Contacts Module

Contacts

class PANDORA.Contacts.Contacts.Contacts(PDB, output_file=False, anchors=False, pept_contacts=False, M_only=list(range(1, 182)), N_only=list(range(1, 92)), cutoff=5)

Bases: object

Calculate atom contacts between different chains of a protein or between peptide anchor residues and the

rest of the MHC structure.

Parameters:

• PDB – (String) or (Bio.PDB) Accepts either the path to the pdb file or a Bio.PDB object

• output_file – (String) Path to output file. If anchors are provided, only write the anchors output

• anchors – (list) list of anchor positions. If this is provided, the atom contacts between the anchor residues of the peptide and the rest of the structure are calculated

• cutoff – Cutoff that considers two atoms contacting. Is 5 Angstrom by default

find_chain_contacts(PDB, cutoff=5)

Calculate atom distances in a pdb object.

Parameters:

• pdb – Bio.PDB object

• cutoff – (int) Distance cutoff that determines atom contact, standard is 5 Angstrom

• all – (Bool) Calculate all atom contacts or just between chains

• specific_chain – (String) Only consider contacts between one specific chain and the rest.

• anchors – (list) list of anchor positions. If such a list is given, only the contacts between the atoms of the peptide anchor residues and the rest of the structure are calculated.

Returns:

list of tuples of: Res 1, Chain 1, Resnr 1, Atom 1, Res 2, Chainm 2, Resnr 2, Atom 2, Distance 1_2

find_pept_chain_contacts(PDB, M_only=list(range(1, 182)), N_only=list(range(1, 92)), cutoff=5)

Calculate atom distances in a pdb object.

Parameters:

• pdb – Bio.PDB object

• cutoff – (int) Distance cutoff that determines atom contact, standard is 5 Angstrom

• all – (Bool) Calculate all atom contacts or just between chains

• specific_chain – (String) Only consider contacts between one specific chain and the rest.

• anchors – (list) list of anchor positions. If such a list is given, only the contacts between the atoms of the peptide anchor residues and the rest of the structure are calculated.

Returns:

list of tuples of: Res 1, Chain 1, Resnr 1, Atom 1, Res 2, Chainm 2, Resnr 2, Atom 2, Distance 1_2

show()

Print the contacts. If anchor contacts have been calculated, only show them