Added position scaling and beta to atoms; centered ssDNA

CanonicalNucleotideAtoms.py

@@ -48,7 +48,8 @@ class CanonicalNucleotideFactory(Group):
                                                 mass   = d['f4'][i])
             p = PointParticle( type_ = atomic_types[tn],
                                position = [xs[i],ys[i],zs[i]],
-                               name = names[i].decode('UTF-8') )
+                               name = names[i].decode('UTF-8'),
+                               beta = 1)
             self.children.append( p )
         
         atoms = self.children

segmentmodel.py

@@ -348,7 +348,7 @@ class Segment(ConnectableElement, Group):
     def _generate_one_bead(self, contour_position, nts):
         raise NotImplementedError
 
-    def _generate_atomic_nucleotide(self, contour_position, is_fwd, seq):
+    def _generate_atomic_nucleotide(self, contour_position, is_fwd, seq, scale):
         """ Seq should include modifications like 5T, T3 Tsinglet; direction matters too """
 
         # print("Generating nucleotide at {}".format(contour_position))
@@ -365,7 +365,7 @@ class Segment(ConnectableElement, Group):
                 angleVec = angleVec/np.linalg.norm(angleVec)
                 y = np.cross(axis,angleVec)
                 orientation = np.array([angleVec,y,axis]).T
-                ## TODOTODO: improve placement of ssDNA
+                ## TODO: improve placement of ssDNA
                 # rot = rotationAboutAxis( axis, contour_position*self.twist_per_nt*self.num_nts, normalizeAxis=True )
                 # orientation = rot.dot(orientation)
             else:
@@ -387,9 +387,24 @@ class Segment(ConnectableElement, Group):
         atoms = nt_dict[ key ].generate() # TODO: clone?
                         
         atoms.orientation = orientation.dot(atoms.orientation)
-        atoms.position = pos
+        if isinstance(self, SingleStrandedSegment):
+            if scale is not None and scale != 1:
+                for a in atoms:
+                    a.position = scale*a.position
+                    a.beta = 0
+            atoms.position = pos - atoms.atoms_by_name["C1'"].collapsed_position()
+        else:
+            if scale is not None and scale != 1:
+                if atoms.sequence in ("A","G"):
+                    r0 = atoms.atoms_by_name["N9"].position
+                else:
+                    r0 = atoms.atoms_by_name["N1"].position
+                for a in atoms:
+                    if a.name[-1] in ("'","P","T"):
+                        a.position = scale*(a.position-r0) + r0
+                        a.beta = 0
+            atoms.position = pos
 
-        ## TODOTODO: scale positions, set beta
         return atoms
 
     def add_location(self, nt, type_, on_fwd_strand=True):
@@ -939,7 +954,7 @@ class Strand(Group):
     #     assert( len(ret) == self.num_nts )
     #     return ret
 
-    def generate_atomic_model(self):
+    def generate_atomic_model(self,scale):
         last = None
         resid = 1
         strand_segment_count = 0
@@ -955,7 +970,7 @@ class Strand(Group):
                 if strand_segment_count == len(s.strand_segments) and c == 1:
                     seq = seq+"3"
 
-                nt = seg._generate_atomic_nucleotide( c, s.is_fwd, seq )
+                nt = seg._generate_atomic_nucleotide( c, s.is_fwd, seq, scale )
                 # if s.is_fwd:                    
                 # else:
                 #     nt = seg._generate_atomic_nucleotide( c, s.is_fwd, "A" )
@@ -1770,10 +1785,10 @@ class SegmentModel(ArbdModel):
             s.update_atomic_orientations(orientation)
 
 
-    def _generate_atomic_model(self):
+    def _generate_atomic_model(self, scale=1):
         self.children = self.strands
         for s in self.strands:
-            s.generate_atomic_model()
+            s.generate_atomic_model(scale)
         return
 
         ## Angle optimization