Merge pull request #126 from peastman/master

Minor enhancements and bug fixes

platforms/cuda/src/CudaKernels.cpp

@@ -5752,7 +5752,7 @@ void CudaRemoveCMMotionKernel::initialize(const System& system, const CMMotionRe
     for (int i = 0; i < numAtoms; i++)
         totalMass += system.getParticleMass(i);
     map<string, string> defines;
-    defines["INVERSE_TOTAL_MASS"] = cu.doubleToString(1.0/totalMass);
+    defines["INVERSE_TOTAL_MASS"] = cu.doubleToString(totalMass == 0 ? 0.0 : 1.0/totalMass);
     CUmodule module = cu.createModule(CudaKernelSources::removeCM, defines);
     kernel1 = cu.getKernel(module, "calcCenterOfMassMomentum");
     kernel2 = cu.getKernel(module, "removeCenterOfMassMomentum");

platforms/opencl/src/OpenCLKernels.cpp

@@ -5978,7 +5978,7 @@ void OpenCLRemoveCMMotionKernel::initialize(const System& system, const CMMotion
     for (int i = 0; i < numAtoms; i++)
         totalMass += system.getParticleMass(i);
     map<string, string> defines;
-    defines["INVERSE_TOTAL_MASS"] = cl.doubleToString(1.0/totalMass);
+    defines["INVERSE_TOTAL_MASS"] = cl.doubleToString(totalMass == 0 ? 0.0 : 1.0/totalMass);
     cl::Program program = cl.createProgram(OpenCLKernelSources::removeCM, defines);
     kernel1 = cl::Kernel(program, "calcCenterOfMassMomentum");
     kernel1.setArg<cl_int>(0, numAtoms);

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

@@ -70,7 +70,10 @@ class PDBFile(object):
 
         # Load the PDB file
 
-        pdb = PdbStructure(open(file), load_all_models=True)
+        inputfile = file
+        if isinstance(file, str):
+            inputfile = open(file)
+        pdb = PdbStructure(inputfile, load_all_models=True)
         PDBFile._loadNameReplacementTables()
 
         # Build the topology
@@ -140,6 +143,7 @@ class PDBFile(object):
         for connect in pdb.models[0].connects:
             i = connect[0]
             for j in connect[1:]:
+                if i in atomByNumber and j in atomByNumber:
                     connectBonds.append((atomByNumber[i], atomByNumber[j]))
         if len(connectBonds) > 0:
             # Only add bonds that don't already exist.