Merge pull request #627 from rmcgibbo/integrator-by-name

CustomIntegrator::get*VariableByName

openmmapi/include/openmm/CustomIntegrator.h

@@ -302,6 +302,13 @@ public:
      * @return the current value of the variable
      */
     double getGlobalVariable(int index) const;
+    /**
+     * Get the current value of a global variable, specified by name.
+     *
+     * @param name    the name of the variable to get
+     * @return the current value of the parameter
+     */
+    double getGlobalVariableByName(const std::string& name) const;
     /**
      * Set the value of a global variable.
      * 
@@ -324,6 +331,14 @@ public:
      *                are stored into this
      */
     void getPerDofVariable(int index, std::vector<Vec3>& values) const;
+    /**
+     * Get the value of a per-DOF variable, specified by name.
+     *
+     * @param name    the name of the variable to get
+     * @param values  the values of the variable for all degrees of freedom
+     *                are stored into this
+     */
+    void getPerDofVariableByName(const std::string& name, std::vector<Vec3>& values) const;
     /**
      * Set the value of a per-DOF variable.
      * 

openmmapi/src/CustomIntegrator.cpp

@@ -124,6 +124,15 @@ double CustomIntegrator::getGlobalVariable(int index) const {
     return globalValues[index];
 }
 
+double CustomIntegrator::getGlobalVariableByName(const string& name) const {
+    for (int i = 0; i < (int) globalNames.size(); i++) {
+        if (name == globalNames[i]) {
+            return getGlobalVariable(i);
+        }
+    }
+    throw OpenMMException("Illegal global variable name: "+name);
+}
+
 void CustomIntegrator::setGlobalVariable(int index, double value) {
     ASSERT_VALID_INDEX(index, globalValues);
     if (owner != NULL && !globalsAreCurrent) {
@@ -152,6 +161,16 @@ void CustomIntegrator::getPerDofVariable(int index, vector<Vec3>& values) const
         kernel.getAs<const IntegrateCustomStepKernel>().getPerDofVariable(*context, index, values);
 }
 
+void CustomIntegrator::getPerDofVariableByName(const string& name,  vector<Vec3>& values) const {
+    for (int i = 0; i < (int) perDofNames.size(); i++) {
+        if (name == perDofNames[i]) {
+            getPerDofVariable(i, values);
+            return;
+        }
+    }
+    throw OpenMMException("Illegal per-DOF variable name: "+name);
+}
+
 void CustomIntegrator::setPerDofVariable(int index, const vector<Vec3>& values) {
     ASSERT_VALID_INDEX(index, perDofValues);
     if (owner != NULL && values.size() != context->getSystem().getNumParticles())

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -161,6 +161,7 @@ UNITS = {
 ("*", "getEwaldErrorTolerance") : (None, ()),
 ("*", "getFriction") : ("1/unit.picosecond", ()),
 ("*", "getGlobalVariable") : (None, ()),
+("*", "getGlobalVariableByName") : (None, ()),
 ("*", "getIntegrator") : (None, ()),
 ("*", "getMapParameters") : (None, ()),
 ("*", "getName") : (None, ()),