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Add CoulombMat calculator (#2993)
* 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>
This commit is contained in:
guillaume godin
GitHub
@@ -1,7 +1,7 @@
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if(RDK_BUILD_DESCRIPTORS3D)
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set(DESC3D_HDRS MolDescriptors3D.h EEM.h PBF.h PMI.h AUTOCORR3D.h RDF.h MORSE.h GETAWAY.h WHIM.h)
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set(DESC3D_SOURCES EEM.cpp PBF.cpp PMI.cpp AUTOCORR3D.cpp RDF.cpp MORSE.cpp GETAWAY.cpp WHIM.cpp)
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set(DESC3D_HDRS MolDescriptors3D.h EEM.h PBF.h PMI.h AUTOCORR3D.h RDF.h MORSE.h GETAWAY.h WHIM.h CoulombMat.h)
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set(DESC3D_SOURCES EEM.cpp PBF.cpp PMI.cpp AUTOCORR3D.cpp RDF.cpp MORSE.cpp GETAWAY.cpp WHIM.cpp CoulombMat.cpp)
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endif(RDK_BUILD_DESCRIPTORS3D)
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@@ -62,6 +62,8 @@ LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges
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LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} )
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rdkit_test(testAUTOCORR3D testAUTOCORR3D.cpp
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LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} )
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rdkit_test(testCoulombMat testCoulombMat.cpp
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LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ForceField ForceFieldHelpers Optimizer DistGeomHelpers ${RDKit_THREAD_LIBS} )
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endif(RDK_BUILD_DESCRIPTORS3D)
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61
Code/GraphMol/Descriptors/CoulombMat.cpp
Normal file
61
Code/GraphMol/Descriptors/CoulombMat.cpp
Normal file
@@ -0,0 +1,61 @@
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//
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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
|
||||
// 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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42
Code/GraphMol/Descriptors/CoulombMat.h
Normal file
42
Code/GraphMol/Descriptors/CoulombMat.h
Normal file
@@ -0,0 +1,42 @@
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//
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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
|
||||
// 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,
|
||||
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
|
||||
// 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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#ifndef CoulombMatRDKIT_H_MAY2018
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#define CoulombMatRDKIT_H_MAY2018
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#ifdef RDK_BUILD_DESCRIPTORS3D
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namespace RDKit {
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class ROMol;
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namespace Descriptors {
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const std::string CoulombMatVersion = "1.0.0";
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RDKIT_DESCRIPTORS_EXPORT void CoulombMat(const ROMol &mol, std::vector<std::vector<double>> &res,
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int confId=-1);
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}
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}
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#endif
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#endif
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@@ -12,6 +12,7 @@
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#ifndef RD_MOLDESCRIPTORS3D_H_SEPT2016
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#define RD_MOLDESCRIPTORS3D_H_SEPT2016
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#include <GraphMol/Descriptors/CoulombMat.h>
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#include <GraphMol/Descriptors/EEM.h>
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#include <GraphMol/Descriptors/PBF.h>
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#include <GraphMol/Descriptors/RDF.h>
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@@ -118,6 +118,16 @@ python::tuple calcCrippenDescriptors(const RDKit::ROMol &mol,
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#ifdef RDK_BUILD_DESCRIPTORS3D
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python::tuple calcCoulombMat(const RDKit::ROMol &mol, int confId) {
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std::vector<std::vector<double>> results;
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RDKit::Descriptors::CoulombMat(mol, results, confId);
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python::list result;
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for (auto &res : results) {
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result.append(res);
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}
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return python::tuple(result);
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}
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python::list calcEEMcharges(RDKit::ROMol &mol, int confId) {
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std::vector<double> res;
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RDKit::Descriptors::EEM(mol, res, confId);
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@@ -332,7 +342,8 @@ double hkAlphaHelper(const RDKit::ROMol &mol, python::object atomContribs) {
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RDKit::SparseIntVect<std::uint32_t> *MorganFingerprintHelper(
