Commit 2161b99c authored by cmaffeo2's avatar cmaffeo2
Browse files

Fixed numerous issues; code seems to work

parent daa829dd
......@@ -21,17 +21,7 @@ def stringToIntTuples(string, tupleLen, offset):
return ret
class CanonicalNucleotide(Group):
# DefaultOrientation = rotationAboutAxis([0,0,1], 68)
# DefaultOrientation = rotationAboutAxis([0,0,1], 68+180)
# DefaultOrientation = rotationAboutAxis([0,0,1], 68+180-20)
DefaultOrientation = rotationAboutAxis([0,0,1], 90)
# DefaultOrientation = rotationAboutAxis([0,0,1], -90)
# DefaultOrientation = rotationAboutAxis([0,0,1], 60)
# DefaultOrientation = rotationAboutAxis([0,0,1], -90)
DefaultOrientation = rotationAboutAxis([0,0,1], -30)
DefaultOrientation = rotationAboutAxis([0,0,1], -120)
DefaultOrientation = rotationAboutAxis([0,0,1], -150)
DefaultOrientation = rotationAboutAxis([0,0,1], 150)
DefaultOrientation = rotationAboutAxis([0,0,1], 80)
def __init__(self, prefix, seq):
self.sequence = seq # TODO: used?
self.resname = resnames[seq]
......
......@@ -100,23 +100,23 @@ class Parent():
def add_bond(self, i,j, bond, exclude=False):
## TODO: how to handle duplicating and cloning bonds
beads = [b for b in self]
for b in (i,j): assert(b in beads)
# beads = [b for b in self]
# for b in (i,j): assert(b in beads)
self.bonds.append( (i,j, bond, exclude) )
def add_angle(self, i,j,k, angle):
beads = [b for b in self]
for b in (i,j,k): assert(b in beads)
# beads = [b for b in self]
# for b in (i,j,k): assert(b in beads)
self.angles.append( (i,j,k, angle) )
def add_dihedral(self, i,j,k,l, dihedral):
beads = [b for b in self]
for b in (i,j,k,l): assert(b in beads)
# beads = [b for b in self]
# for b in (i,j,k,l): assert(b in beads)
self.dihedrals.append( (i,j,k,l, dihedral) )
def add_improper(self, i,j,k,l, dihedral):
beads = [b for b in self]
for b in (i,j,k,l): assert(b in beads)
# beads = [b for b in self]
# for b in (i,j,k,l): assert(b in beads)
self.impropers.append( (i,j,k,l, dihedral) )
def add_exclusion(self, i,j):
......
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