stage/include/ost/mol/alg/local_dist_diff_test.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
#ifndef OST_MOL_ALG_LOCAL_DIST_TEST_HH
#define OST_MOL_ALG_LOCAL_DIST_TEST_HH

#include <ost/mol/alg/module_config.hh>
#include <ost/seq/alignment_handle.hh>
#include <ost/mol/alg/distance_test_common.hh>

namespace ost { namespace mol { namespace alg {
  
std::pair<long int,long int> DLLEXPORT_OST_MOL_ALG 
LocalDistDiffTest(const EntityView& mdl, const GlobalRDMap& dist_list,
                  std::vector<Real> cutoff_list, int sequence_separation = 0, 
                  const String& local_ldt_property_string="");

Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& mdl,
                                         const EntityView& target,
                                         Real cutoff, 
                                         Real max_dist,
                                         const String& local_ldt_property_string="");
Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const ost::seq::AlignmentHandle& aln,
                                         Real cutoff, Real max_dist,
                                         int ref_index=0, int mdl_index=1);

Real DLLEXPORT_OST_MOL_ALG LDDTHA(EntityView& v, const GlobalRDMap& global_dist_list, int sequence_separation=0);

GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceList(const EntityView& ref,Real max_dist);

GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceListFromMultipleReferences(const std::vector<EntityView>& ref_list,std::vector<Real>& cutoff_list, int sequence_separation, Real max_dist);

void DLLEXPORT_OST_MOL_ALG PrintGlobalRDMap(const GlobalRDMap& glob_dist_list);

void DLLEXPORT_OST_MOL_ALG PrintResidueRDMap(const ResidueRDMap& res_dist_list);

// required by some helper function. Cannot reuse similar functions in other modules without creating
// circular dependencies
bool DLLEXPORT_OST_MOL_ALG IsStandardResidue(String rn);

}}}

#endif

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