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const RDKit::ROMol &mol, int radius, int nBits, python::object invariants,
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python::object fromAtoms, bool useChirality, bool useBondTypes,
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bool useFeatures, bool useCounts, python::object bitInfo, bool includeRedundantEnvironments) {
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bool useFeatures, bool useCounts, python::object bitInfo,
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bool includeRedundantEnvironments) {
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std::vector<boost::uint32_t> *invars = nullptr;
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if (invariants) {
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unsigned int nInvar =
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@@ -371,7 +382,8 @@ RDKit::SparseIntVect<std::uint32_t> *MorganFingerprintHelper(
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if (nBits < 0) {
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res = RDKit::MorganFingerprints::getFingerprint(
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mol, static_cast<unsigned int>(radius), invars, froms, useChirality,
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useBondTypes, useCounts, false, bitInfoMap, includeRedundantEnvironments);
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useBondTypes, useCounts, false, bitInfoMap,
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includeRedundantEnvironments);
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} else {
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res = RDKit::MorganFingerprints::getHashedFingerprint(
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mol, static_cast<unsigned int>(radius),
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@@ -402,22 +414,20 @@ RDKit::SparseIntVect<std::uint32_t> *MorganFingerprintHelper(
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return res;
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}
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#ifdef RDK_HAS_EIGEN3
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std::pair<double,double> BCUT2D_list(const RDKit::ROMol &m, python::list atomprops)
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{
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#ifdef RDK_HAS_EIGEN3
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std::pair<double, double> BCUT2D_list(const RDKit::ROMol &m,
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python::list atomprops) {
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std::vector<double> dvec;
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for (int i = 0; i < len(atomprops); ++i)
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{
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for (int i = 0; i < len(atomprops); ++i) {
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dvec.push_back(boost::python::extract<double>(atomprops[i]));
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}
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return RDKit::Descriptors::BCUT2D(m, dvec);
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}
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std::pair<double,double> BCUT2D_tuple(const RDKit::ROMol &m, python::tuple atomprops)
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{
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std::pair<double, double> BCUT2D_tuple(const RDKit::ROMol &m,
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python::tuple atomprops) {
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std::vector<double> dvec;
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for (int i = 0; i < len(atomprops); ++i)
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{
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for (int i = 0; i < len(atomprops); ++i) {
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dvec.push_back(boost::python::extract<double>(atomprops[i]));
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}
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return RDKit::Descriptors::BCUT2D(m, dvec);
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@@ -426,43 +436,40 @@ std::pair<double,double> BCUT2D_tuple(const RDKit::ROMol &m, python::tuple atomp
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// From boost::python examples
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// Converts a std::pair instance to a Python tuple.
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template <typename T1, typename T2>
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struct std_pair_to_tuple
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{
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static PyObject* convert(std::pair<T1, T2> const& p)
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{
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struct std_pair_to_tuple {
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static PyObject *convert(std::pair<T1, T2> const &p) {
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return boost::python::incref(
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boost::python::make_tuple(p.first, p.second).ptr());
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boost::python::make_tuple(p.first, p.second).ptr());
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}
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static PyTypeObject const *get_pytype () {return &PyTuple_Type; }
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static PyTypeObject const *get_pytype() { return &PyTuple_Type; }
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};
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// Helper for convenience.
