AdjacencyFiles

CoDIAC.AdjacencyFiles.BinaryFeatures(PDB_ID, PATH, translate_resid=False)

Produces an adjacency file for intra (domain-domain) and inter (liagnd) protein contacts that are represented as binary features. Contacts merged across and within protein entities and chains using defined thresholds.

Parameters:

PDB_IDstr

Input a PDB ID

PATHstr

Path to write the output file

translate_residbool

chose whether to update structure sequence residue positions to the ones in the Uniprot Reference

Returns:

OUTFILEstr

binarized version of the adjacency txt file is created

CoDIAC.AdjacencyFiles.ProcessArpeggio(input_file_path, outfile_path, mmCIF_file, small_molecule=False)

This function generates a text file of contacts that is a processed version of contact information extracted using Arpeggio (json file)

Parameters:

input_file_pathstr

Input a .json file generated by running Arpeggio

outfile_pathstr

Path to save the output .txt contactmap file

mmCIF_filestr

Path to fetch the mmCIF file

small_moleculebool

Whether to include or exclude protein interactions with any small molecules that may be present in the structure complex

Returns:

Adjacency file ‘{PDB_ID}.txt’ to the specified path in outfile variable