Fixed multiple issues; 3-prime ends of nucleotides now terminate correctly;...

Fixed multiple issues; 3-prime ends of nucleotides now terminate correctly; strands not cleared unless atoms exist; strands regenerated with atomic model; cadnano models initialized with more correct azimuthal angle

mrdna/model/arbdmodel.py

@@ -1105,13 +1105,12 @@ cellBasisVector3 0 0 {cellZ}
 
 if {{$nLast == 0}} {{
     temperature 300
-    fixedAtoms on
-    fixedAtomsForces on
-    fixedAtomsFile $prefix.pdb
-    fixedAtomsCol B
-    minimize 2400
-
-    fixedAtoms off
+    # fixedAtoms on
+    # fixedAtomsForces on
+    # fixedAtomsFile $prefix.pdb
+    # fixedAtomsCol B
+    # minimize 2400
+    # fixedAtoms off
     minimize 2400
 }} else {{
     bincoordinates  {output_directory}/$prefix-$nLast.restart.coor

mrdna/model/nbPot.py

@@ -3,8 +3,8 @@ import scipy.optimize as opt
 from scipy.interpolate import interp1d
 from scipy.signal import savgol_filter as savgol
 
-from .nonbonded import NonbondedScheme
-from .. import get_resource_path
+from mrdna.model.nonbonded import NonbondedScheme
+from mrdna import get_resource_path
 
 dxParam = -1
 
@@ -33,7 +33,7 @@ y0 = d[:,0]                     # kcal/mol for 10bp with 10bp, according to JY
 y0 = y0 - np.mean(y0[x0>(38.5 + dxParam)])    # set 0 to tail of potential
 y0 = savgol(y0, int(5.0/(x0[1]-x0[0])), 3) # smooth potential
 
-def pot(x,*parms):
+def parametric_potential(x,*parms):
     x = np.array(x)
     u = interp1d(x0, np.array(parms),
                  bounds_error = False, fill_value="extrapolate",
@@ -41,7 +41,7 @@ def pot(x,*parms):
     u[x>np.max(x0)] = 0
     return u
 
-def potForBp(potfn,x,numBp,*parms):
+def integrated_potential(potfn,x,numBp,*parms):
     u = np.zeros(np.shape(x))
     for h in range(-numBp,numBp+1):
         r = np.sqrt(x**2 + (3.4*h)**2)
@@ -50,7 +50,8 @@ def potForBp(potfn,x,numBp,*parms):
     return u
 
 def fitFun(x,*parms):
-    return 10 * potForBp(pot,x,20,*parms)
+    ## 1-turn iteracting with 4 turns (more is not needed)
+    return 10 * integrated_potential(parametric_potential,x,20,*parms)
 
 xinterp = np.linspace(np.min(x0),np.max(x0),1000) # interpolate potentialb
 yinterp = interp1d(x0,y0)(xinterp)
@@ -62,9 +63,9 @@ def nbPot(x,bps1,bps2):
     if larger >= 2:
         largerInt = int(0.5*larger)
         smaller *= larger/(2*largerInt)
-        y = smaller * potForBp(pot,x,largerInt,*popt)
+        y = smaller * integrated_potential(parametric_potential,x,largerInt,*popt)
     else:
-        y = smaller * larger * pot(x,*popt)
+        y = smaller * larger * parametric_potential(x,*popt)
     y = maxForce(x,y, 100)
     y = savgol(y, int(5.0/(x0[1]-x0[0])), 3)    
     return y
@@ -99,3 +100,10 @@ class nbDnaScheme(NonbondedScheme):
             u = nbPot(r, 0.5*typeA.nts, 0.5*typeB.nts)
         return u
 nbDnaScheme = nbDnaScheme()
+
+if __name__ == "__main__":
+    ## run some tests
+    np.savetxt("jj-filtered.dat", np.array((x0,y0)).T)
+    y = fitFun(x,*popt)
+    np.savetxt("1-bp-fit.dat", np.array((x,y)).T),
+    

mrdna/readers/cadnano_segments.py

@@ -5,7 +5,7 @@ import os,sys
 from glob import glob
 import re
 
-from ..coords import readArbdCoords, readAvgArbdCoords
+from ..coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
 from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
 from ..model.dna_sequence import m13 as m13seq
 
