def on_ppi(self, receptor_path, ligand_path, fold_name=None):
'''
Compute the split potentials for a ppi
receptor_path = Complete path to the structure of the receptor
ligand_path = Complete path to the structure of the ligand
fold_name = Optional parameter, name given to the PPI
'''
# Get PDB structure (fold structure)
receptor = PDB.read_pdb(receptor_path)
ligand = PDB.read_pdb(ligand_path)
receptor_name = self.get_fold_name_from_fold_path(receptor_path)
ligand_name = self.get_fold_name_from_fold_path(ligand_path)
if not fold_name:
fold_name = '{}-{}'.format(receptor_name, ligand_name)
if isinstance(receptor, list): # if the structure obtained is an instance of a list, it means that it is not a unique structure: it is a COMPLEX of more than one chain
receptor = PDB.read_pdb(receptor_path, merge_chains=True) # The complex will always be merged
if isinstance(ligand, list): # if the structure obtained is an instance of a list, it means that it is not a unique structure: it is a COMPLEX of more than one chain
ligand = PDB.read_pdb(ligand_path, merge_chains=True) # The complex will always be merged
receptor.set_dssp()
receptor.clean()
receptor.normalize_residues()
ligand.set_dssp()
ligand.clean()
ligand.normalize_residues()
ppi = Interaction(receptor, ligand)
# Compute split potentials
if self.pot_type == 'CB':
cutoff = 12
else:
cutoff = 5
split_potentials = SplitPotentialsPPI(c_type=self.pot_type, cutoff=cutoff) # definition of SplitPotentialsPPI class (BioLib.Docking)
#global_energies = []
global_energies = split_potentials.calculate_global_energies(ppi, Zscores=True) # calculation of global energies using the method of the SplitPotentialsPPI class
print('\nGLOBAL ENERGIES')
#residues_energies = []
residues_energies = split_potentials.calculate_residue_energies_between_pairs(ppi, 'R', Zscores=True) # same for residues energies
print('\nRESIDUE ENERGIES')
self.ppi_xml(fold_name, global_energies, residues_energies, receptor, ligand) # creation of xml results file
return
def check_pdb_format(self, structure_path):
file_name = self.get_fold_name_from_fold_path(structure_path)
try:
struct = PDB.read_pdb(structure_path)
except:
self.print_error(8, file_name)
self.write_output_file(self.xml_errors, self.xml_err_file)
self.write_output_file(self.xml_result, self.xml_out_file) # Output an empty results file
sys.exit(10)
return