Likely fixed most backmapping bugs

arbdmodel.py

@@ -710,7 +710,7 @@ class ArbdModel(PdbModel):
     def _writeArbdParticleFile(self, filename):
         with open(filename,'w') as fh:
             for p in self.particles:
-                data = tuple([p.idx,p.name] + [x for x in p.collapsedPosition()])
+                data = tuple([p.idx,p.type_.name] + [x for x in p.collapsedPosition()])
                 fh.write("ATOM %d %s %f %f %f\n" % data)
 
         

cadnano_segments.py

@@ -199,7 +199,8 @@ class cadnano_part(SegmentModel):
         self.part = part
         self._cadnano_part_to_segments(part)
         # SegmentModel.__init__(self,...)
-        self.segments = [seg for hid,segs in self.helices.items() for seg in segs]
+        # self.segments = [seg for hid,segs in self.helices.items() for seg in segs]
+        self.segments = [seg for hid,segs in sorted(self.helices.items()) for seg in segs]
         self._add_intrahelical_connections()
         self._add_crossovers()
         self._add_prime_ends()
@@ -227,7 +228,10 @@ class cadnano_part(SegmentModel):
         vh_list = []
         strand_list = []
         self.xover_list = xover_list = []
-        numHID = part.getIdNumMax() + 1
+        try:
+            numHID = part.getMaxIdNum() + 1
+        except:
+            numHID = part.getIdNumMax() + 1
 
         for id_num in range(numHID):
             offset_and_size = part.getOffsetAndSize(id_num)
@@ -527,14 +531,13 @@ def run_simulation_protocol( output_name, job_id, json_data,
                              remove_long_bonds=False,
                              gpu = 0,
                              directory=None,
-                             coarse_steps = 1e6,
-                             fine_steps = 1e6
+                             coarse_steps = 1e5+1,
+                             fine_steps = 1e5+1
                          ):
 
     ret = None
     d_orig = os.getcwd()
     try:
-        directory = "/dev/shm/origami-job-robot_v1.9_bent--0f4axf4k"
         if directory is None:
             import tempfile
             directory = tempfile.mkdtemp(prefix='origami-%s-' % job_id, dir='/dev/shm/')
@@ -594,7 +597,7 @@ def run_simulation_protocol( output_name, job_id, json_data,
         else:
             output_prefix = "%s-1" % output_name
             full_output_prefix = "%s/%s" % (output_directory,output_prefix)
-            # model.simulate( outputPrefix = output_prefix, numSteps=coarse_steps, **simargs )
+            model.simulate( outputPrefix = output_prefix, numSteps=coarse_steps, **simargs )
         coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
 
 
@@ -605,7 +608,7 @@ def run_simulation_protocol( output_name, job_id, json_data,
         model._update_segment_positions(coordinates)
         model._clear_beads()
         model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
-        # model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
+        model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
         coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
 
 

run.py

@@ -19,7 +19,7 @@ if __name__ == '__main__':
             print("WARNING: skipping unreadable json file {}".format(f))
             continue
             
-        run_simulation_protocol( out, "job-"+out+"-", data, gpu=0 )
+        run_simulation_protocol( out, "job-"+out+"-", data, gpu=1 )
         # try:
         #     run_simulation_protocol( out, "job-"+out+"-", data, gpu=0 )
         # except: