Merge branch 'master' of https://github.com/SimTk/openmm into exclusions

wrappers/python/simtk/openmm/app/charmmcrdfiles.py

@@ -13,7 +13,7 @@ Copyright (c) 2014 the Authors
 
 Author: Jason Deckman
 Contributors: Jason M. Swails
-Date: April 19, 2014
+Date: June 6, 2014
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -105,7 +105,7 @@ class CharmmCrdFile(object):
                 self.resname.append(line[2])
                 self.attype.append(line[3])
                 pos = Vec3(float(line[4]), float(line[5]), float(line[6]))
-                self.positions.append(pos * u.angstroms)
+                self.positions.append(pos)
                 self.segid.append(line[7])
                 self.resid.append(int(line[8]))
                 self.weighting.append(float(line[9]))
@@ -120,6 +120,10 @@ class CharmmCrdFile(object):
         except (ValueError, IndexError), e:
             raise CharmmFileError('Error parsing CHARMM coordinate file')
 
+        # Apply units to the positions now. Do it this way to allow for
+        # (possible) numpy functionality in the future.
+        self.positions = u.Quantity(self.positions, u.angstroms)
+
 class CharmmRstFile(object):
     """
     Reads and parses data, velocities and coordinates from a CHARMM restart
@@ -209,8 +213,9 @@ class CharmmRstFile(object):
         self.velocities = [v * ONE_TIMESCALE for v in self.velocities]
 
         # Add units to positions and velocities
-        self.positions *= u.angstroms
-        self.velocities *= u.angstroms / u.picoseconds
+        self.positions = u.Quantity(self.positions, u.angstroms)
+        self.positionsold = u.Quantity(self.positionsold, u.angstroms)
+        self.velocities = u.Quantity(self.velocities, u.angstroms/u.picoseconds)
 
     def _scan(self, handle, str, r=0): # read lines in file until str is found
         scanning = True

wrappers/python/simtk/openmm/app/modeller.py

@@ -952,14 +952,14 @@ class Modeller(object):
                                     # This is a virtual site.  Compute its position by the correct rule.
 
                                     if site.type == 'average2':
-                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]]
+                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]]
                                     elif site.type == 'average3':
-                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
+                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]] + site.weights[2]*templateAtomPositions[site.atoms[2]]
                                     elif site.type == 'outOfPlane':
-                                        v1 = templateAtomPositions[index+site.atoms[1]] - templateAtomPositions[index+site.atoms[0]]
-                                        v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+site.atoms[0]]
+                                        v1 = templateAtomPositions[site.atoms[1]] - templateAtomPositions[site.atoms[0]]
+                                        v2 = templateAtomPositions[site.atoms[2]] - templateAtomPositions[site.atoms[0]]
                                         cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
-                                        position = templateAtomPositions[index+site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
+                                        position = templateAtomPositions[site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
                             if position is None and atom.type in drudeTypeMap:
                                 # This is a Drude particle.  Put it on top of its parent atom.