diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py index 5e698c4c68dce2626e6eed6c55428ec6b468312e..e9fb79239fc2d9bd8c68a3c83ffcdd7d1df699b1 100644 --- a/mrdna/segmentmodel.py +++ b/mrdna/segmentmodel.py @@ -2755,10 +2755,6 @@ class SegmentModel(ArbdModel): nt1.basepair = nt2 nt2.basepair = nt1 - def _update_orientations(self,orientation): - for s in self.strands: - s.update_atomic_orientations(orientation) - def write_atomic_ENM(self, output_name, lattice_type=None): ## TODO: ensure atomic model was generated already if lattice_type is None: @@ -2997,26 +2993,6 @@ proc calcforces {} { for s in self.strands: first_atomic_index = s.generate_atomic_model(scale,first_atomic_index) self._assign_basepairs() - return - - ## Angle optimization - angles = np.linspace(-180,180,180) - score = [] - for a in angles: - o = rotationAboutAxis([0,0,1], a) - sum2 = count = 0 - for s in self.strands: - s.update_atomic_orientations(o) - for s1,s2 in zip(s.strand_segments[:-1],s.strand_segments[1:]): - nt1 = s1.children[-1] - nt2 = s2.children[0] - o3 = nt1.atoms_by_name["O3'"] - p = nt2.atoms_by_name["P"] - sum2 += np.sum((p.collapsedPosition()-o3.collapsedPosition())**2) - count += 1 - score.append(sum2/count) - print(angles[np.argmin(score)]) - print(score) def vmd_tube_tcl(self, file_name="drawTubes.tcl"): with open(file_name, 'w') as tclFile: