Beads positions/orientations now generated from contour_position in _generate_one_bead()

segmentmodel.py

@@ -127,8 +127,8 @@ class Segment(ConnectableElement, Group):
 
     def contour_to_tangent(self,s):
         t = interpolate.splev( s, self.position_spline_params, der=1 )
-        if len(t) > 1: t = np.array(t).T
-        return t
+        t = (t / np.linalg.norm(t,axis=0))
+        return t.T
         
 
     def contour_to_orientation(self,s):
@@ -136,8 +136,7 @@ class Segment(ConnectableElement, Group):
             # axis = self.start_orientation.dot( np.array((0,0,1)) )
             if self.quaternion_spline_params is None:
                 axis = self.contour_to_tangent(s)
-                # orientation = rotationAboutAxis( axis, s*self.twist_per_nt*self.num_nts, normalizeAxis=False )
-                orientation = rotationAboutAxis( axis, s*self.twist_per_nt*self.num_nts, normalizeAxis=False )
+                orientation = rotationAboutAxis( axis, s*self.twist_per_nt*self.num_nts, normalizeAxis=True )
                 ## TODO: ensure this is correct
                 # orientation = self.start_orientation.dot(orientation) # .dot( self.start_orientation )
                 orientation = orientation.dot( self.start_orientation )
@@ -152,7 +151,7 @@ class Segment(ConnectableElement, Group):
     def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead ):
         raise NotImplementedError
 
-    def _generate_one_bead(self, pos, nts, orientation=None):
+    def _generate_one_bead(self, contour_position, nts):
         raise NotImplementedError
 
     def _assign_particles_to_locations(self):
@@ -212,44 +211,27 @@ class Segment(ConnectableElement, Group):
         if num_beads <= 2:
             ## not yet implemented for dsDNA
             assert( isinstance(self, SingleStrandedSegment) )
-            b = self._generate_one_bead(0.5, 
-                                        self.start_position,
-                                        self.num_nts,
-                                        self.start_orientation)
+            b = self._generate_one_bead(0.5, self.num_nts)
             self.children.append(b)
             self.beads.append(b) # don't add orientation bead
             self._assign_particles_to_locations()
             return
 
-
         for i in range(num_beads+1):
             nts = nts_per_bead
             if i == 0 or i == num_beads: 
                 nts *= 0.5
 
             s = i*float(nts_per_bead)/(self.num_nts) # contour
-            pos = self.contour_to_position(s)
-            if self.start_orientation is not None:
-                axis = self.start_orientation.dot( np.array((0,0,1)) )
-                orientation = rotationAboutAxis( axis, s*self.twist_per_nt*self.num_nts, normalizeAxis=False )
-                ## TODO: ensure this is correct
-                # orientation = self.start_orientation.dot(orientation) # .dot( self.start_orientation )
-                orientation = orientation.dot( self.start_orientation )
-            else:
-                orientation = None
-
-            b = self._generate_one_bead(s,pos,nts,orientation)
+            b = self._generate_one_bead(s,nts)
             self.children.append(b)
             self.beads.append(b) # don't add orientation bead
 
-            if "orientation_bead" in b.__dict__:
+            if "orientation_bead" in b.__dict__: # TODO: think of a cleaner approach
                 o = b.orientation_bead
                 self.children.append(o)
                 self.add_bond(b,o, Segment.orientation_bond, exclude=True)
                 
-            # if last is not None:
-            #     self.add_bond( i=last, j=b, bond="ssdna" )
-            # last = b
         self._assign_particles_to_locations()
 
     def _regenerate_beads(self, max_nts_per_bead=4, ):
@@ -337,10 +319,10 @@ class DoubleStrandedSegment(Segment):
     def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead):
         return (self.num_nts // max_basepairs_per_bead) + 1
 
-    def _generate_one_bead(self, contour_position, pos, nts, orientation=None):
+    def _generate_one_bead(self, contour_position, nts):
+        pos = self.contour_to_position(contour_position)
         if self.local_twist:
-            assert(orientation is not None)
-            # opos = pos + np.array((2,0,0)).dot(orientation)
+            orientation = self.contour_to_orientation(contour_position)
             opos = pos + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
             o = PointParticle( Segment.orientation_particle, opos, nts,
                                num_nts=nts, parent=self )
@@ -424,7 +406,8 @@ class SingleStrandedSegment(Segment):
         #     pdb.set_trace()
         return (self.num_nts // max_nucleotides_per_bead) + 1
 
-    def _generate_one_bead(self, contour_position, pos, nts, orientation=None):
+    def _generate_one_bead(self, contour_position, nts):
+        pos = self.contour_to_position(contour_position)
         return PointParticle( Segment.ssDNA_particle, pos, nts,
                               num_nts=nts, parent=self,
                               contour_position=contour_position )