builder.hh

Go to the documentation of this file.

//------------------------------------------------------------------------------
// 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_BUILDER_HH
#define OST_CONOP_BUILDER_HH

/*
   Author: Marco Biasini
 */
#include <ost/mol/mol.hh>

#include <ost/conop/module_config.hh>
#include <ost/conop/builder_fw.hh>

namespace ost { namespace conop {

typedef enum {
  PDB_DIALECT,
  CHARMM_DIALECT
} Dialect;
class DLLEXPORT_OST_CONOP Builder {
public:
  
  Builder(): dialect_(PDB_DIALECT), strict_(false) { }
  virtual ~Builder();
  
  virtual void CompleteAtoms(mol::ResidueHandle rh);

  virtual void SetDialect(Dialect dialect) { dialect_=dialect; }
  
  virtual void SetStrictHydrogenMode(bool strict) { strict_=strict; }
  bool GetStrictHydrogenMode() const { return strict_; }
  
  Dialect GetDialect() const { return dialect_; }
  virtual void CheckResidueCompleteness(const mol::ResidueHandle& rh);

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

  virtual void FillResidueProps(mol::ResidueHandle residue);

  virtual void FillAtomProps(mol::AtomHandle atom);
  virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
  virtual void ConnectResidueToPrev(mol::ResidueHandle rh,
                                    mol::ResidueHandle prev);
  virtual void ConnectResidueToNext(mol::ResidueHandle rh, 
                                    mol::ResidueHandle next);

  virtual void AssignTorsions(mol::ChainHandle ch);
  
  virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
  
  void AssignBackBoneTorsionsToResidue(mol::ResidueHandle res);
  
  virtual bool DoesPeptideBondExist(const mol::AtomHandle& n, 
                                    const mol::AtomHandle& c);
  
  virtual bool IsBondFeasible(const mol::AtomHandle& atom_a,
                              const mol::AtomHandle& atom_b);  

  static String GuessAtomElement(const String& atom_name, bool hetatm);
   
  static bool AreResiduesConsecutive(const mol::ResidueHandle& r1, 
                                     const mol::ResidueHandle& r2);
  void GuessChemClass(mol::ResidueHandle res);
  void DistanceBasedConnect(mol::AtomHandle atom);
private:
  Dialect dialect_;
  bool    strict_;
};


}} // ns

#endif