PProtein.h

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/*
    LoopTK: Protein Loop Kinematic Toolkit
    Copyright (C) 2007 Stanford University

    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    This program 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 General Public License for more details.

    You should have received a copy of the GNU General Public License along
    with this program; if not, write to the Free Software Foundation, Inc.,
    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef __P_PROTEIN_H
#define __P_PROTEIN_H

#include "PChain.h"
#include "PProteinResidue.h"


class PProtein: public PChain {
 public:
  
  PProtein();

  PProtein(const string &firstResidueName); 

  PProtein(const string &firstResidueName, PResidueSpec &firstResidueSpec);

  PProtein(PProtein *protein, int resStartIndex, int resEndIndex);

  PProtein(int numResidues);
  
  PProtein *getParent() { return (PProtein *) PChain::getParent(); }
  
  PProtein *getTopLevelProtein();

  PProteinResidue *getResidue(int localIndex) { return (PProteinResidue *) PChain::getResidue(localIndex); }

  PProteinResidue *getResidueByPdbIndex(int pdbIndex);

  PProtein *getSubchainByPdbIndices(int startPdbIndex, int endPdbIndex);

  int NumBackboneDOFs() const;

  int NumSidechainDOFs() const;

  void RandomizeSidechainAtRes(int resIndex);

  void RandomizeAllSidechains();

  void GetEndEffectors(ProteinSide side, PAtom *&endAtom, PAtom *&endPriorAtom);

  void GetAnchors(ProteinSide side, PAtom *&endAnchor, PAtom *&endPriorAnchor);
  
  void DisableSidechains();

  void DisableSidechains(int resIndex1, int resIndex2);
  
  void EnableSidechains();

  void EnableSidechains(int resIndex1, int resIndex2);

  void RotateBackbone(int DOF_index, BondDirection dir, Real numDegrees);

  void RotateSidechain(int DOF_index, float numDegrees);

  PProtein *Clone();

  void RandomizeBackbone();

protected:
  virtual PResidue *CreateResidue(const string &name) {
    return new PProteinResidue(this, name);
  }

  virtual PResidue *CreateResidue(const string &name, PResidueSpec &spec) {
    return new PProteinResidue(this, name, spec); 
  }

  virtual PResidue *CreateResidue(const string &name, PResidue *res) {
    return new PProteinResidue(this, name, res);
  }

  virtual PResidue *CreateResidue(const string &name, PResidueSpec &spec, PResidue *res) {
    return new PProteinResidue(this, name, spec, res);
  }
};



#endif  // __P_PROTEIN_H

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