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