RotamerLibrary.h

Go to the documentation of this file.

/**
 * \file IMP/rotamer/RotamerLibrary.h
 * \brief Object representing rotamer library.
 *
 * Copyright 2007-2015 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPROTAMER_ROTAMER_LIBRARY_H
#define IMPROTAMER_ROTAMER_LIBRARY_H

#include <string>
#include <vector>
#include <boost/range/iterator_range.hpp>
#include <IMP/base/Object.h>
#include <IMP/atom/Residue.h>
#include <IMP/rotamer/rotamer_config.h>

IMPROTAMER_BEGIN_NAMESPACE

//! A simple class storing chi angles and their probability
class IMPROTAMEREXPORT RotamerAngleTuple {
 public:
  //! default constructor. Build identity rotations with zero probability
  RotamerAngleTuple()
      : chi1_(0), chi2_(0), chi3_(0), chi4_(0), probability_(0) {}

  //! constructor. build rotamer data corresponding to 1 line from
  // the library file
  RotamerAngleTuple(float chi1, float chi2, float chi3, float chi4,
                    float probability)
      : chi1_(chi1),
        chi2_(chi2),
        chi3_(chi3),
        chi4_(chi4),
        probability_(probability) {}

  //! query the chi1 angle
  float get_chi1() const { return chi1_; }

  //! query the chi2 angle
  float get_chi2() const { return chi2_; }

  //! query the chi3 angle
  float get_chi3() const { return chi3_; }

  //! query the chi4 angle
  float get_chi4() const { return chi4_; }

  //! query the probability
  float get_probability() const { return probability_; }

  IMP_SHOWABLE_INLINE(RotamerAngleTuple, {
    out << "RotamerAngleTuple: " << chi1_ << ' ' << chi2_ << ' ' << chi3_ << ' '
        << chi4_ << ' ' << probability_;
  });

 private:
  float chi1_;
  float chi2_;
  float chi3_;
  float chi4_;
  float probability_;
};

IMP_VALUES(RotamerAngleTuple, RotamerAngleTuples);

//! A class storing a whole rotamer library read from a file
class IMPROTAMEREXPORT RotamerLibrary : public IMP::base::Object {
 public:
  //! constructor. Build an empty library object
  /** \param[in] angle_step bucket size in degrees */
  RotamerLibrary(unsigned angle_step = 10);

#ifndef SWIG
  typedef RotamerAngleTuples::const_iterator RotamerIterator;
  typedef boost::iterator_range<RotamerIterator> RotamerRange;

  //! query the rotamer library for the rotamer data
  /** This function returns a range of iterators to the queried contents.
      The range can be used in the following way:
      \code{.cpp}
      RotamerLibrary rl;
      // ....
      RotamerLibrary::RotamerRange r = rl.get_rotamers_fast(...);
      for ( RotamerLibrary::RotamerIterator p = r.begin(); p != r.end(); ++p )
      {
        const RotamerAngleTuple &ra = *p;
        // process ra ...
      }
      \endcode
      \param[in] residue the residue to query about
      \param[in] phi first backbone angle
      \param[in] psi second backbone angle
      \param[in] probability_thr threshold on the sum of probabilities.
  */
  RotamerRange get_rotamers_fast(IMP::atom::ResidueType residue, float phi,
                                 float psi, float probability_thr) const;
#endif

  //! query the rotamer library for the rotamer data
  /** This function returns a vector with the queried contents (and is
      therefore slower than get_rotamers_fast). It is however more useful in
      Python code
      \param[in] residue the residue to query about
      \param[in] phi first backbone angle
      \param[in] psi second backbone angle
      \param[in] probability_thr threshold on the sum of probabilities.
  */
  RotamerAngleTuples get_rotamers(IMP::atom::ResidueType residue, float phi,
                                  float psi, float probability_thr) const;

  //! load the library from file
  /** \param[in] lib_file_name file name */
  void read_library_file(const std::string &lib_file_name);

  IMP_OBJECT_METHODS(RotamerLibrary);

 private:
  unsigned backbone_angle_to_index(float phi, float psi) const;

  typedef std::vector<RotamerAngleTuples> RotamerAngleTuplesByBackbone;
  typedef std::vector<RotamerAngleTuplesByBackbone> RotamersByResidue;
  RotamersByResidue library_;

  unsigned angle_step_;
  unsigned rotamers_by_backbone_size_;
};

IMPROTAMER_END_NAMESPACE

#endif /* IMPROTAMER_ROTAMER_LIBRARY_H */