Fixed python wrapping procedure

Author: Charlles Abreu

python/openmmcppforces/CMakeLists.txt

@@ -1,7 +1,10 @@
 # Execute SWIG to generate source code for the Python module.
 
-add_custom_target(PythonWrapper DEPENDS "${MODULE_NAME}.i")
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${MODULE_NAME}.i ${CMAKE_CURRENT_BINARY_DIR})
+file(GLOB SWIG_SOURCE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.i)
+add_custom_target(PythonWrapper DEPENDS ${SWIG_SOURCE_FILES})
+foreach(file ${SWIG_SOURCE_FILES})
+    configure_file(${file} ${CMAKE_CURRENT_BINARY_DIR})
+endforeach(file ${SWIG_SOURCE_FILES})
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/__init__.py ${CMAKE_CURRENT_BINARY_DIR})
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/py.typed ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
 

python/openmmcppforces/header.i

@@ -0,0 +1,33 @@
+%header %{
+namespace OpenMM {
+
+PyObject *copyVVec3ToList(std::vector<Vec3> vVec3) {
+  int i, n;
+  PyObject *pyList;
+
+  n=vVec3.size();
+  pyList=PyList_New(n);
+  PyObject* mm = PyImport_AddModule("openmm");
+  PyObject* vec3 = PyObject_GetAttrString(mm, "Vec3");
+  for (i=0; i<n; i++) {
+    OpenMM::Vec3& v = vVec3.at(i);
+    PyObject* args = Py_BuildValue("(d,d,d)", v[0], v[1], v[2]);
+    PyObject* pyVec = PyObject_CallObject(vec3, args);
+    Py_DECREF(args);
+    PyList_SET_ITEM(pyList, i, pyVec);
+  }
+  return pyList;
+}
+
+int isNumpyAvailable() {
+    static bool initialized = false;
+    static bool available = false;
+    if (!initialized) {
+        initialized = true;
+        available = (_import_array() >= 0);
+    }
+    return available;
+}
+
+} // namespace OpenMM
+%}

python/openmmcppforces/openmmcppforces.i

@@ -1,19 +1,5 @@
-
 %module openmmcppforces
 
-%import(module="openmm") "swig/OpenMMSwigHeaders.i"
-%include "swig/typemaps.i"
-%include <std_string.i>
-%include <std_vector.i>
-%include <std_map.i>
-
-namespace std {
-  %template(vectord) vector<double>;
-  %template(vectorstring) vector<string>;
-  %template(mapstringstring) map<string,string>;
-  %template(mapstringdouble) map<string,double>;
-};
-
 %{
 #define SWIG_PYTHON_CAST_MODE
 #include "ConcertedRMSDForce.h"
@@ -22,8 +8,22 @@ namespace std {
 #include "OpenMMDrude.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/RPMDMonteCarloBarostat.h"
+#include "openmm/Force.h"
+#include "openmm/Vec3.h"
+#include <numpy/ndarrayobject.h>
+
+using namespace OpenMM;
 %}
 
+%import(module="openmm") "swig/OpenMMSwigHeaders.i"
+%include "swig/typemaps.i"
+%include "header.i"
+%include "std_vector.i"
+
+namespace std {
+  %template(vectori) vector<int>;
+};
+
 %pythoncode %{
 __version__ = "@CMAKE_PROJECT_VERSION@"
 %}
@@ -64,11 +64,11 @@ namespace OpenMMCPPForces {
  */
 class ConcertedRMSDForce : public OpenMM::Force {
 public:
-    explicit ConcertedRMSDForce(const std::vector<OpenMM::Vec3>& referencePositions);
+    explicit ConcertedRMSDForce(const std::vector<Vec3>& referencePositions);
     /**
      * Get the reference positions to compute the deviation from.
      */
-    const std::vector<OpenMM::Vec3>& getReferencePositions() const;
+    const std::vector<Vec3>& getReferencePositions() const;
     /**
      * Set the reference positions to compute the deviation from.
      *
@@ -79,7 +79,7 @@ public:
      *     vector must equal the number of particles in the system, even if not all
      *     particles are used in computing the concerted RMSD.
      */
-    void setReferencePositions(const std::vector<OpenMM::Vec3>& positions);
+    void setReferencePositions(const std::vector<Vec3>& positions);
     /**
      * Add a group of particles to be included in the concerted RMSD calculation.
      *
@@ -125,12 +125,12 @@ public:
     void setGroup(int index, const std::vector<int>& particles);
     /**
      * Update the reference positions and particle groups in a Context to match those stored
-     * in this Force object.  This method provides an efficient way to update these parameters
+     * in this OpenMM::Force object.  This method provides an efficient way to update these parameters
      * in an existing Context without needing to reinitialize it.  Simply call setReferencePositions()
      * and setGroup() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      */
-    void updateParametersInContext(OpenMM::Context& context);
+    void updateParametersInContext(Context& context);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
@@ -139,7 +139,7 @@ public:
      */
     bool usesPeriodicBoundaryConditions();
     /*
-     * Add methods for casting a Force to an ExtendedCustomCVForce.
+     * Add methods for casting a OpenMM::Force to an ExtendedCustomCVForce.
     */
     %extend {
         static OpenMMCPPForces::ConcertedRMSDForce& cast(OpenMM::Force& force) {

python/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools", "numpy >= 1.19"]
 build-backend = "setuptools.build_meta"
 
 [project]

python/setup.py

@@ -1,6 +1,7 @@
 from setuptools import setup, Extension
 import os
 import platform
+import numpy as np
 
 openmm_dir = '@OPENMM_DIR@'
 header_dir = '@PLUGIN_HEADER_DIR@'
@@ -26,7 +27,7 @@
             name='@MODULE_NAME@._@MODULE_NAME@',
             sources=[os.path.join(module_dir, '@WRAP_FILE@')],
             libraries=['OpenMM', '@PLUGIN_LIBRARY_NAME@'],
-            include_dirs=[os.path.join(openmm_dir, 'include'), header_dir],
+            include_dirs=[os.path.join(openmm_dir, 'include'), header_dir, np.get_include()],
             library_dirs=[os.path.join(openmm_dir, 'lib'), library_dir],
             extra_compile_args=extra_compile_args,
             extra_link_args=extra_link_args,