rule_based_builder.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_CONOP_RULE_BASED_BUILDER_HH
#define OST_CONOP_RULE_BASED_BUILDER_HH

/*
   Author: Marco Biasini
 */
#include <set>
#include <map>

#include "builder.hh"
#include "compound_lib.hh"

namespace ost { namespace conop {

class DLLEXPORT_OST_CONOP RuleBasedBuilder: public Builder {
public:
  RuleBasedBuilder(const CompoundLibPtr& compound_lib)
    : compound_lib_(compound_lib), last_compound_() {
  }
  
  virtual void SetDialect(Dialect dialect) {
    if (this->GetDialect()!=dialect) {
      Builder::SetDialect(dialect);
      last_compound_=CompoundPtr();
      compound_lib_->ClearCache();
    }
  }
  
  virtual void FillAtomProps(mol::AtomHandle atom);
  
  virtual void CompleteAtoms(mol::ResidueHandle rh);

  virtual void CheckResidueCompleteness(const mol::ResidueHandle& rh);

  virtual mol::ResidueKey IdentifyResidue(const mol::ResidueHandle& rh);


  virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);

  virtual void ConnectResidueToNext(mol::ResidueHandle rh,
                                    mol::ResidueHandle next);
  virtual void AssignTorsions(mol::ChainHandle ch);
  virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
  virtual bool OnUnknownAtom(mol::AtomHandle atom);

  virtual void OnMissingAtom(const mol::ResidueHandle& residue,
                              const String& atom_name) { }
                              
  virtual void FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec);

  virtual void FillResidueProps(mol::ResidueHandle residue);

  mol::AtomHandleList GetUnknownAtoms(mol::ResidueHandle res);
  
  virtual bool IsResidueComplete(const mol::ResidueHandle& residue);
  
  CompoundLibPtr GetCompoundLib() const { return compound_lib_; }
    
private:
  CompoundLibPtr      compound_lib_;
  CompoundPtr         last_compound_;
  mol::ResidueHandle  last_residue_;
  bool                unknown_atoms_;
  bool HasUnknownAtoms(mol::ResidueHandle res);

  void LookupCompound(const mol::ResidueHandle& rh);
  void ReorderAtoms(mol::ResidueHandle residue, CompoundPtr compound);

  mol::AtomHandle LocateAtom(const mol::AtomHandleList& ahl, int ordinal);

  void AssignBackBoneTorsionsToResidue(mol::ResidueHandle residue);

};

typedef boost::shared_ptr<RuleBasedBuilder> RuleBasedBuilderPtr;

}}

#endif