Fixed numerous issues; code seems to work

CanonicalNucleotideAtoms.py

@@ -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]

arbdmodel.py

@@ -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):