Adds method for copy and deepcopy to work with CompositeRMSDForce (#13)

* Improved docstring

* Fixed comments

* Bug fix

* Added __copy__ magic method

Author: Charlles Abreu

openmmcppforces/include/CompositeRMSDForce.h

@@ -8,7 +8,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+ *  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "internal/windowsExportOpenMMCPPForces.h"

openmmcppforces/include/internal/CompositeRMSDForceImpl.h

@@ -8,7 +8,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "CompositeRMSDForce.h"

openmmcppforces/src/CompositeRMSDForce.cpp

@@ -5,7 +5,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "CompositeRMSDForce.h"

openmmcppforces/src/CompositeRMSDForceImpl.cpp

@@ -5,7 +5,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "internal/CompositeRMSDForceImpl.h"

python/openmmcppforces/openmmcppforces.i

@@ -34,7 +34,7 @@ Add units to function outputs.
 */
 
 %pythonappend OpenMMCPPForces::CompositeRMSDForce::getReferencePositions() const %{
-    val= unit.nanometers
+    val *= unit.nanometers
 %}
 
 /*
@@ -56,20 +56,21 @@ namespace OpenMMCPPForces {
 This is a force whose energy equals the root mean squared deviation (RMSD) between the
 current coordinates of multiple particle groups and reference structures defined for
 each group. The composite RMSD is computed after aligning every particle group to its
-reference while keeping the relative orientations of all groups fixed. Therefore, it is
-not a mere composition of independent RMSD calculations done in the usual way.
+reference while keeping the relative orientations of all groups fixed. In other words,
+every group can translate independently in search for the best alignment, but all
+groups must rotate in unison.
 
 Consider `m` particle groups, with each group :math:`{\bf g}_j` containing
 :math:`n_j` particles. The centroid of each group is given by
 
 .. math::
 
-   {\bf c}_j = \frac{1}{n_j} \sum_{k \in {\bf g}_j} {\bf r}_k
+   {\bf c}_j = \frac{1}{n_j} \sum_{i \in {\bf g}_j} {\bf r}_i
 
-where :math:`{\bf r}_k` is the position of particle :math:`k` and the sum is over
+where :math:`{\bf r}_i` is the position of particle :math:`k` and the sum is over
 all particles in the group. Analogously, :math:`{\bf c}_j^{\rm ref}` is the
 centroid of the reference structure for group :math:`j`, whose each particle
-:math:`k` is located at :math:`{\bf r}_k^{\rm ref}`.
+:math:`k` is located at :math:`{\bf r}_i^{\rm ref}`.
 
 The composite RMSD is then defined as
 
@@ -78,9 +79,9 @@ The composite RMSD is then defined as
     d_{\rm crms}({\bf r}) = \sqrt{
         \frac{1}{n} \min_{
             \bf q \in \mathbb{R}^4 \atop \|{\bf q}\| = 1
-        } \sum_{j=1}^m \sum_{k \in {\bf g}_j} \left\|
-            {\bf A}({\bf q})\left({\bf r}_k - {\bf c}_j\right) -
-                {\bf r}_k^{\rm ref} + {\bf c}_j^{\rm ref}
+        } \sum_{j=1}^m \sum_{i \in {\bf g}_j} \left\|
+            {\bf A}({\bf q})\left({\bf r}_i - {\bf c}_j\right) -
+                {\bf r}_i^{\rm ref} + {\bf c}_j^{\rm ref}
         \right\|^2
     }
 
@@ -217,14 +218,23 @@ public:
     %}
     bool usesPeriodicBoundaryConditions();
 
+
     %extend {
+        %feature("docstring") %{Cast a :OpenMM:`Force` to a :class:`CompositeRMSDForce`.%}
         static OpenMMCPPForces::CompositeRMSDForce& cast(OpenMM::Force& force) {
             return dynamic_cast<OpenMMCPPForces::CompositeRMSDForce&>(force);
         }
 
+        %feature("docstring") %{Check if a :OpenMM:`Force` is a :class:`CompositeRMSDForce`.%}
         static bool isinstance(OpenMM::Force& force) {
             return (dynamic_cast<OpenMMCPPForces::CompositeRMSDForce*>(&force) != NULL);
         }
+
+        %feature("docstring") %{Clone a :class:`CompositeRMSDForce` object.%}
+        %newobject __copy__;
+        OpenMMCPPForces::CompositeRMSDForce* __copy__() {
+            return OpenMM::XmlSerializer::clone<OpenMMCPPForces::CompositeRMSDForce>(*self);
+        }
     }
 };
 

serialization/include/CompositeRMSDForceProxy.h

@@ -8,7 +8,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "internal/windowsExportOpenMMCPPForces.h"

serialization/src/OpenMMCPPForcesSerializationProxyRegistration.cpp

@@ -5,7 +5,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #ifdef WIN32

serialization/tests/TestSerializeCompositeRMSDForce.cpp

@@ -5,7 +5,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "CompositeRMSDForce.h"

tests/TestCompositeRMSDForce.cpp

@@ -5,7 +5,7 @@
  *  A plugin for distributing platform-agnostic OpenMM Forces                 *
  *                                                                            *
  *  Copyright (c) 2024 Charlles Abreu                                         *
- *  https://github.com/RedesignScience/openmm-cpp-forces                             *
+*  https://github.com/RedesignScience/openmm-cpp-forces                      *
  * -------------------------------------------------------------------------- */
 
 #include "CompositeRMSDForce.h"