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template <typename T1, typename T2>
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struct std_pair_to_python_converter
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{
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std_pair_to_python_converter()
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{
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boost::python::to_python_converter<
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std::pair<T1, T2>,
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std_pair_to_tuple<T1, T2>,
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true //std_pair_to_tuple has get_pytype
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>();
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struct std_pair_to_python_converter {
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std_pair_to_python_converter() {
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boost::python::to_python_converter<std::pair<T1, T2>,
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std_pair_to_tuple<T1, T2>,
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true // std_pair_to_tuple has get_pytype
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>();
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}
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};
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#endif
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#endif
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} // namespace
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RDKit::SparseIntVect<std::uint32_t> *GetMorganFingerprint(
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const RDKit::ROMol &mol, int radius, python::object invariants,
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python::object fromAtoms, bool useChirality, bool useBondTypes,
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bool useFeatures, bool useCounts, python::object bitInfo, bool includeRedundantEnvironments) {
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return MorganFingerprintHelper(mol, radius, -1, invariants, fromAtoms,
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useChirality, useBondTypes, useFeatures,
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useCounts, bitInfo, includeRedundantEnvironments);
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bool useFeatures, bool useCounts, python::object bitInfo,
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bool includeRedundantEnvironments) {
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return MorganFingerprintHelper(
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mol, radius, -1, invariants, fromAtoms, useChirality, useBondTypes,
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useFeatures, useCounts, bitInfo, includeRedundantEnvironments);
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}
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RDKit::SparseIntVect<std::uint32_t> *GetHashedMorganFingerprint(
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const RDKit::ROMol &mol, int radius, int nBits, python::object invariants,
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python::object fromAtoms, bool useChirality, bool useBondTypes,
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bool useFeatures, python::object bitInfo, bool includeRedundantEnvironments) {
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bool useFeatures, python::object bitInfo,
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bool includeRedundantEnvironments) {
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return MorganFingerprintHelper(mol, radius, nBits, invariants, fromAtoms,
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useChirality, useBondTypes, useFeatures, true,
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bitInfo, includeRedundantEnvironments);
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@@ -471,7 +478,8 @@ RDKit::SparseIntVect<std::uint32_t> *GetHashedMorganFingerprint(
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ExplicitBitVect *GetMorganFingerprintBV(
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const RDKit::ROMol &mol, int radius, unsigned int nBits,
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python::object invariants, python::object fromAtoms, bool useChirality,
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bool useBondTypes, bool useFeatures, python::object bitInfo, bool includeRedundantEnvironments) {
