protein-design-tools 0.1.21

A library of tools for protein design.

Protein-Design Tools

A library of tools for protein design.

Installation

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pip install protein-design-tools

Usage

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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

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MIT