Preparation: Remove Hydrogens

Briefs

This science API, named enzy_htp.preparation.remove_hydrogens, removes hydrogen atoms from the supplied enzy_htp.structure.Structure class instance (hereafter referred to as Structure instance).

Input/Output

input: A Structure instance (no matter it’s a protein, polypeptite, or ligand).

How to obtain

A Structure instance can be obtained by these APIs.

OR using the output of Remove Solvent. (Recommended, otherwise the water molecules will be left with a bunch of oxygen atoms after the hydrogen atoms are removed.)

output: A Structure instance with hydrogen atoms removed (in-place modification, not as return value).

preparation_remove_solvent

Arguments

stru

The input Structure instance (no matter it’s a protein, polypeptite, or ligand).

(See Input/Output section)

polypeptide_only

whether only remove hydrogen atoms from polypeptide.

(Boolean, optional, default True)

in_place

Apply the change in place (to the supplied instance) or in a copy (create a new instance).

(Boolean, optional, default True)

Examples

Prepare the Input: Load Structure

In order to make use of the API, we should have structure loaded.

import enzy_htp.structure as struct

sp = struct.PDBParser()

pdb_filepath = "/path/to/your/structure.pdb"
stru = sp.get_structure(pdb_filepath)

Execute API

Use preparation.remove_hydrogens to remove hydrogen atoms from your structure.

The simpliest use of remove_hydrogens is as follows.

Where the polypeptide_only and in_place are both set to True.

from enzy_htp.preparation import remove_hydrogens

stru = remove_hydrogens(stru=stru)
We can also customize the arguments passed to this function.

Do you want to remove hydrogens from both polypeptide(s) and ligand(s)? Customize polypeptide_only.

Do you want to create a new Structure instance while keeping the supplied instance still? Customize in_place.

stru_no_hydrogen = remove_hydrogens(stru=stru, polypeptide_only=False, in_place=False)

Note

This API modifies the Structure instance (what we passed as argument stru) itself or create a new Structure instance (while keeping the supplied instance still) depending on the in_place argument you choose. Both circumstances will return a reference value.

Thus, if you set in_place=False so as to have two Structure instances (one with hydrogens, and the other without hydrogens), you’d better define a new variable to receive the response.

Check the Output

Let’s try executing the API here and check if there’s any changes taking place.

We choose the crystal structure of small protein crambin at 0.48 Angstrom resolution for example.

Now, we can go through the procedure (picking up after the “Remove Solvent” step).

import enzy_htp.structure as struct
from enzy_htp.preparation import remove_solvent, remove_hydrogens

sp = struct.PDBParser()

# Read PDB file here.
pdb_filepath = "3NIR.pdb"
stru = sp.get_structure(pdb_filepath)

# Remove solvents here.
print(stru.num_atoms)       # 742.
remove_solvent(stru=stru)   # <enzy_htp.structure.structure.Structure object at 0x7fa383c4aa30>
print(stru.num_atoms)       # 644.

# Remove hydrogen atoms here.
stru = remove_hydrogens(stru=stru, polypeptide_only=False)
print(stru.num_atoms)       # 327.

We may notice that, after executing the API remove_hydrogens, the number of atoms (num_atoms) in the structure decreased, indicating that the hydrogen atoms have been removed from the structure.

Author: Zhong, Yinjie <yinjie.zhong@vanderbilt.edu>