PDBontheGō

WARNING: This is an highly experimental package which assumes specific cases when reading PDB files. Use it cautiously.

Set of functions for extracting parameters from a PDB file to construct a coarse-grained, Gō-model, of the analyzed protein. They allow you to compute: bond lengths, dihedral angles, contact map (gemetrical definition, more details in contactmap.py), etc.

The porject is divided into:

• parser which contains a Bio.PDB.PDBParser() wrapper from the Biopython project and it is used to extract residues objects from the PDB file
• parameters contains functions to extract bond lengths, bond angles, dihedral angles and disulfite bonds lengths
• contactmap helps you to compute the native contact map as define here and plot it.

Each function has a detailed docstring explaning what it does, arguments and its result.

Installation

git clone https://github.com/loscati/pdbonthego.git

Usage example

Clone this repository into the project directory and make sure to let the interpreter know where these scripts are located (e.g. by adding them to the __path__ variable).

import parser
import parameters
import contactmap 

prot_name = '1ucs' # PDB name example
path_pdb = f'/path/to/pdbfile/{prot_name}.pdb'

# Parameters to select model-chain-altloc (see Biopython wiki and pdb101.rcsb.org/)
altloc = 'A' # alternative location
model = 0 # model index
chain = 0 # chain index
residues_to_remove = 0 # from the beginning of the chain (N-terminus)
threshold = 4.5 # threshold for the contact map, same lenght units of the PDB file (usually Angstrom)

res = parser.get_residues(path_pdb, altloc, model, chain, residues_to_remove)
bonds = parameters.get_residue_dists(path_pdb, altloc, model, chain, residues_to_remove)
contact_map = contactmap.get_contact_map(path_pdb, threshold, altloc, model, chain, residues_to_remove)

In order to select the right model-chain-altloc you have to know the structure of the PDB file, this site contain a complete introduction to this datastructure. More info about how parser, and all other function which uses it, handle these arguments can be found in the The Structure Object section of the Bio.PDB package.

Compatibility

The package is tested with Python 3.9.5 and biopython version 1.79