def test_calculate_interface(self):
atoms, residues, chains = parse_complex_from_file(
self.golden_data_path + '1PPErec.pdb')
receptor = Complex(chains, atoms)
atoms, residues, chains = parse_complex_from_file(
self.golden_data_path + '1PPElig.pdb')
ligand = Complex(chains, atoms)
adapter = DFIREAdapter(receptor, ligand)
receptor_residue_indexes, ligand_residue_indexes, dist_matrix, atom_indexes = get_interface_residues(
adapter.receptor_model, adapter.ligand_model, max_cutoff=1.)
receptor_residues = []
for residue_index in receptor_residue_indexes:
residue = receptor.residues[residue_index]
receptor_residues.append("%s.%d" % (residue.name, residue.number))
ligand_residues = []
for residue_index in ligand_residue_indexes:
residue = ligand.residues[residue_index]
ligand_residues.append("%s.%d" % (residue.name, residue.number))
# Checked according to UCSF chimera
expected_receptor = [
'SER.61', 'ALA.56', 'TYR.59', 'TYR.94', 'GLY.62', 'ILE.63',
'MET.104', 'ILE.106'
]
expected_ligand = [
'LEU.7', 'LEU.8', 'GLU.24', 'HIS.25', 'GLY.26', 'TYR.27', 'CYS.28'
]
assert len(set(expected_receptor) & set(receptor_residues)) == 8
assert len(set(expected_ligand) & set(ligand_residues)) == 7
def test_calculate_DFIRE_1AY7(self):
atoms, residues, chains = parse_complex_from_file(
self.golden_data_path + '1AY7rec.pdb')
receptor = Complex(chains, atoms)
atoms, residues, chains = parse_complex_from_file(
self.golden_data_path + '1AY7lig.pdb')
ligand = Complex(chains, atoms)
adapter = DFIREAdapter(receptor, ligand)
assert_almost_equal(
-20.7486309727,
self.dfire(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
def test_calculate_DFIRE_1EAW(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1EAWrec.pdb')
receptor = Complex(chains, atoms)
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1EAWlig.pdb')
ligand = Complex(chains, atoms)
adapter = DFIREAdapter(receptor, ligand)
assert_almost_equal(
-16.2182794457,
self.dfire(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
def usage():
print("Usage: %s receptor.pdb ligand.pdb" % sys.argv[0])
if __name__ == "__main__":
if len(sys.argv[1:]) != 2:
usage()
raise SystemExit('Wrong command line')
atoms, residues, chains = parse_complex_from_file(sys.argv[1])
receptor = Complex(chains, atoms)
atoms, residues, chains = parse_complex_from_file(sys.argv[2])
ligand = Complex(chains, atoms)
adapter = DFIREAdapter(receptor, ligand)
# 5A of cutoff to be in the same line as the ASA value used in the original paper
receptor_residue_indexes, ligand_residue_indexes, dist_matrix, atom_indexes = get_interface_residues(
adapter.receptor_model, adapter.ligand_model, max_cutoff=5.)
rotamer_library = InterfaceSurfaceLibrary()
print("%d receptor interface residues" % len(receptor_residue_indexes))
receptor_residues = []
for residue_index in receptor_residue_indexes:
residue = receptor.residues[residue_index]
chi_angles = calculate_chi_angles(residue)
for chi, angle in chi_angles.items():
try:
chi_angles[chi] = math.degrees(angle)
except TypeError: