Merge pull request #388 from peastman/master

Exposed getMolecules() in the public API

openmmapi/include/openmm/Context.h

@@ -247,6 +247,15 @@ public:
      * @param stream    an input stream the checkpoint data should be read from
      */
     void loadCheckpoint(std::istream& stream);
+    /**
+     * Get a description of how the particles in the system are grouped into molecules.  Two particles are in the
+     * same molecule if they are connected by constraints or bonds, where every Force object can define bonds
+     * in whatever way are appropriate to that force.
+     *
+     * Each element lists the indices of all particles in a single molecule.  Every particle is guaranteed to
+     * belong to exactly one molecule.
+     */
+    const std::vector<std::vector<int> >& getMolecules() const;
 private:
     friend class Force;
     friend class Platform;

openmmapi/src/Context.cpp

@@ -278,3 +278,7 @@ void Context::loadCheckpoint(istream& stream) {
 ContextImpl& Context::getImpl() {
     return *impl;
 }
+
+const vector<vector<int> >& Context::getMolecules() const {
+    return impl->getMolecules();
+}

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -297,6 +297,7 @@ UNITS = {
 ("AmoebaWcaDispersionForce",              "getShctd")                                      :  ( None, ()),
 
 ("Context", "getParameter") : (None, ()),
+("Context", "getMolecules") : (None, ()),
 ("CMAPTorsionForce", "getMapParameters") : (None, ()),
 ("CMAPTorsionForce", "getTorsionParameters") : (None, ()),
 ("CMMotionRemover", "getFrequency") : (None, ()),