Minor API additions needed for the Normal Mode Langevin plugin

openmmapi/include/openmm/Vec3.h

@@ -80,6 +80,12 @@ public:
         return Vec3(lhs[0] + rhs[0], lhs[1] + rhs[1], lhs[2] + rhs[2]);
     }
     
+    Vec3 operator+=(const Vec3& rhs) {
+        data[0] += rhs[0];
+        data[1] += rhs[1];
+        data[2] += rhs[2];
+    }
+
     // unary minus
     Vec3 operator-() const {
         const Vec3& lhs = *this;
@@ -92,18 +98,35 @@ public:
         return Vec3(lhs[0] - rhs[0], lhs[1] - rhs[1], lhs[2] - rhs[2]);
     }
 
+    Vec3 operator-=(const Vec3& rhs) {
+        data[0] -= rhs[0];
+        data[1] -= rhs[1];
+        data[2] -= rhs[2];
+    }
+
     // scalar product
     Vec3 operator*(double rhs) const {
         const Vec3& lhs = *this;
         return Vec3(lhs[0]*rhs, lhs[1]*rhs, lhs[2]*rhs);
     }
 
+    Vec3 operator*=(double rhs) {
+        data[0] *= rhs;
+        data[1] *= rhs;
+        data[2] *= rhs;
+    }
+    
     // dot product
     double dot(const Vec3& rhs) const {
         const Vec3& lhs = *this;
         return lhs[0]*rhs[0] + lhs[1]*rhs[1] + lhs[2]*rhs[2];
     }
 
+    // cross product
+    Vec3 cross(const Vec3& rhs) const {
+        return Vec3(data[1]*rhs[2]-data[2]*rhs[1], data[2]*rhs[0]-data[0]*rhs[2], data[0]*rhs[1]-data[1]*rhs[0]);
+    }
+    
 private:
     double data[3];
 };

openmmapi/include/openmm/internal/ContextImpl.h

@@ -175,6 +175,10 @@ public:
      * ForceImpl in the system, allowing them to modify the values of state variables.
      */
     void updateContextState();
+    /**
+     * Get the list of ForceImpls belonging to this ContextImpl.
+     */
+    const std::vector<ForceImpl*>& getForceImpls() const;
     /**
      * Get the platform-specific data stored in this context.
      */

openmmapi/include/openmm/internal/CustomBondForceImpl.h

@@ -60,7 +60,7 @@ public:
     double calcEnergy(ContextImpl& context);
     std::map<std::string, double> getDefaultParameters();
     std::vector<std::string> getKernelNames();
-    std::vector<std::pair<int, int> > getBondedParticles();
+    std::vector<std::pair<int, int> > getBondedParticles() const;
 private:
     CustomBondForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/ForceImpl.h

@@ -105,7 +105,7 @@ public:
      * Get pairs of particles connected by bonds by this force.  This is used to determine which particles
      * are part of the same molecule.
      */
-    std::vector<std::pair<int, int> > getBondedParticles() {
+    virtual std::vector<std::pair<int, int> > getBondedParticles() const {
         return std::vector<std::pair<int, int> >(0);
     }
 };

openmmapi/include/openmm/internal/HarmonicBondForceImpl.h

@@ -62,7 +62,7 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
-    std::vector<std::pair<int, int> > getBondedParticles();
+    std::vector<std::pair<int, int> > getBondedParticles() const;
 private:
     HarmonicBondForce& owner;
     Kernel kernel;

openmmapi/src/ContextImpl.cpp

@@ -169,6 +169,10 @@ void ContextImpl::updateContextState() {
         forceImpls[i]->updateContextState(*this);
 }
 
+const vector<ForceImpl*>& ContextImpl::getForceImpls() const {
+    return forceImpls;
+}
+
 void* ContextImpl::getPlatformData() {
     return platformData;
 }

openmmapi/src/CustomBondForceImpl.cpp

@@ -103,7 +103,7 @@ map<string, double> CustomBondForceImpl::getDefaultParameters() {
     return parameters;
 }
 
-vector<pair<int, int> > CustomBondForceImpl::getBondedParticles() {
+vector<pair<int, int> > CustomBondForceImpl::getBondedParticles() const {
     int numBonds = owner.getNumBonds();
     vector<pair<int, int> > bonds(numBonds);
     for (int i = 0; i < numBonds; i++) {

openmmapi/src/HarmonicBondForceImpl.cpp

@@ -63,7 +63,7 @@ std::vector<std::string> HarmonicBondForceImpl::getKernelNames() {
     return names;
 }
 
-vector<pair<int, int> > HarmonicBondForceImpl::getBondedParticles() {
+vector<pair<int, int> > HarmonicBondForceImpl::getBondedParticles() const {
     int numBonds = owner.getNumBonds();
     vector<pair<int, int> > bonds(numBonds);
     for (int i = 0; i < numBonds; i++) {