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bool useBondTypes, bool useFeatures, python::object bitInfo,
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bool includeRedundantEnvironments) {
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std::vector<boost::uint32_t> *invars = nullptr;
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if (invariants) {
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unsigned int nInvar =
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@@ -501,7 +509,8 @@ ExplicitBitVect *GetMorganFingerprintBV(
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ExplicitBitVect *res;
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res = RDKit::MorganFingerprints::getFingerprintAsBitVect(
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mol, static_cast<unsigned int>(radius), nBits, invars, froms.get(),
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useChirality, useBondTypes, false, bitInfoMap, includeRedundantEnvironments);
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useChirality, useBondTypes, false, bitInfoMap,
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includeRedundantEnvironments);
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if (bitInfoMap) {
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bitInfo.attr("clear")();
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for (RDKit::MorganFingerprints::BitInfoMap::const_iterator iter =
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@@ -521,15 +530,13 @@ ExplicitBitVect *GetMorganFingerprintBV(
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return res;
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}
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python::list GetAtomFeatures(const RDKit::ROMol &mol,
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int atomid,
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bool addchiral) {
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python::list GetAtomFeatures(const RDKit::ROMol &mol, int atomid,
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bool addchiral) {
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std::vector<double> res;
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RDKit::Descriptors::AtomFeatVect(mol, res, atomid, addchiral );
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RDKit::Descriptors::AtomFeatVect(mol, res, atomid, addchiral);
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python::list pyres;
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for( auto iv : res ) {
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pyres.append(iv);
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for (auto iv : res) {
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pyres.append(iv);
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}
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return pyres;
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}
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@@ -1413,12 +1420,13 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
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(python::arg("mol")), docString.c_str(),
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python::return_value_policy<python::manage_new_object>());
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python::scope().attr("_GetAtomFeatures_version") = RDKit::Descriptors::AtomFeatVersion;
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python::scope().attr("_GetAtomFeatures_version") =
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RDKit::Descriptors::AtomFeatVersion;
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docString = "Returns the Atom Features vector";
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python::def(
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"GetAtomFeatures", GetAtomFeatures,
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(python::arg("mol"), python::arg("atomid"), python::arg("addchiral") = false),
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docString.c_str());
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python::def("GetAtomFeatures", GetAtomFeatures,
|
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(python::arg("mol"), python::arg("atomid"),
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python::arg("addchiral") = false),
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docString.c_str());
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python::scope().attr("_CalcNumSpiroAtoms_version") =
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RDKit::Descriptors::NumSpiroAtomsVersion;
