obconformersearch_default.cpp

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obconformersearch_default.cpp

    #include <openbabel/obconversion.h>
    #include <openbabel/mol.h>
    #include <openbabel/shared_ptr.h>
    #include <openbabel/conformersearch.h>

    #include <iostream>

    using namespace OpenBabel;

    // Helper function to read molecule from file
    shared_ptr<OBMol> GetMol(const std::string &filename)
    {
      // Create the OBMol object.
      shared_ptr<OBMol> mol(new OBMol);

      // Create the OBConversion object.
      OBConversion conv;
      OBFormat *format = conv.FormatFromExt(filename.c_str());
      if (!format || !conv.SetInFormat(format)) {
        std::cout << "Could not find input format for file " << filename << std::endl;
        return mol;
      }

      // Open the file.
      std::ifstream ifs(filename.c_str());
      if (!ifs) {
        std::cout << "Could not open " << filename << " for reading." << std::endl;
        return mol;
      }
      // Read the molecule.
      if (!conv.Read(mol.get(), &ifs)) {
        std::cout << "Could not read molecule from file " << filename << std::endl;
        return mol;
      }

      return mol;
    }

    int main(int argc, char **argv)
    {
      if (argc < 2) {
        std::cout << "Usage: " << argv[0] << " <filename>" << std::endl;
        return 1;
      }

      // Read the file
      shared_ptr<OBMol> mol = GetMol(argv[1]);

      // Create the OBConformerSearch object
      OBConformerSearch cs;

      // Setup
      std::cout << "Setting up conformer searching..." << std::endl
                << "   conformers:  30" << std::endl
                << "   children:    5" << std::endl
                << "   mutability:  5" << std::endl
                << "   convergence: 25" << std::endl;
      cs.Setup(*mol.get(),
               30, // numConformers
               5, // numChildren
               5, // mutability
               25); // convergence

      // Perform searching
      cs.Search();

      // Print the rotor keys
      RotorKeys keys = cs.GetRotorKeys();
      for (RotorKeys::iterator key = keys.begin(); key != keys.end(); ++key) {
        for (unsigned int i = 1; i < key->size(); ++i)
          std::cout << key->at(i) << " ";
        std::cout << std::endl;
      }

      // Get the conformers
      cs.GetConformers(*mol.get());

      std::cout << mol->NumConformers() << std::endl;
      OBConversion conv;
      conv.SetOutFormat("sdf");
      for (unsigned int c = 0; c < mol->NumConformers(); ++c) {
        mol->SetConformer(c);
        conv.Write(mol.get(), &std::cerr);
      }

    }

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