def setRigidBodyConstraints(self, universe=None):
"""
Sets distance constraints that make the object fully rigid.
"""
if universe is None:
universe = self.universe()
if universe is None:
import Universe
universe = Universe.InfiniteUniverse()
atoms = self.atomList()
if len(atoms) > 1:
self.addDistanceConstraint(atoms[0], atoms[1],
universe.distance(atoms[0], atoms[1]))
if len(atoms) > 2:
self.addDistanceConstraint(atoms[0], atoms[2],
universe.distance(atoms[0], atoms[2]))
self.addDistanceConstraint(atoms[1], atoms[2],
universe.distance(atoms[1], atoms[2]))
if len(atoms) > 3:
for a in atoms[3:]:
self.addDistanceConstraint(atoms[0], a,
universe.distance(atoms[0], a))
self.addDistanceConstraint(atoms[1], a,
universe.distance(atoms[1], a))
self.addDistanceConstraint(atoms[2], a,
universe.distance(atoms[2], a))
def phiPsi(self, conf=None):
"Returns the values of the backbone dihedral angles phi and psi."
universe = self.universe()
if universe is None:
universe = Universe.InfiniteUniverse()
C = None
for a in self.peptide.N.bondedTo():
if a.parent.parent != self:
C = a
break
if C is None:
phi = None
else:
phi = universe.dihedral(self.peptide.C, self.peptide.C_alpha,
self.peptide.N, C, conf)
N = None
for a in self.peptide.C.bondedTo():
if a.parent.parent != self:
N = a
break
if N is None:
psi = None
else:
psi = universe.dihedral(N, self.peptide.C, self.peptide.C_alpha,
self.peptide.N, conf)
return phi, psi
def write(self, object, configuration=None, distance=None):
if distance is None:
try:
distance = object.universe().distanceVector
except AttributeError:
distance = Universe.InfiniteUniverse().distanceVector
if not ChemicalObjects.isChemicalObject(object):
for o in object:
self.write(o, configuration, distance)
else:
for bu in object.bondedUnits():
for a in bu.atomList():
self.writeAtom(a, configuration)
if hasattr(bu, 'bonds'):
for b in bu.bonds:
self.writeBond(b, configuration, distance)
def phiPsi(self, conf=None):
"""Returns a list of the (phi, psi) backbone angle pairs
for each residue."""
universe = self.universe()
if universe is None:
universe = Universe.InfiniteUniverse()
angles = []
for i in range(len(self)):
r = self[i]
if i == 0:
phi = None
else:
phi = universe.dihedral(r.peptide.C, r.peptide.C_alpha,
r.peptide.N, self[i - 1].peptide.C,
conf)
if i == len(self) - 1:
psi = None
else:
psi = universe.dihedral(self[i + 1].peptide.N, r.peptide.C,
r.peptide.C_alpha, r.peptide.N, conf)
angles.append((phi, psi))
return angles