mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
d15efc1ac9
* auto generate coords in mol block writer if includeChirality = True * default to include chirality when writing mol blocks/files * make isomeric smiles the default; note that not all tests are passing at the moment * update a reaction test * update expected cartridge search results at this point all python, c++, and cartridge tests pass * docs * update incompatibility docs * update doctests * these now build * minor example update * update expected c++ * typo * make allowCXSMILES=true the default * add auto perception of chirality when reading 3D structures from mol blocks * explain changes in release notes * further doc update
47 lines
1.7 KiB
C++
47 lines
1.7 KiB
C++
//
|
|
// 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);
|
|
}
|