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@@ -1548,6 +1556,13 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
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python::return_value_policy<python::manage_new_object>());
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#ifdef RDK_BUILD_DESCRIPTORS3D
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python::scope().attr("_CalcCoulombMat_version") =
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RDKit::Descriptors::CoulombMatVersion;
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docString = "Returns severals Coulomb randomized matrices";
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python::def("CalcCoulombMat", calcCoulombMat,
|
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(python::arg("mol"), python::arg("confId") = -1),
|
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docString.c_str());
|
||||
|
||||
python::scope().attr("_CalcEMMcharges_version") =
|
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RDKit::Descriptors::EEMVersion;
|
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docString = "Returns EEM atomic partial charges";
|
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@@ -1688,31 +1703,34 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
|
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docString.c_str());
|
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|
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#endif
|
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|
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|
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#ifdef RDK_HAS_EIGEN3
|
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python::scope().attr("_BCUT2D_version") =
|
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RDKit::Descriptors::BCUT2DVersion;
|
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std::vector<double> (*BCUT)(const RDKit::ROMol&) = & RDKit::Descriptors::BCUT2D;
|
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std::pair<double,double> (*BCUT_atomprops)(const RDKit::ROMol&, const std::string&) = & RDKit::Descriptors::BCUT2D;
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docString = \
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"Implements BCUT descriptors From J. Chem. Inf. Comput. Sci., Vol. 39, No. 1, 1999" \
|
||||
"Diagonal elements are (currently) atomic mass, gasteiger charge,"\
|
||||
"crippen logP and crippen MRReturns the 2D BCUT2D descriptors vector as described in\n"\
|
||||
"returns [mass eigen value high, mass eigen value low,\n"\
|
||||
" gasteiger charge eigenvalue high, gasteiger charge low,\n"\
|
||||
" crippen lowgp eigenvalue high, crippen lowgp low,\n"\
|
||||
" crippen mr eigenvalue high, crippen mr low]\n"\
|
||||
"";
|
||||
|
||||
python::def("BCUT2D", BCUT,
|
||||
(python::arg("mol")),
|
||||
docString.c_str());
|
||||
python::scope().attr("_BCUT2D_version") = RDKit::Descriptors::BCUT2DVersion;
|
||||
std::vector<double> (*BCUT)(const RDKit::ROMol &) =
|
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&RDKit::Descriptors::BCUT2D;
|
||||
std::pair<double, double> (*BCUT_atomprops)(
|
||||
const RDKit::ROMol &, const std::string &) = &RDKit::Descriptors::BCUT2D;
|
||||
docString =
|
||||
"Implements BCUT descriptors From J. Chem. Inf. Comput. Sci., Vol. 39, "
|
||||
"No. 1, 1999"
|
||||
"Diagonal elements are (currently) atomic mass, gasteiger charge,"
|
||||
"crippen logP and crippen MRReturns the 2D BCUT2D descriptors vector as "
|
||||
"described in\n"
|
||||
"returns [mass eigen value high, mass eigen value low,\n"
|
||||
" gasteiger charge eigenvalue high, gasteiger charge low,\n"
|
||||
" crippen lowgp eigenvalue high, crippen lowgp low,\n"
|
||||
" crippen mr eigenvalue high, crippen mr low]\n"
|
||||
"";
|
||||
|
||||
python::def("BCUT2D", BCUT, (python::arg("mol")), docString.c_str());
|
||||
|
||||
std_pair_to_python_converter<double, double>();
|
||||
docString = \
|
||||
"Returns a 2D BCUT (eigen value hi, eigenvalue low) given the molecule and the specified atom props\n"\
|
||||
" there length ot atom_props must a list or tuple of floats equal in size to the number of atoms in mol";
|
||||
|
||||
docString =
|
||||
"Returns a 2D BCUT (eigen value hi, eigenvalue low) given the molecule "
|
||||
"and the specified atom props\n"
|
||||
" atom_props must be a list or tuple of floats equal in "
|
||||
"size to the number of atoms in mol";
|
||||
|
||||
python::def("BCUT2D", BCUT2D_list,
|
||||
(python::arg("mol"), python::arg("atom_props")),
|
||||
docString.c_str());
|
||||
@@ -1720,12 +1738,12 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
