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. For instance, X-ray crystal structures deposited in the Protein Data Bank often exclude hydrogens, and histidine residues can adopt different protonation states depending on the pH.

In the build module of MolSysMT, the function molsysmt.build.add_missing_hydrogens() allows you to add missing hydrogens to any molecular system supported by the library. Let’s demonstrate how it works with the following example:

Added in version 1.0.0.

How this function works#

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects: molsysmt.build.add_missing_hydrogens().

This function identifies atoms that are missing from the selected residues or molecules and restores them based on predefined topological templates and standard protonation patterns. It applies chemical rules and structural constraints to determine plausible positions for the new hydrogen atoms, integrating them consistently into the molecular system.

We start by loading a protein structure from the Protein Data Bank. This system lacks hydrogen atoms, as is typical for X-ray crystallography models.

import molsysmt as msm

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

msm.info(molecular_system)

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 molecular system was obtained from a PDB structure and, as expected, it does not contain hydrogen atoms.

msm.build.has_hydrogens(molecular_system)

False

We now add the missing hydrogen atoms, using standard protonation patterns at pH 7.4:

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

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

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