Get acceptor atoms#

Identifying hydrogen bond acceptor atoms based on chemical rules and electronegative centers.

The function molsysmt.interactions.hbonds.get_acceptor_atoms() identifies potential hydrogen bond acceptor atoms within molecular systems using customizable chemical inclusion and exclusion selection 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.interactions.hbonds.get_acceptor_atoms().

Basic usage#

Let’s identify the hydrogen bond acceptor atoms in a protein structure:

import molsysmt as msm

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 inspect the built-in default inclusion and exclusion rules defined in MolSysMT:

print('Default inclusion rules:', msm.interactions.hbonds.acceptor_inclusion_rules)
print('Default exclusion rules:', msm.interactions.hbonds.acceptor_exclusion_rules)

Default inclusion rules: ["atom_type=='O'", "atom_type=='N'", "atom_type=='S'"]
Default exclusion rules: ["atom_name=='NE2' and group_name=='GLN'", "(atom_name=='NE2' and group_name=='HIS') bonded to (atom_type=='H')", "(atom_name=='ND1' and group_name=='HIS') bonded to (atom_type=='H')"]

Now let’s find all acceptor atoms within the first three residues (group_index in [1, 2, 3]):

acceptor_atoms = msm.interactions.hbonds.get_acceptor_atoms(molsys, selection='group_index==[1, 2, 3]')
print('Acceptor atom indices:', acceptor_atoms)

Acceptor atom indices: [ 6 11 18 23 28 42 47 51]

Inspecting acceptor atom metadata#

We can query detailed attribute information for the identified acceptor atoms:

msm.info(molsys, element='atom', selection=acceptor_atoms)
index id name type group index group id group name group type component index chain index molecule index molecule type entity index entity name
6 7 N N 1 41 MET amino acid 0 0 0 peptide 0 VILLIN
11 12 O O 1 41 MET amino acid 0 0 0 peptide 0 VILLIN
18 19 SD S 1 41 MET amino acid 0 0 0 peptide 0 VILLIN
23 24 N N 2 42 LEU amino acid 0 0 0 peptide 0 VILLIN
28 29 O O 2 42 LEU amino acid 0 0 0 peptide 0 VILLIN
42 43 N N 3 43 SER amino acid 0 0 0 peptide 0 VILLIN
47 48 O O 3 43 SER amino acid 0 0 0 peptide 0 VILLIN
51 52 OG O 3 43 SER amino acid 0 0 0 peptide 0 VILLIN

Custom inclusion and exclusion rules#

Users can specify custom inclusion or exclusion rules to tailor acceptor definitions for non-standard molecules or specific chemical centers:

custom_acceptors = msm.interactions.hbonds.get_acceptor_atoms(molsys, selection='group_index==[1, 2, 3]',
                                                 inclusion_rules="atom_name=='O'")
msm.info(molsys, element='atom', selection=custom_acceptors)
index id name type group index group id group name group type component index chain index molecule index molecule type entity index entity name
6 7 N N 1 41 MET amino acid 0 0 0 peptide 0 VILLIN
11 12 O O 1 41 MET amino acid 0 0 0 peptide 0 VILLIN
18 19 SD S 1 41 MET amino acid 0 0 0 peptide 0 VILLIN
23 24 N N 2 42 LEU amino acid 0 0 0 peptide 0 VILLIN
28 29 O O 2 42 LEU amino acid 0 0 0 peptide 0 VILLIN
42 43 N N 3 43 SER amino acid 0 0 0 peptide 0 VILLIN
47 48 O O 3 43 SER amino acid 0 0 0 peptide 0 VILLIN
51 52 OG O 3 43 SER amino acid 0 0 0 peptide 0 VILLIN

See also

Related Tools & References