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46 lines
1.7 KiB
C++
46 lines
1.7 KiB
C++
//
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// Working with 3D molecules - example11.cpp
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#include <iostream>
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#include <map>
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#include <string>
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#include <vector>
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#include <Geometry/point.h>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/DistGeomHelpers/Embedder.h>
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#include <GraphMol/ForceFieldHelpers/MMFF/MMFF.h>
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#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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int main(int main, char **argv) {
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std::shared_ptr<RDKit::ROMol> mol(RDKit::SmilesToMol("C1CCC1OC"));
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std::shared_ptr<RDKit::ROMol> mol1(RDKit::MolOps::addHs(*mol));
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std::shared_ptr<RDKit::ROMol> mol2(RDKit::MolOps::addHs(*mol));
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// Original distance geometry embedding
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RDKit::DGeomHelpers::EmbedMolecule(*mol1, 0, 1234);
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RDKit::UFF::UFFOptimizeMolecule(*mol1);
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// new Riniker and Landrum CSD-based method
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// using the parameters class
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RDKit::DGeomHelpers::EmbedParameters params(RDKit::DGeomHelpers::ETKDG);
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params.randomSeed = 1234;
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RDKit::DGeomHelpers::EmbedMolecule(*mol2, params);
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// Multiple conformations
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RDKit::INT_VECT mol1_cids =
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RDKit::DGeomHelpers::EmbedMultipleConfs(*mol1, 10);
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std::cout << "Number of conformations : " << mol1_cids.size() << std::endl;
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RDKit::INT_VECT mol2_cids;
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int numConfs = 20;
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RDKit::DGeomHelpers::EmbedMultipleConfs(*mol2, mol2_cids, numConfs, params);
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std::cout << "Number of conformations : " << mol2_cids.size() << std::endl;
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std::vector<double> rms_list;
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std::vector<unsigned int> m2cids(mol2_cids.begin(), mol2_cids.end());
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RDKit::MolAlign::alignMolConformers(*mol2, nullptr, &m2cids, nullptr, false,
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50, &rms_list);
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}
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