|
||||
(python::arg("mol"), python::arg("atom_props")),
|
||||
docString.c_str());
|
||||
|
||||
docString = \
|
||||
"Returns a 2D BCUT (eigen value high, eigen value low) given the molecule and the specified atom prop name\n" \
|
||||
"atom_propname must exist on each aton and be convertable to a float";
|
||||
docString =
|
||||
"Returns a 2D BCUT (eigen value high, eigen value low) given the "
|
||||
"molecule and the specified atom prop name\n"
|
||||
"atom_propname must exist on each atom and be convertible to a float";
|
||||
python::def("BCUT2D", BCUT_atomprops,
|
||||
(python::arg("mol"), python::arg("atom_propname")),
|
||||
docString.c_str());
|
||||
#endif
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
86
Code/GraphMol/Descriptors/testCoulombMat.cpp
Normal file
86
Code/GraphMol/Descriptors/testCoulombMat.cpp
Normal file
@@ -0,0 +1,86 @@
|
||||
// Created by Guillaume GODIN
|
||||
// Copyright (C) 2012-2018 Greg Landrum
|
||||
// @@ All Rights Reserved @@
|
||||
//
|
||||
// This file is part of the RDKit.
|
||||
// The contents are covered by the terms of the BSD license
|
||||
// which is included in the file license.txt, found at the root
|
||||
// of the RDKit source tree.
|
||||
|
||||
#include <RDGeneral/Invariant.h>
|
||||
#include <GraphMol/RDKitBase.h>
|
||||
#include <GraphMol/FileParsers/MolSupplier.h>
|
||||
#include <GraphMol/FileParsers/FileParsers.h>
|
||||
#include <RDGeneral/RDLog.h>
|
||||
#include <vector>
|
||||
#include <algorithm>
|
||||
#include <fstream>
|
||||
#include <string>
|
||||
#include <sstream>
|
||||
#include <iterator>
|
||||
#include <GraphMol/GraphMol.h>
|
||||
#include <GraphMol/MolOps.h>
|
||||
#include <boost/tokenizer.hpp>
|
||||
#include <GraphMol/PeriodicTable.h>
|
||||
#include <GraphMol/Descriptors/CoulombMat.h>
|
||||
#include <GraphMol/SmilesParse/SmilesParse.h>
|
||||
#include <GraphMol/DistGeomHelpers/Embedder.h>
|
||||
#include <GraphMol/ForceFieldHelpers/MMFF/MMFF.h>
|
||||
#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
|
||||
|
||||
|
||||
std::vector<std::string> tokenize(const std::string &s) {
|
||||
boost::char_separator<char> sep(", \n\r\t");
|
||||
boost::tokenizer<boost::char_separator<char>> tok(s, sep);
|
||||
std::vector<std::string> tokens;
|
||||
std::copy(tok.begin(), tok.end(), std::back_inserter<std::vector<std::string> >(tokens));
|
||||
return tokens;
|
||||
}
|
||||
|
||||
|
||||
|
||||
void testCoulombMat1(){
|
||||
std::cerr << "===================== Testing CoulombMat =======================\n";
|
||||
|
||||
std::string pathName = getenv("RDBASE");
|
||||
|
||||
// CM test 1
|
||||
std::string fNameCM =
|
||||
pathName + "/Code/GraphMol/Descriptors/test_data/CM1.out";
|
||||
|
||||
std::string mol_file =
|
||||
pathName + "/Code/GraphMol/Descriptors/test_data/bobmol.sdf";
|
||||
|
||||
std::ifstream instrmCM(fNameCM.c_str());
|
||||
std::string line;
|
||||
std::vector<std::string> tokens;
|
||||
|
||||
RDKit::ROMOL_SPTR mol( RDKit::MolFileToMol( mol_file , true, false) );
|
||||
|
||||
|
||||
std::vector<std::vector<double>> Mres;
|
||||
int confId = -1;
|
||||
RDKit::Descriptors::CoulombMat(*mol, Mres, confId);
|
||||
|
||||
for ( const auto &v : Mres ) {
|
||||
std::getline(instrmCM, line);
|
||||
tokens = tokenize(line);
|
||||
|
||||
unsigned int ti = 0;
|
||||
for ( double x : v ) {
|
||||
// std::cout << x << ",";
|
||||
TEST_ASSERT(std::fabs(std::stof(tokens[ti]) - x)< 0.001);
|
||||
ti++;
|
||||
}
|
||||
// std::cout << "\n";
|
||||
}
|
||||
// std::cout << "\n";
|
||||
|
||||
std::cerr << "CM test 1 mat Done\n";
|
||||
}
|
||||
|
||||
|
||||
int main() {
|
||||
RDLog::InitLogs();
|
||||
testCoulombMat1();
|
||||
}
|
||||
20
Code/GraphMol/Descriptors/test_data/CM1.out
Normal file
20
Code/GraphMol/Descriptors/test_data/CM1.out
Normal file
@@ -0,0 +1,20 @@
|
||||
53.3587,28.8825,17.6339,11.2255,8.72554,6.8079,8.65217,6.58329,6.60033,3.37463,3.27199,2.63155,2.64092,1.74263,1.72194,1.44489,1.42311,1.00482,1.09884,1.07798,
|
||||
28.8825,36.8581,23.6974,14.4435,9.49153,7.21172,9.20791,2.98292,2.9352,5.42428,5.50323,2.73963,2.77078,2.22406,2.18813,1.49618,1.46838,1.01732,1.17144,1.16919,
|
||||
17.6339,23.6974,36.8581,23.6352,14.7987,9.45274,11.3184,2.45891,2.31393,2.82976,2.77261,5.45955,5.43053,2.81015,2.76517,2.31103,2.2502,1.30863,1.46182,1.36136,
|
||||
11.2255,14.4435,23.6352,36.8581,23.8652,14.3849,16.7549,1.54952,1.5025,2.19477,2.21189,2.81032,2.82206,5.44131,5.4622,2.83714,2.76358,1.73626,2.2004,2.03985,
|
||||
8.72554,9.49153,14.7987,23.8652,36.8581,23.7572,20.3322,1.2663,1.22377,1.46916,1.46352,2.30132,2.2869,2.75577,2.78271,5.41015,5.41041,2.78637,2.80358,2.07202,
