def calc_RMSD(self, list1, list2, keys):
''' Calculates RMSD between two atoms lists. The two lists have to have the same length.
'''
superpose = sp.RotamerSuperpose(list1, list2)
list2 = superpose.run()
array1, array2 = np.array([0, 0, 0]), np.array([0, 0, 0])
for a1, a2, k in zip(list1, list2, keys):
array1 = np.vstack((array1, list(a1.get_coord())))
array2 = np.vstack((array2, list(a2.get_coord())))
rmsd = np.sqrt(
sum(sum((array1[1:] - array2[1:])**2)) / array1[1:].shape[0])
return rmsd
def non_conserved_switcher(self, cgn, AA, ref_atoms, template):
try:
rot = Rotamer.objects.get(
structure=template, residue__display_generic_number__label=cgn)
if rot.residue.amino_acid != AA or rot.missing_atoms:
return False
parse = GPCRDBParsingPDB()
parsed_atoms = parse.parse_rotamer_pdb(rot)
superpose = sp.RotamerSuperpose(ref_atoms, parsed_atoms)
new_atoms = superpose.run()
if self.debug:
print(template, cgn, superpose.backbone_rmsd)
if superpose.backbone_rmsd > 0.45:
return False
return new_atoms
except Exception as msg:
return False
def non_conserved_switcher(self, cgn, AA, ref_atoms, template):
try:
print(cgn, template, AA, ref_atoms[0].get_parent().get_resname())
rot = Rotamer.objects.get(structure=template, residue__display_generic_number__label=cgn)
print(rot.residue.amino_acid)
if rot.residue.amino_acid!=AA or rot.missing_atoms:
return False
parse = GPCRDBParsingPDB()
parsed_atoms = parse.parse_rotamer_pdb(rot)
superpose = sp.RotamerSuperpose(ref_atoms, parsed_atoms)
new_atoms = superpose.run()
if self.debug:
print(template, cgn, superpose.backbone_rmsd)
if superpose.backbone_rmsd>0.45:
return False
return new_atoms
except Exception as msg:
if self.debug:
print("WARNING: Rotamer swap-in {} at {} failed with {}".format(template, cgn, msg))
return False
def superpose(self, list1, list2, TM_keys=None):
"""Superposition, supply TM_keys (list of sequence residue numbers) when superimposing on only those atoms."""
superpose = sp.RotamerSuperpose(list1, list2, TM_keys)
return superpose.run(), superpose.num_atoms_used_for_superposition