@@ -311,7 +311,8 @@ class cadnano_part(SegmentModel):
                 ## TODO get sequence from cadnano api
                 if zMid in strandOccupancies[0] and zMid in strandOccupancies[1]:
                     kwargs['num_bp'] = numBps
-                    seg = DoubleStrandedSegment(**kwargs,**posargs1)
+                    start_orientation = rotationAboutAxis(np.array((0,0,1)), (zid1-3.25)*34)
+                    seg = DoubleStrandedSegment(**kwargs,**posargs1, start_orientation = start_orientation)
                 elif zMid in strandOccupancies[0]:
                     kwargs['num_nt'] = numBps
                     seg = SingleStrandedSegment(**kwargs,**posargs1)

mrdna/segmentmodel.py

@@ -506,6 +506,9 @@ class Segment(ConnectableElement, Group):
             else:
                 orientation0 = np.eye(3) if axis.dot(zAxis) > 0 else \
                                rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
+            if self.start_orientation is not None:
+                orientation0 = orientation0.dot(self.start_orientation)
+
             orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
             orientation = orientation.dot(orientation0)
         else:
@@ -572,7 +575,7 @@ class Segment(ConnectableElement, Group):
             if scale is not None and scale != 1:
                 for a in atoms:
                     a.position = scale*a.position
-                    a.beta = 0
+                    a.fixed = 1
             atoms.position = pos - atoms.atoms_by_name["C1'"].collapsedPosition()
         else:
             if scale is not None and scale != 1:
@@ -583,7 +586,7 @@ class Segment(ConnectableElement, Group):
                 for a in atoms:
                     if a.name[-1] in ("'","P","T"):
                         a.position = scale*(a.position-r0) + r0
-                        a.beta = 0
+                        a.fixed = 1
             atoms.position = pos
         
         atoms.contour_position = contour_position
@@ -1321,14 +1324,15 @@ class Strand(Group):
             #     pdb.set_trace()
             # assert(s.end != s.start)
             assert( s.num_nt == 1 or (np.linalg.norm( seg.contour_to_position(contour[-1]) - seg.contour_to_position(contour[0]) ) > 0.1) )
+            nucleotide_count = 0
             for c,seq in zip(contour,s.get_sequence()):
+                nucleotide_count += 1
                 if last is None and not self.is_circular:
                     seq = "5"+seq
-                if strand_segment_count == len(s.strand_segments) and c == 1 and not self.is_circular:
+                if strand_segment_count == len(s.strand_segments) and nucleotide_count == s.num_nt and not self.is_circular:
                     seq = seq+"3"
 
                 nt = seg._generate_atomic_nucleotide( c, s.is_fwd, seq, scale, s )
-                s.add(nt)
 
                 ## Join last basepairs
                 if last is not None:
@@ -1515,6 +1519,7 @@ class SegmentModel(ArbdModel):
         for seg in self.segments:
             for d in ('fwd','rev'):
                 seg.strand_pieces[d] = []
+        self._generate_strands()
 
     def clear_beads(self):
         return self._clear_beads()
@@ -1525,7 +1530,8 @@ class SegmentModel(ArbdModel):
             s.clear_all()
         self.clear_all(keep_children=True)
 
-        self.clear_atomic()
+        if len(self.strands[0].children[0].children) > 0:
+            self.clear_atomic()
 
         ## Check that it worked
         assert( len([b for b in self]) == 0 )
@@ -2355,6 +2361,9 @@ class SegmentModel(ArbdModel):
         try:
             for s in self.strands:
                 self.children.remove(s)
+            for seg in self.segments:
+                for d in ('fwd','rev'):
+                    seg.strand_pieces[d] = []
         except:
             ...
         self.strands = strands = []
@@ -2674,7 +2683,7 @@ class SegmentModel(ArbdModel):
                                 # print("WARNING: could not find 'P' atom in {}:{} or {}:{}".format( segI, ntI_idx, segJ, ntJ_idx ))
                                 ...
 
-        print("PUSH BONDS:", len(push_bonds))
+        # print("PUSH BONDS:", len(push_bonds))
 
         if not self.useTclForces:
             with open("%s.exb" % output_name, 'a') as fh: