Add Molecular Interaction Fields (#7993)

* Add RealValueVect.

* Add UniformRealValueGrid3D

* Add Molecular Interaction Fields (MIFs)

* line endings

* cherry-pick f1bc94a4c8

* format

* Adapt tests for python3.

* Adapt RealValueVector pickling for python3.

* Speed-up of MIF calculations.

* Bugfix in MIFDescriptors.cpp.

* all tests pass

* clean up some memory leaks

* update copyrights

* rename

* rename the library

* complete the rename

* lost file

* another forgotten file

* cleanup

* clang-tidy

* clang-tidy

* windows DLL builds work

* python wrapper and tests cleanup

* convert to catch2 testing

* switch RealValueVect to use std::vector

* remove obsolete friend

* - Replace explicit loops with stdlib implicit equivalents
- Replace explicit types with auto where possible
- Avoid unnecessary copy operations where possible
- Replace raw pointers with exception-safe unique_ptr
- Replace C-style #define with constexpr
- Replace C-style casts with C++ casts
- Replace C-style arrays with std::vector
- Avoid code duplication with templated operators
- Replace VdWaals class taking multiple atom type definitions and force-field name as string parameter with force-field-specific classes deriving from an abstract VdWaals class
- Replace x,y,z doubles with Point3D class where possible
- Removed unused (and untested) DistanceToClosestAtom class
- Renamed some variables and functions for better clarity
- Converted tabs to spaces
- Made the mol parameter in cube read/write functions optional for convenience
- Made the Python wrappers more pythonic (e.g., avoid C++-style passing objects as parameters which are modified in place)
- Implemented alternative Python class constructors using boost::python::make_constructor rather than with external non-class functions
- The Python wrappers taking a sequence of Point3D now take a sequence of sequences, such that the output of Conformer.GetPositions() can be passed
- Made the Python wrapper sequence parsing more robust
- Removed duplicated code from Python wrappers

* - avoid an unnecessary copy

* progress

* works

* more cleanup

* all tests pass

* changes in response to review

---------

Co-authored-by: dfhahn <dfhahn@users.noreply.github.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>

Code/DataStructs/Wrap/DataStructs.cpp

@@ -15,7 +15,7 @@
 #include <DataStructs/BitVects.h>
 #include <DataStructs/DiscreteValueVect.h>
 #include <DataStructs/SparseIntVect.h>
-
+#include <DataStructs/RealValueVect.h>
 #include <RDBoost/boost_numpy.h>
 #include <numpy/npy_common.h>
 #include <RDBoost/import_array.h>
@@ -28,11 +28,13 @@ void wrap_EBV();
 void wrap_BitOps();
 void wrap_Utils();
 void wrap_discreteValVect();
+void wrap_realValVect();
 void wrap_sparseIntVect();
 void wrap_FPB();
 
-template <typename T>
-void convertToNumpyArray(const T &v, python::object destArray) {
+namespace {
+template <typename T, typename U>
+void converter(const T &v, python::object destArray, U func) {
   if (!PyArray_Check(destArray.ptr())) {
     throw_value_error("Expecting a Numeric array object");
   }
@@ -44,12 +46,22 @@ void convertToNumpyArray(const T &v, python::object destArray) {
   dims.len = 1;
   PyArray_Resize(destP, &dims, 0, NPY_ANYORDER);
   for (unsigned int i = 0; i < v.size(); ++i) {
-    PyObject *iItem = PyInt_FromLong(v[i]);
+    PyObject *iItem = func(v[i]);
     PyArray_SETITEM(destP, static_cast<char *>(PyArray_GETPTR1(destP, i)),
                     iItem);
     Py_DECREF(iItem);
   }
 }
+}  // namespace
+
+template <typename T>
+void convertToIntNumpyArray(const T &v, python::object destArray) {
+  converter(v, destArray, PyLong_FromLong);
+}
+template <typename T>
+void convertToDoubleNumpyArray(const T &v, python::object destArray) {
+  converter(v, destArray, PyFloat_FromDouble);
+}
 
 BOOST_PYTHON_MODULE(cDataStructs) {
   rdkit_import_array();
@@ -72,31 +84,36 @@ BOOST_PYTHON_MODULE(cDataStructs) {
   wrap_EBV();
   wrap_BitOps();
   wrap_discreteValVect();
+  wrap_realValVect();
   wrap_sparseIntVect();
   wrap_FPB();
 
   python::def(
       "ConvertToNumpyArray",
-      (void (*)(const ExplicitBitVect &, python::object))convertToNumpyArray,
+      (void (*)(const ExplicitBitVect &, python::object))convertToIntNumpyArray,
       (python::arg("bv"), python::arg("destArray")));
   python::def("ConvertToNumpyArray",
               (void (*)(const RDKit::DiscreteValueVect &,
-                        python::object))convertToNumpyArray,
+                        python::object))convertToIntNumpyArray,
               (python::arg("bv"), python::arg("destArray")));
   python::def("ConvertToNumpyArray",
               (void (*)(const RDKit::SparseIntVect<std::int32_t> &,
-                        python::object))convertToNumpyArray,
+                        python::object))convertToIntNumpyArray,
               (python::arg("bv"), python::arg("destArray")));
   python::def("ConvertToNumpyArray",
               (void (*)(const RDKit::SparseIntVect<boost::int64_t> &,
-                        python::object))convertToNumpyArray,
+                        python::object))convertToIntNumpyArray,
               (python::arg("bv"), python::arg("destArray")));
   python::def("ConvertToNumpyArray",
               (void (*)(const RDKit::SparseIntVect<std::uint32_t> &,
-                        python::object))convertToNumpyArray,
+                        python::object))convertToIntNumpyArray,
               (python::arg("bv"), python::arg("destArray")));
   python::def("ConvertToNumpyArray",
               (void (*)(const RDKit::SparseIntVect<boost::uint64_t> &,
-                        python::object))convertToNumpyArray,
+                        python::object))convertToIntNumpyArray,
               (python::arg("bv"), python::arg("destArray")));
+  python::def("ConvertToNumpyArray",
+              (void (*)(const RDKit::RealValueVect &,
+                        python::object))convertToDoubleNumpyArray,
+              (python::arg("rvv"), python::arg("destArray")));
 }