protein-design-tools 0.1.26

A library of tools for protein design.

Protein-Design Tools

A library of tools for protein design.

Installation

Describe how to install your package. For example:

pip install protein-design-tools

Usage

This package provides tools for protein design projects, including handling and manipulating metadata associated with those types of projects.

Some examples of how to use this package. For example:

Examples

In the example below, we demonstrate how to calculate the radius of gyration for a protein. This can be useful when selecting proteins with a more spherical structure.

from protein_design_tools import protein_structure, protein_structure_utils

protein = protein_structure.ProteinStructure()
protein.read_pdb("example.pdb")

# Display the amino acid sequence of the protein
# Get the sequence of each chain in the protein
sequence_dict = protein.get_sequence_dict()
for chain_id, sequence in sequence_dict.items():
    print(f"Chain {chain_id}: {sequence}")

# What is the radius of gyration of the backbone of chain A in our protein structure?
rgA = protein_structure_utils.get_radgyr(protein, chains='A', atom_type="backbone")
print(f"protein structure chain A rg : {rgA:.4f}")

# What is the radius of gyration of the backbone of an ideal alanine helix?
ideal_helix_seq_length = len(sequence_dict['A'])
rg_ideal_helix = protein_structure_utils.get_radgyr_alanine_helix(ideal_helix_seq_length, atom_type="backbone")
print(f"ideal alanine helix rg : {rg_ideal_helix:.4f}")

# What is the radius of gyration ratio of the protein structure to an ideal alanine helix?
rg_ratio = protein_structure_utils.get_radgyr_ratio(protein, chains='A', atom_type="backbone")
print(f"rg ratio : {rg_ratio:.4f}")

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

License

Include information about the license. For example:

MIT