Has hydrogens#

Checking whether a molecular system or selection contains hydrogen atoms.

The function molsysmt.build.has_hydrogens() evaluates whether hydrogen atoms are present in a molecular system or within a specific selection, returning True or False.

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.has_hydrogens().

Basic usage#

Let’s show how this function works using T4 lysozyme (PDB ID: 181L):

import molsysmt as msm

molsys = msm.convert(msm.systems['T4 lysozyme L99A']['181l.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.

Let’s check the number of hydrogen atoms using molsysmt.basic.get():

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

We check if the system contains hydrogen atoms using molsysmt.build.has_hydrogens():

msm.build.has_hydrogens(molsys)

False

We can also restrict the check to a specific selection (such as protein molecules):

msm.build.has_hydrogens(molsys, selection='molecule_type=="protein"')

False

Now let’s complete terminal cappings, heavy atoms, and add hydrogen atoms to the system:

molsys = msm.build.add_missing_terminal_cappings(molsys)
molsys = msm.build.add_missing_heavy_atoms(molsys)
molsys = msm.build.add_missing_hydrogens(molsys)

We check again to confirm that hydrogen atoms are now present:

msm.build.has_hydrogens(molsys)

True

msm.build.has_hydrogens(molsys, selection='molecule_type=="protein"')

True