|
||||
6.8079,7.21172,9.45274,14.3849,23.7572,36.8581,34.6815,0.974949,0.9523,1.16749,1.17062,1.48822,1.48602,2.14083,2.17601,2.74887,2.79197,5.41823,5.35397,3.00643,
|
||||
8.65217,9.20791,11.3184,16.7549,20.3322,34.6815,73.5167,1.25019,1.1738,1.5804,1.47696,1.67679,1.85156,3.07811,2.46567,2.40036,3.0276,3.9189,3.87097,8.10652,
|
||||
6.58329,2.98292,2.45891,1.54952,1.2663,0.974949,1.25019,0.5,0.582079,0.428958,0.337355,0.35725,0.447337,0.245789,0.2247,0.206959,0.217354,0.1458,0.153006,0.15277,
|
||||
6.60033,2.9352,2.31393,1.5025,1.22377,0.9523,1.1738,0.582079,0.5,0.338807,0.412752,0.414909,0.33205,0.221307,0.23854,0.213156,0.196437,0.142353,0.155748,0.145129,
|
||||
3.37463,5.42428,2.82976,2.19477,1.46916,1.16749,1.5804,0.428958,0.338807,0.5,0.551678,0.326312,0.416222,0.404512,0.319664,0.219255,0.235493,0.16426,0.186241,0.203829,
|
||||
3.27199,5.50323,2.77261,2.21189,1.46352,1.17062,1.47696,0.337355,0.412752,0.551678,0.5,0.388841,0.325132,0.331923,0.39925,0.236454,0.21549,0.16411,0.199393,0.192683,
|
||||
2.63155,2.73963,5.45955,2.81032,2.30132,1.48822,1.67679,0.35725,0.414909,0.326312,0.388841,0.5,0.557344,0.329364,0.399923,0.438276,0.340401,0.214469,0.236977,0.199229,
|
||||
2.64092,2.77078,5.43053,2.82206,2.2869,1.48602,1.85156,0.447337,0.33205,0.416222,0.325132,0.557344,0.5,0.412667,0.327377,0.341573,0.421277,0.213861,0.217612,0.215306,
|
||||
1.74263,2.22406,2.81015,5.44131,2.75577,2.14083,3.07811,0.245789,0.221307,0.404512,0.331923,0.329364,0.412667,0.5,0.558072,0.326758,0.393978,0.262764,0.317627,0.398743,
|
||||
1.72194,2.18813,2.76517,5.4622,2.78271,2.17601,2.46567,0.2247,0.23854,0.319664,0.39925,0.399923,0.327377,0.558072,0.5,0.405057,0.324055,0.265435,0.397947,0.324765,
|
||||
1.44489,1.49618,2.31103,2.83714,5.41015,2.74887,2.40036,0.206959,0.213156,0.219255,0.236454,0.438276,0.341573,0.326758,0.405057,0.5,0.562862,0.396722,0.401525,0.260011,
|
||||
1.42311,1.46838,2.2502,2.76358,5.41041,2.79197,3.0276,0.217354,0.196437,0.235493,0.21549,0.340401,0.421277,0.393978,0.324055,0.562862,0.5,0.407749,0.326456,0.297044,
|
||||
1.00482,1.01732,1.30863,1.73626,2.78637,5.41823,3.9189,0.1458,0.142353,0.16426,0.16411,0.214469,0.213861,0.262764,0.265435,0.396722,0.407749,0.5,0.546132,0.353014,
|
||||
1.09884,1.17144,1.46182,2.2004,2.80358,5.35397,3.87097,0.153006,0.155748,0.186241,0.199393,0.236977,0.217612,0.317627,0.397947,0.401525,0.326456,0.546132,0.5,0.452921,
|
||||
1.07798,1.16919,1.36136,2.03985,2.07202,3.00643,8.10652,0.15277,0.145129,0.203829,0.192683,0.199229,0.215306,0.398743,0.324765,0.260011,0.297044,0.353014,0.452921,0.5,
|
||||
44
Code/GraphMol/Descriptors/test_data/bobmol.sdf
Normal file
44
Code/GraphMol/Descriptors/test_data/bobmol.sdf
Normal file
@@ -0,0 +1,44 @@
|
||||
|
||||
RDKit 3D
|
||||
|
||||
20 19 0 0 0 0 0 0 0 0999 V2000
|
||||
3.3709 -0.4775 0.3706 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.0231 -1.0195 0.3052 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0808 0.1720 0.2902 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.3637 -0.3063 0.2221 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2298 0.9287 0.2108 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.7029 0.5798 0.1440 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.9424 -0.1384 -1.0146 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.4168 0.2414 -0.4115 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.4680 0.0361 1.2934 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.9149 -1.5221 -0.6742 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.7832 -1.6968 1.1252 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.1861 0.8040 1.1831 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2583 0.7881 -0.6096 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.4776 -0.9003 -0.6999 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.6039 -0.9393 1.0871 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.9864 1.4993 1.1301 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.9764 1.5878 -0.6443 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.3013 1.5115 0.1327 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.9476 -0.0336 1.0494 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.9701 -1.1150 -0.8754 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0
|
||||
2 3 1 0
|
||||
3 4 1 0
|
||||
4 5 1 0
|
||||
5 6 1 0
|
||||
6 7 1 0
|
||||
1 8 1 0
|
||||
1 9 1 0
|
||||
2 10 1 0
|
||||
2 11 1 0
|
||||
3 12 1 0
|
||||
3 13 1 0
|
||||
4 14 1 0
|
||||
4 15 1 0
|
||||
5 16 1 0
|
||||
5 17 1 0
|
||||
6 18 1 0
|
||||
6 19 1 0
|
||||
7 20 1 0
|
||||
M END
|
||||
Reference in New Issue
Block a user