = msm.topology.get_dihedral_quartets(molsys, chi5=True)
print('Total chi5 quartets found:', len(chi5_quartets))
print('First 3 chi5 quartets:', chi5_quartets[:3])

Total chi5 quartets found: 26
First 3 chi5 quartets: [[391, 392, 393, 394], [516, 517, 518, 519], [731, 732, 733, 734]]

Multiple dihedral angles can be queried simultaneously:

phi_q, psi_q, omega_q, chi1_q = msm.topology.get_dihedral_quartets(molsys, selection='group_index==10', phi=True, psi=True, omega=True, chi1=True)
print('phi:', phi_q)
print('psi:', psi_q)
print('omega:', omega_q)
print('chi1:', chi1_q)

phi: []
psi: []
omega: []
chi1: [[77, 78, 81, 82]]

Summary of dihedral angle definitions#

The tables below summarize the standard atom quartet definitions used by MolSysMT:

Angle	Atoms Definition	Standard Range
\(\\phi\)	\(C_{i-1} - N_i - C\\alpha_i - C_i\)	\([-180^\\circ, 180^\\circ]\)
\(\\psi\)	\(N_i - C\\alpha_i - C_i - N_{i+1}\)	\([-180^\\circ, 180^\\circ]\)
\(\\omega\)	\(C\\alpha_i - C_i - N_{i+1} - C\\alpha_{i+1}\)	\([-180^\\circ, 180^\\circ]\)
\(\\chi_1\)	\(N_i - C\\alpha_i - C\\beta_i - C\\gamma_i\)	\([-180^\\circ, 180^\\circ]\)

Extracting atom blocks attached to dihedral quartets#

Using with_blocks=True, molsysmt.topology.get_dihedral_quartets() returns both the dihedral quartet and the two sets of atoms that move rigidly as blocks around the rotatable bond:

molsys_peptide = msm.convert(msm.systems['Met-enkephalin']['met_enkephalin.h5msm'])
phi_chains, phi_blocks = msm.topology.get_dihedral_quartets(molsys_peptide, with_blocks=True, phi=True)

print('Quartet 1 atom indices:', phi_chains[1])
print(f'Block 0 contains {len(phi_blocks[1][0])} atoms.')
print(f'Block 1 contains {len(phi_blocks[1][1])} atoms.')

Quartet 1 atom indices: [26, 28, 30, 33]
Block 0 contains 30 atoms.
Block 1 contains 42 atoms.

We can visualize the peptide with MolSysViewer:

msm.view(molsys_peptide)