Get covalent paths#

Finding paths of covalently bonded atoms matching specified element patterns.

The function molsysmt.topology.get_covalent_paths() identifies all linear sequences of covalently bonded atoms that match a specified pattern of atom names or element criteria.

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_covalent_paths().

Basic usage#

Let’s show how to find covalent paths matching atom name patterns using TcTIM (PDB ID: 1TCD):

import molsysmt as msm

molsys = msm.convert(msm.systems['TcTIM']['1tcd.h5msm'], to_form='molsysmt.MolSys')

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 inspect structural information with molsysmt.basic.info():

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_proteins	n_structures
molsysmt.MolSys	3983	662	167	4	167	2	165	2	1

We search for all 3-atom covalent paths matching the sequence C -> N -> CA using molsysmt.topology.get_covalent_paths():

covalent_paths = msm.topology.get_covalent_paths(molsys, path=['atom_name=="C"', 'atom_name=="N"', 'atom_name=="CA"'])

covalent_paths.shape

(495, 3)

covalent_paths

array([[   2,    9,   10],
       [  11,   16,   17],
       [  18,   25,   26],
       ...,
       [3789, 3796, 3797],
       [3798, 3801, 3802],
       [3803, 3808, 3809]], shape=(495, 3))

We check the atom names along the first retrieved covalent path using molsysmt.basic.get():

msm.get(molsys, element='atom', selection=covalent_paths[0], name=True)

['C', 'N', 'CA']

Using multi-name atom selections#

Selection strings at each position can match multiple atom names:

covalent_paths = msm.topology.get_covalent_paths(molsys, path=['atom_name==["C", "N"]', 'atom_name=="CA"', 'atom_name=="C"'])

covalent_paths

array([[   0,    1,    2],
       [   2,    1,    2],
       [   9,   10,   11],
       ...,
       [3803, 3802, 3803],
       [3808, 3809, 3810],
       [3810, 3809, 3810]], shape=(994, 3))

msm.get(molsys, element='atom', selection=covalent_paths[0], name=True)

['N', 'CA', 'C']

msm.get(molsys, element='atom', selection=covalent_paths[1], name=True)

['C', 'CA', 'C']