docktprep

This is a work in progress and the code is not yet stable.

Create DockThor input files from PDB, mmCIF and MOL2 formats. Prepare and fix common issues in the PDB files.

Accepted input formats:

• Receptor: PDB, PDBx/mmCIF ⏳.
• Ligand: PDB ⏳, PDBx/mmCIF ⏳, MOL2 ⏳.

Features:

• Handles disordered atom positions.¹
• Handles amino acid residue insertions.¹
• Handles non-standard amino acids nomenclatures (e.g. HISD, HSD). ⏳
• Allows for structure model selection.¹
• Supports DNA/RNA receptors.¹
• Replaces non-standard amino acids/nucleotides with standard ones.²
• Adds missing heavy atoms to the structure.²
• Adds missing residues to the structure.² ⏳
• Adds missing hydrogens to the structure.²

Features originally implemented in ¹Biopython and ²PDBFixer.

Installation and usage as a command-line tool

To install the application as a command-line tool, you'll need conda.

Clone the repository:

git clone https://github.com/gmmsb-lncc/docktprep.git
cd docktprep

Create a new conda environment from the environment.yml file:

conda env create --file environment.yml --prefix ./venv/

You will always need to activate the environment before running the application:

conda activate ./venv/

Install the application:

python -m pip install .

That's it. For a complete list of options, run:

docktprep --help

Development setup

Follow the instructions below to set up the development environment.

Installation

Clone the repository and install the dependencies using conda.

# create a new conda environment from the environment.yml file
conda env create --file environment.yml --prefix ./venv/
conda activate ./venv/

Run tests

python -m pytest -vs tests/ --log-cli-level=INFO

Execute main script

python -m docktprep.main --help