Add missing hydrogens#

Adding missing hydrogen atoms to a molecular system.

Many molecular systems lack hydrogen atoms or require protonation adjustments to reflect a specific chemical or physical environment. The function molsysmt.build.add_missing_hydrogens() adds missing hydrogen atoms to any molecular system based on standard protonation rules and residue templates at a specified pH.

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.build.add_missing_hydrogens().

Basic usage#

Let’s show how this function works using a protein structure loaded from T4 lysozyme (PDB ID: 181L):

import molsysmt as msm

molsys = msm.convert('181L', selection='molecule_type=="protein"')

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_proteins	n_structures
molsysmt.MolSys	1289	162	1	1	1	1	1	1

This protein system was obtained from a PDB X-ray structure and does not contain hydrogen atoms. Let’s verify this using molsysmt.build.has_hydrogens():

msm.build.has_hydrogens(molsys)

False

Now we add the missing hydrogen atoms using standard protonation patterns at pH 7.4:

molsys = msm.build.add_missing_hydrogens(molsys, pH=7.4)

Let’s confirm the addition of hydrogen atoms by counting how many atoms of type 'H' are now present:

msm.get(molsys, element='atom', selection='atom_type=="H"', n_atoms=True)