Hydride - Adding hydrogen atoms to molecular models

Many tasks in structural biology ranging from simulations and hydrogen bond detection to mere visual analysis, require complete molecular models. However, most experimentally determined structures do not include the position of hydrogen atoms, due to their small size and electron density.

Hydride is an easy-to-use program and library written in Python that adds missing hydrogen atoms to molecular models based on known bond lengths and angles. Since it does not require force-field parameters for the specific molecule(s), it can be used for adding hydrogen atoms to almost any organic molecule - from small ligands to large protein complexes.

Installation

In order to use Hydride you need to have Python (at least 3.7) installed.

You can install Hydride via

$ pip install hydride

Usage

In its basic invocation Hydride reads an input structure file, adds hydrogen atoms to the molecular model and writes the resulting model into an output structure file.

$ hydride -i input_structure.pdb -o output_structure.pdb

Python API

Hydride also provides a Python API to add hydrogen atoms to AtomArray objects from Biotite.

atom_array, _ = hydride.add_hydrogen(atom_array)
atom_array.coord = hydride.relax_hydrogen(atom_array)