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// (c) Copyright BCL @ Vanderbilt University 2014
// (c) BCL Homepage: http://www.meilerlab.org/bclcommons
// (c) BCL Code Repository: https://github.com/BCLCommons/bcl
// (c)
// (c) The BioChemical Library (BCL) was originally developed by contributing members of the Meiler Lab @ Vanderbilt University.
// (c)
// (c) The BCL is now made available as an open-source software package distributed under the permissive MIT license,
// (c) developed and maintained by the Meiler Lab at Vanderbilt University and contributing members of the BCL Commons.
// (c)
// (c) External code contributions to the BCL are welcome. Please visit the BCL Commons GitHub page for information on how you can contribute.
// (c)
// (c) This file is part of the BCL software suite and is made available under the MIT license.
// (c)
// include example header
#include "example.h"
// include the header of the class which this example is for
#include "descriptor/bcl_descriptor_maccs.h"
// includes from bcl - sorted alphabetically
#include "chemistry/bcl_chemistry_fragment_ensemble.h"
#include "descriptor/bcl_descriptor_atom_vcharge.h"
#include "io/bcl_io_file.h"
#include "sdf/bcl_sdf_fragment_factory.h"
// external includes - sorted alphabetically
namespace bcl
{
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//!
//! @example example_descriptor_maccs.cpp
//!
//! @author mendenjl
//! @date Aug 27, 2014
//! @remarks status complete
//! @remarks reviewed by nobody on
//!
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
class ExampleDescriptorMaccs :
public ExampleInterface
{
public:
ExampleDescriptorMaccs *Clone() const
{
return new ExampleDescriptorMaccs( *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
{
/////////////////
// preparation //
/////////////////
// Read in small molecule
io::IFStream input_sdf;
BCL_ExampleMustOpenInputFile( input_sdf, AddExampleInputPathToFilename( e_Chemistry, "taxol.sdf"));
// load information into small_mol
chemistry::FragmentComplete taxol( sdf::FragmentFactory::MakeFragment( input_sdf));
io::File::CloseClearFStream( input_sdf);
//////////////////////////////////
// construction and destruction //
//////////////////////////////////
// prepare atom properties vector
descriptor::CheminfoProperty atom_property( "MACCS");
// test empty constructor
descriptor::MACCS maccs_code;
BCL_ExampleCheck( maccs_code.GetAlias(), "MACCS");
/////////////////
// data access //
/////////////////
static const size_t s_maccs_key_size( 938);
BCL_ExampleCheck( maccs_code.GetNormalSizeOfFeatures(), s_maccs_key_size);
// Generate the VDW RDF code
BCL_ExampleCheck( maccs_code( taxol).GetSize(), s_maccs_key_size);
float expected_vec_array [ s_maccs_key_size] =
{
1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 1, 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,
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, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 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, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0,
0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0,
0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0,
1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1,
0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1,
0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1,
1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0,
1, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 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, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 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
};
linal::Vector< float> expected_vector( s_maccs_key_size, expected_vec_array);
BCL_ExampleCheckWithinAbsTolerance( maccs_code( taxol), expected_vector, 0.001);
//////////////////////
// input and output //
//////////////////////
// check i/o
BCL_ExampleIndirectCheck
(
TestBCLObjectIOForSymmetry( maccs_code, descriptor::MACCS()),
true,
"Maccs I/O"
);
//////////////////////
// helper functions //
//////////////////////
return 0;
} // Run
static const ExampleClass::EnumType s_Instance;
}; //end ExampleDescriptorMaccs
const ExampleClass::EnumType ExampleDescriptorMaccs::s_Instance
(
GetExamples().AddEnum( ExampleDescriptorMaccs())
);
} // namespace bcl