Get Luzar-Chandler hydrogen bonds#

Detecting hydrogen bonds based on combined distance and angle criteria (Luzar & Chandler).

The function molsysmt.hbonds.get_luzard_chandler_hbonds() evaluates hydrogen bonds using the joint donor–acceptor distance and D–H···A linearity angle thresholds established by Luzar & Chandler.

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.hbonds.get_luzard_chandler_hbonds().

Basic usage#

Let’s detect hydrogen bonds in a protein structure using the Luzar-Chandler distance and angle criteria:

import molsysmt as msm
import pyunitwizard as puw

molsys = msm.convert(msm.systems['chicken villin HP35']['chicken_villin_HP35.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 evaluate hydrogen bonds with a distance cutoff of 3.5 Å and an angle tolerance of 30°:

hbonds, distances, angles = msm.hbonds.get_luzard_chandler_hbonds(molsys,
                                                                  distance_threshold='3.5 angstroms',
                                                                  angle_threshold='30.0 degrees')
print('Total Luzar-Chandler hydrogen bonds detected:', len(hbonds[0]))
print('First 5 H-bond triplets [donor_heavy, bonded_H, acceptor]:\n', hbonds[0][:5])
print('First 5 distances:\n', distances[0][:5])
print('First 5 angles:\n', angles[0][:5])

Total Luzar-Chandler hydrogen bonds detected: 36
First 5 H-bond triplets [donor_heavy, bonded_H, acceptor]:
 [[ 42  43  91]
 [ 51  52  90]
 [ 80  81  90]
 [ 92  93  47]
 [112 113  58]]
First 5 distances:
 [0.29376070029188095 0.25604054035224855 0.27401248994459554 0.2834160516724867 0.2878586446826376] nanometer
First 5 angles:
 [0.35409470074619875 0.10517367420842096 0.5053429033349056 0.30326356925490494 0.20589640163446343] radian

Hydrogen bonds between selections#

Hydrogen bonds can also be evaluated across two distinct subsets or candidate selections using selection and selection_2. Here we demonstrate this general feature with an example of interfacial hydrogen bonds formed between the two binding partners in the Barnase–Barstar complex:

complex_sys = msm.convert(msm.systems['Barnase-Barstar']['barnase_barstar.h5msm'])
inter_hbonds, inter_dist, inter_ang = msm.hbonds.get_luzard_chandler_hbonds(complex_sys,
                                                                            selection='molecule_name=="BARNASE"',
                                                                            selection_2='molecule_name=="BARSTAR"')
print('Interfacial hydrogen bonds detected:', len(inter_hbonds[0]))
print('Interface H-bond triplets:\n', inter_hbonds[0][:5])

Interfacial hydrogen bonds detected: 15
Interface H-bond triplets:
 [[ 431  432 2400]
 [ 431  433 2361]
 [ 858  859 2296]
 [ 876  878 2969]
 [ 879  880 2969]]