def __init__(self, b1, b2, ca):
self.b1 = b1 # bond 1
self.b2 = b2 # bond 2
self.ca = ca # common atom
if Utility.uniqueID(self.b2) < Utility.uniqueID(self.b1):
self.b1, self.b2 = self.b2, self.b1
self.a1 = b1.otherAtom(ca)
self.a2 = b2.otherAtom(ca)
Utility.uniqueID.registerObject(self)
def __init__(self, b1, b2, ca):
self.b1 = b1 # bond 1
self.b2 = b2 # bond 2
self.ca = ca # common atom
if Utility.uniqueID(self.b2) < Utility.uniqueID(self.b1):
self.b1, self.b2 = self.b2, self.b1
self.a1 = b1.otherAtom(ca)
self.a2 = b2.otherAtom(ca)
Utility.uniqueID.registerObject(self)
def __init__(self, blueprint, memo=None):
if type(blueprint) is type(()):
self.a1 = blueprint[0]
self.a2 = blueprint[1]
else:
self.a1 = Database.instantiate(blueprint.a1, memo)
self.a2 = Database.instantiate(blueprint.a2, memo)
if Utility.uniqueID(self.a2) < Utility.uniqueID(self.a1):
self.a1, self.a2 = self.a2, self.a1
Utility.uniqueID.registerObject(self)
def __init__(self, blueprint, memo = None):
if type(blueprint) is type(()):
self.a1 = blueprint[0]
self.a2 = blueprint[1]
else:
self.a1 = Database.instantiate(blueprint.a1, memo)
self.a2 = Database.instantiate(blueprint.a2, memo)
if Utility.uniqueID(self.a2) < Utility.uniqueID(self.a1):
self.a1, self.a2 = self.a2, self.a1
Utility.uniqueID.registerObject(self)
def __init__(self, ba1, ba2, cb):
self.ba1 = ba1 # bond angle 1
self.ba2 = ba2 # bond angle 2
# cb is the common bond, i.e. the central bond for a proper dihedral
if Utility.uniqueID(self.ba2) < Utility.uniqueID(self.ba1):
self.ba1, self.ba2 = self.ba2, self.ba1
self.improper = (self.ba1.ca is self.ba2.ca)
if self.improper:
self.b1 = self.ba1.otherBond(cb)
self.b2 = cb
self.b3 = self.ba2.otherBond(cb)
self.a1 = self.ba1.ca # central atom
self.a2 = self.b1.otherAtom(self.ba1.ca)
self.a3 = cb.otherAtom(self.ba1.ca)
self.a4 = self.b3.otherAtom(self.ba2.ca)
# each improper dihedral will come in three versions;
# identify an arbitrary unique one for constructing the list
self.normalized = Utility.uniqueID(cb) < Utility.uniqueID(self.b1)\
and Utility.uniqueID(cb) < \
Utility.uniqueID(self.b3)
else:
self.b1 = self.ba1.otherBond(cb)
self.b2 = cb
self.b3 = self.ba2.otherBond(cb)
self.a1 = self.b1.otherAtom(self.ba1.ca)
self.a2 = self.ba1.ca # these two are
self.a3 = self.ba2.ca # on the common bond
self.a4 = self.b3.otherAtom(self.ba2.ca)
self.normalized = self.a1 is not self.a4
def __init__(self, ba1, ba2, cb):
self.ba1 = ba1 # bond angle 1
self.ba2 = ba2 # bond angle 2
# cb is the common bond, i.e. the central bond for a proper dihedral
if Utility.uniqueID(self.ba2) < Utility.uniqueID(self.ba1):
self.ba1, self.ba2 = self.ba2, self.ba1
self.improper = (self.ba1.ca is self.ba2.ca)
if self.improper:
self.b1 = self.ba1.otherBond(cb)
self.b2 = cb
self.b3 = self.ba2.otherBond(cb)
self.a1 = self.ba1.ca # central atom
self.a2 = self.b1.otherAtom(self.ba1.ca)
self.a3 = cb.otherAtom(self.ba1.ca)
self.a4 = self.b3.otherAtom(self.ba2.ca)
# each improper dihedral will come in three versions;
# identify an arbitrary unique one for constructing the list
self.normalized = Utility.uniqueID(cb) < Utility.uniqueID(self.b1)\
and Utility.uniqueID(cb) < \
Utility.uniqueID(self.b3)
else:
self.b1 = self.ba1.otherBond(cb)
self.b2 = cb
self.b3 = self.ba2.otherBond(cb)
self.a1 = self.b1.otherAtom(self.ba1.ca)
self.a2 = self.ba1.ca # these two are
self.a3 = self.ba2.ca # on the common bond
self.a4 = self.b3.otherAtom(self.ba2.ca)
self.normalized = self.a1 is not self.a4
