bis_protein_structure.DISULFIDE.get_SS_ver5

bis_protein_structure.DISULFIDE.get_SS_ver5(chain_id, chain, res_length, residue_idx_edit, criteria)[source]

Extracts the spatial coordinates of the alpha carbon (CA) or sulfur gamma (SG) atoms of residues in a protein chain and computes pairwise distances.

Parameters:

  • chain_id (str) – Chain ID to process.

  • chain (Bio.PDB.Chain) – The chain object containing residues to process.

  • res_length (int) – The total number of residues in the chain.

  • residue_idx_edit (dict) – A dictionary mapping residue numbers to indices for the chain.

  • criteria (str) – The atom type to use for distance calculations. Valid options are ‘CA’ (alpha carbon) and ‘SG’ (sulfur gamma).

Returns:

  • filter_disto (numpy.ndarray) – A filtered distogram (distance matrix) that contains distances between Cysteine residues that meet the distance criteria. The shape is (res_length, res_length, 1).

  • pair_list (numpy.ndarray) – List of residue index pairs where the distance between Cysteine residues satisfies the specified distance criteria.

Notes

  • The function computes the pairwise Euclidean distance between alpha carbons (CA) or sulfur gamma atoms (SG) in the given chain.

  • For the ‘CA’ criteria, the distance threshold is set between 3.0 and 7.5 Å, while for ‘SG’ criteria, it is set between 2.0 and 3.0 Å.

  • Only Cysteine residues are considered for the distance calculation in the case of ‘SG’ criteria.