Pinyili2

New Features:

• scadnano Support:

Integrated support for scadnano, enabling users to read in model from scadnano designs.

• Pandas-Compatible List Reading:

Added functionality to read in model in pd.DataFrame format and retrieve its own DataFrame.

Enhancements:

• oxDNA Bonds and Base Pairing Localization:

Implemented the ability to locate oxDNA bonds and analyze base-pairing behavior using the virt2nuc file (generated by tacoxDNA.

• Cadnano Data Retrieval for oxDNA Generation:

Enhanced the system to retrieve relevant caDNAno information, facilitating the generation of oxDNA structures.

mrdna/segmentmodel.py

@@ -2316,6 +2316,29 @@ class SegmentModel(ArbdModel):
                 tck, u = interpolate.splprep( quats.T, u=contours, s=0, k=1 )
                 s.quaternion_spline_params = (tck,u)
 
+    def update_reader_list_coordinates(self):
+        new_coords = np.empty(self._reader_list_coordinates.shape)
+        new_orientations = np.empty(self._reader_list_orientation.shape)
+
+        for seg in self.segments:
+            c = seg.nt_pos_to_contour(np.arange(seg.num_nt))
+            sl0 = (self._reader_list_hmap == seg._helix_idx)
+            pos = seg.contour_to_position( c )
+            orientation = seg.contour_to_orientation( c )
+
+            sl1 = (self._reader_list_fwd == True)
+            order = np.argsort( self._reader_list_hmap_hrank[sl0 & sl1] )
+            new_coords[sl0 & sl1][order] = pos
+            new_orientations[sl0 & sl1][order] = orientation
+
+            sl1 = (self._reader_list_fwd == False)
+            order = np.argsort( self._reader_list_hmap_hrank[sl0 & sl1] )
+            new_coords[sl0 & sl1][order] = pos
+            new_orientations[sl0 & sl1][order] = np.array([o.dot(rotationAboutAxis((1,0,0),180)) for o in orientation])
+
+        self._reader_list_coordinates = new_coords
+        self._reader_list_orientation = new_orientations
+
     def get_segments_matching(self, pattern):
         """ Returns a list of all segments that match the regular expression 'pattern' """