local_dist_test.hh

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

namespace ost { namespace mol { namespace alg {
  
  
class UniqueAtomIdentifier
{
  
public:
  UniqueAtomIdentifier(const String& chain,const ResNum& residue,const String& residue_name, const String& atom): chain_(chain),residue_(residue),residue_name_(residue_name),atom_(atom) {}  
  
  String GetChainName() const { return chain_; } 
  ResNum GetResNum() const { return residue_; }  
  String GetResidueName() const { return residue_name_; }
  String GetAtomName() const { return atom_; }
  bool operator==(const UniqueAtomIdentifier& rhs) const;
    
private:

  String chain_;
  ResNum residue_;
  String residue_name_;
  String atom_;    
};

class ReferenceDistance
{
  
public:
  
  ReferenceDistance(const UniqueAtomIdentifier& first_atom, const UniqueAtomIdentifier& second_atom, Real mind, Real maxd):
       first_atom_(first_atom),second_atom_(second_atom),mind_(mind),maxd_(maxd) {}
  UniqueAtomIdentifier GetFirstAtom() const {return first_atom_;}
  UniqueAtomIdentifier GetSecondAtom() const {return second_atom_;}
  Real GetMinDistance() const {return mind_ ;}
  Real GetMaxDistance() const {return maxd_ ;}
  bool IsValid() const; 
  void Print() const; 
  bool operator==(const ReferenceDistance& rhs) const;
  
private:
  
  UniqueAtomIdentifier first_atom_;
  UniqueAtomIdentifier second_atom_;
  Real mind_;
  Real maxd_;
};

typedef std::vector<ReferenceDistance> ResidueDistanceList;
typedef std::vector<ResidueDistanceList> GlobalDistanceList;
  
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const EntityView& mdl,
                                         const GlobalDistanceList& dist_list,
                                         Real cutoff, 
                                         const String& local_ldt_property_string="");

Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const ost::seq::AlignmentHandle& aln,
                                         Real cutoff, Real max_dist,
                                         int ref_index=0, int mdl_index=1);


Real DLLEXPORT_OST_MOL_ALG LDTHA(EntityView& v, const GlobalDistanceList& global_dist_list);

GlobalDistanceList CreateDistanceList(const EntityView& ref,Real max_dist);


}}}

#endif