example_descriptor_atom_is_sp3.cpp

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//
//// include example header
//#include "example.h"
//
//// include the header of the class which this example is for
//#include "descriptor/bcl_descriptor_atom_is_sp3.h"
//
//// includes from bcl - sorted alphabetically
//#include "chemistry/bcl_chemistry_fragment_ensemble.h"
//#include "io/bcl_io_file.h"
//#include "sdf/bcl_sdf_fragment_factory.h"
//
//// external includes - sorted alphabetically
//
//namespace bcl
//{
//  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//  //!
//  //! @example example_descriptor_atom_is_sp3.cpp
//  //!
//  //! @author brownbp1, mendenjl
//  //! @date Jun 19, 2020
//  //! @remarks status complete
//  //! @remarks reviewed by nobody on
//  //!
//  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//
//  class ExampleDescriptorAtomIsSP3 :
//    public ExampleInterface
//  {
//  public:
//
//    ExampleDescriptorAtomIsSP3 *Clone() const
//    {
//      return new ExampleDescriptorAtomIsSP3( *this);
//    }
//
//  /////////////////
//  // data access //
//  /////////////////
//
//    //! @brief returns class name
//    //! @return the class name as const ref std::string
//    const std::string &GetClassIdentifier() const
//    {
//      return GetStaticClassName( *this);
//    }
//
//    int Run() const
//    {
//    //////////////////////////////////
//    // construction and destruction //
//    //////////////////////////////////
//
//      // test default constructor
//      descriptor::AtomIsSP3 stereocenters_a;
//
//      // test Clone
//      descriptor::AtomIsSP3 stereocenters_cp( stereocenters_a);
//
//    ////////////////////////////////////////
//    //  read Small molecule Stereocenters //
//    ////////////////////////////////////////
//
//      // use SmallMoleculeFactory to load molecule information into SmallMolecule
//      // this requires SmallMolecule and input stream
//      io::IFStream input_sdf;
//      BCL_ExampleMustOpenInputFile( input_sdf, AddExampleInputPathToFilename( e_Chemistry, "corina_taxol.sdf"));
//      chemistry::FragmentComplete taxol = sdf::FragmentFactory::MakeFragment( input_sdf);
//      io::File::CloseClearFStream( input_sdf);
//
//      //calculate stereocenters for taxol
//      linal::Vector< float> calculated_stereocenters( stereocenters_a.CollectValuesOnEachElementOfObject( taxol));
//
//      float expected_vec_array [] =
//      {
//          0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,-1,-1,1,-1,1,-1,0,0,0,0,0,0,0,-1,-1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,
//          0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
//        0,0,0,0,0
//      };
//      linal::Vector< float> expected_vector( 113, expected_vec_array);
//      BCL_ExampleCheckWithinAbsTolerance( calculated_stereocenters, expected_vector, 0.001);
//
//      return 0;
//      } // Run
//
//    static const ExampleClass::EnumType s_Instance;
//
//  }; //end ExampleDescriptorAtomIsSP3
//
//  const ExampleClass::EnumType ExampleDescriptorAtomIsSP3::s_Instance
//  (
//    GetExamples().AddEnum( ExampleDescriptorAtomIsSP3())
//  );
//
//} // namespace bcl