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df609d45f8
* Coulomb Mat v0.1 issue on linux * use static 3D molecule instead of generating 3D conf for testing * fix tokenize * fix issue removeHs * update test for sdf 3D molecule * strip things back to just do the basic coulomb matrix * add RDKIT_DESCRIPTORS_EXPORT * fix 3 typos and a missing const * Update rdMolDescriptors.cpp Co-authored-by: greg landrum <greg.landrum@gmail.com> Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
61 lines
2.3 KiB
C++
61 lines
2.3 KiB
C++
//
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// Copyright (c) 2018, Guillaume GODIN
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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// Modified by Greg Landrum, March 2020
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//
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#include <GraphMol/RDKitBase.h>
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#include <cmath>
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#include "CoulombMat.h"
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namespace RDKit {
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namespace Descriptors {
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void CoulombMat(const ROMol &mol, std::vector<std::vector<double>> &res, int confId) {
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PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
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unsigned int numAtoms = mol.getNumAtoms();
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const auto conf = mol.getConformer(confId);
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res.resize(numAtoms);
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for(unsigned int i=0;i<numAtoms;++i){
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res[i].resize(numAtoms);
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const auto at = mol.getAtomWithIdx(i);
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double Zi = at->getAtomicNum();
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res[i][i] = 0.5 * pow(Zi,2.4);
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const auto Pi = conf.getAtomPos(i);
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for(unsigned int j=0;j<i;++j){
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const auto Pj = conf.getAtomPos(j);
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double Zj = mol.getAtomWithIdx(j)->getAtomicNum();
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res[i][j] = res[j][i] = Zi*Zj / (Pi-Pj).length();
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}
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}
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}
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} // namespace Descriptors
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} // namespace RDKit
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