arbdmodel now preserves particle order

arbdmodel.py

@@ -491,8 +491,8 @@ class ArbdModel(PdbModel):
 
     def _updateParticleOrder(self):
         ## Create ordered list
-        particles = [p for p in self]
-        self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
+        self.particles = [p for p in self]
+        # self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
         
         ## Update particle indices
         for p,i in zip(self.particles,range(len(self.particles))):
@@ -509,7 +509,7 @@ class ArbdModel(PdbModel):
         assert(type(gpu) is int)
         numSteps = int(numSteps)
 
-        if self.cacheUpToDate == False:
+        if self.cacheUpToDate == False: # TODO: remove cache?
             self._countParticleTypes()
             self._updateParticleOrder()
 
@@ -566,7 +566,8 @@ class ArbdModel(PdbModel):
         self._dihedral_filename = "%s/%s.dihedrals.txt" % (d, prefix)
         self._exclusion_filename = "%s/%s.exculsions.txt" % (d, prefix)
         
-        self._writeArbdCoordFile( prefix + ".coord.txt" )
+        # self._writeArbdCoordFile( prefix + ".coord.txt" )
+        self._writeArbdParticleFile( prefix + ".particles.txt" )
         self._writeArbdBondFile()
         self._writeArbdAngleFile()
         self._writeArbdDihedralFile()
@@ -574,10 +575,17 @@ class ArbdModel(PdbModel):
         self._writeArbdPotentialFiles( prefix, directory = d )
         self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod )
         
-    def _writeArbdCoordFile(self, filename):
+    # def _writeArbdCoordFile(self, filename):
+    #     with open(filename,'w') as fh:
+    #         for p in self.particles:
+    #             fh.write("%f %f %f\n" % tuple(x for x in p.collapsedPosition()))
+
+    def _writeArbdParticleFile(self, filename):
         with open(filename,'w') as fh:
             for p in self.particles:
-                fh.write("%f %f %f\n" % tuple(x for x in p.collapsedPosition()))
+                data = tuple([p.idx,p.name] + [x for x in p.collapsedPosition()])
+                fh.write("ATOM %d %s %f %f %f\n" % data)
+
         
     def _writeArbdConf(self, prefix, randomSeed=None, numSteps=100000000, outputPeriod=10000, restartCoordinateFile=None):
         ## TODO: raise exception if _writeArbdPotentialFiles has not been called
@@ -592,7 +600,8 @@ class ArbdModel(PdbModel):
             params['randomSeed'] = "seed %s" % randomSeed
         params['numSteps']       = int(numSteps)
 
-        params['coordinateFile'] = "%s.coord.txt" % prefix
+        # params['coordinateFile'] = "%s.coord.txt" % prefix
+        params['particleFile'] = "%s.particles.txt" % prefix
         if restartCoordinateFile is None:
             params['restartCoordinates'] = ""
         else:
@@ -646,7 +655,7 @@ diffusion {diffusivity}
             ## Write coordinates and interactions
             fh.write("""
 ## Input coordinates
-inputCoordinates {coordinateFile}
+inputParticles {particleFile}
 {restartCoordinates}
 
 ## Interaction potentials