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644296fe13
* 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>
74 lines
2.6 KiB
C++
Executable File
74 lines
2.6 KiB
C++
Executable File
//
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// Copyright (c) 2014-2024, Novartis Institutes for BioMedical Research and
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// other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <boost/python.hpp>
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#include <RDGeneral/types.h>
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#include <RDGeneral/Invariant.h>
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#include <RDBoost/PySequenceHolder.h>
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#include <DataStructs/RealValueVect.h>
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using namespace RDKit;
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struct rvv_pickle_suite : rdkit_pickle_suite {
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static python::tuple getinitargs(const RealValueVect &self) {
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std::string res = self.toString();
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python::object retval = python::object(
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python::handle<>(PyBytes_FromStringAndSize(res.c_str(), res.length())));
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return python::make_tuple(retval);
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};
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};
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std::string realValVectDoc =
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"A container class for storing real\n\
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values.\n\
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\n\
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The length of the vector is set at construction time.\n\
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\n\
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As you would expect, _RealValueVects_ support a set of binary operations\n\
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so you can do things like:\n\
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rvv3 = rvv1 & rvv2 the result contains the smallest value in each entry\n\
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rvv3 = rvv1 | rvv2 the result contains the largest value in each entry\n\
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rvv1 += rvv2 \n\
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rvv3 = rvv1 + rvv2 \n\
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rvv1 -= rvv3 \n\
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rvv3 = rvv1 - rvv2 \n\
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\n\
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Elements can be set and read using indexing (i.e. bv[i] = 4 or val=bv[i])\n\
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\n";
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struct realValVec_wrapper {
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static void wrap() {
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python::class_<RealValueVect>("RealValueVect", realValVectDoc.c_str(),
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python::init<unsigned int>("Constructor"))
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.def(python::init<std::string>())
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.def("__len__", &RealValueVect::getLength,
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"Get the number of entries in the vector")
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.def("__setitem__", &RealValueVect::setVal,
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"Set the value at a specified location")
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.def("__getitem__", &RealValueVect::getVal,
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"Get the value at a specified location")
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.def(python::self & python::self)
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.def(python::self | python::self)
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.def(python::self - python::self)
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.def(python::self -= python::self)
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.def(python::self + python::self)
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.def(python::self += python::self)
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.def("GetTotalVal", &RealValueVect::getTotalVal,
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"Get the sum of the values in the vector, basically L1 norm")
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.def_pickle(rvv_pickle_suite());
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python::def("ComputeL1Norm", computeL1Norm,
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"Compute the distance between two real vector values\n");
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}
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};
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void wrap_realValVect() { realValVec_wrapper::wrap(); }
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