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/Geometry/UniformGrid3D.cpp

@@ -73,11 +73,11 @@ void UniformGrid3D::initGrid(
 
 UniformGrid3D::UniformGrid3D(const std::string &pkl) {
   dp_storage = nullptr;
-  this->initFromText(pkl.c_str(), pkl.size());
+  initFromText(pkl.c_str(), pkl.size());
 }
 UniformGrid3D::UniformGrid3D(const char *pkl, const unsigned int len) {
   dp_storage = nullptr;
-  this->initFromText(pkl, len);
+  initFromText(pkl, len);
 }
 
 UniformGrid3D::~UniformGrid3D() {
@@ -181,7 +181,7 @@ bool UniformGrid3D::compareParams(const UniformGrid3D &other) const {
 void UniformGrid3D::setSphereOccupancy(const Point3D &center, double radius,
                                        double stepSize, int maxNumLayers,
                                        bool ignoreOutOfBound) {
-  int ptIndex = this->getGridPointIndex(center);
+  int ptIndex = getGridPointIndex(center);
   if (ptIndex == -1) {
     if (ignoreOutOfBound) {
       return;