DNAMutator.h

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/*
 * File: BALL/STRUCTURE/DNAMutator.h
 * Created: 23.10.2008
 *
 * Author: Daniel Stoeckel
 */

#ifndef DNAMUTATOR_H
#define DNAMUTATOR_H

#include <BALL/COMMON/exception.h>
#include <BALL/MATHS/vector3.h>
#include <BALL/STRUCTURE/mutator.h>
#include <BALL/STRUCTURE/nucleotideMapping.h>

#include <deque>
#include <map>

namespace BALL
{
  class Chain;
  class Residue;
  class FragmentDB;
  class EnergyMinimizer;
  class ForceField;
  class Fragment;
  class AtomContainer;
  class Atom;

  class BALL_EXPORT DNAMutator
    : public Mutator
  {
    public:
      enum MatchingMode
      {
        MINIMUM_ANGLE,
        MATCH_TORSION
      };
      DNAMutator(EnergyMinimizer* mini = NULL, ForceField* ff = NULL, FragmentDB* frag = NULL);

      ~DNAMutator();

      virtual void setup();

      void setMinimizer(EnergyMinimizer* mini);

      void setForceField(ForceField* ff);

      void setMaxOptimizationSteps(Size steps);

      void setUsedProperty(Property p);

      bool optimize();

      void setStrands(Chain* s1, Chain* s2);

      void setFirstStrand(Chain* s1);

      void setSecondStrand(Chain* s2);

      void setNucleotideMapping(const NucleotideMapping& bij);

      void addMutation(Index i, const String& new_frag_name);

      void clearMutations();

      void setMatchingMode(MatchingMode mmode);

    protected:
      virtual void mutate_impl_(MutatorOptions opt);

    private:
      typedef std::map<Residue*, String> Mutations;
      typedef Mutations::iterator MutIterator;

      bool keep_ff_;

      ForceField* ff_;
      EnergyMinimizer* minimizer_;

      Size num_steps_;
      Property prop_;

      Chain* first_strand_;
      Chain* second_strand_;

      NucleotideMapping mapping_;
      MatchingMode matching_mode_;

      void mutateSingleBase_(Residue* res, const String& basename) const;

      void freeFF_();

      void mark_(AtomContainer* atoms) const;
      void unmark_(AtomContainer* atoms) const;

      bool optimize_(Fragment* frag);

      Atom* getAttachmentAtom(AtomContainer* res) const;

      Atom* markBaseAtoms_(AtomContainer* res) const;

      void alignBases_(AtomContainer* from, const Vector3& from_connection, const Vector3& to_connection, Atom* from_at) const;

      Atom* getTorsionDefiningAtom_(Atom* atom) const;
      const Atom* getTorsionDefiningAtom_(const Atom* atom) const;

      void rotateBasesMatchTorsion_(AtomContainer* from, const Atom* to_connection_at, Atom* from_at, const Atom* to_at) const;
      void rotateBasesMinAngle_    (AtomContainer* from, const Vector3& to_connection,   Atom* from_at, const Atom* to_at) const;
      void rotateSameBases_(AtomContainer* from, AtomContainer* to) const;

      Vector3 getNormalVector_(const Atom* at) const;
      Atom* getConnectionAtom_(Atom* at) const;

      String canonizeName_(const String& frag_name) const;

      bool isPurine_(const Atom& baseNitrogen) const;
      bool isPyrimidine_(const Atom& baseNitrogen) const;

      static const char* bases_[];
      static const Size default_num_steps_;

      String getComplement_(const String& s) const;

      std::map<Residue*, String> mutations_;
      std::deque<Atom*> to_optimize_;
  };
}

#endif