StubGenerator.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file
/// @brief
/// @author Alex Ford (fordas@u.washington.edu)
//
#ifndef INCLUDED_protocols_hotspot_hashing_StubGenerator_hh
#define INCLUDED_protocols_hotspot_hashing_StubGenerator_hh

// Unit headers
#include <protocols/hotspot_hashing/StubGenerator.fwd.hh>
#include <core/kinematics/Stub.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>

// Utility Headers
#include <core/types.hh>
#include <numeric/xyzVector.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/pointer/owning_ptr.hh>

#include <utility/vector1.hh>

namespace protocols {
namespace hotspot_hashing {

class StubGenerator
{
  public:
    typedef  numeric::xyzMatrix< core::Real > Matrix;
    typedef  numeric::xyzVector< core::Real > Vector;

  public:
    static core::conformation::ResidueOP getStubByName( std::string name );

    static void placeResidueAtTransform( core::pose::Pose & pose, core::conformation::ResidueCOP sourceResidue, core::kinematics::Stub transform, core::Size & residuejumpindex, core::Size & residueindex);

    static void placeResidueOnPose(core::pose::Pose & pose, core::conformation::ResidueCOP residue);

    //@brief Moves residue into the transform's reference frame via local2global.
    static void moveIntoStubFrame(core::conformation::ResidueOP residue, core::kinematics::Stub transform);

    //@brief Moves residue from transform's reference frame via global2local.
    static void moveFromStubFrame(core::conformation::ResidueOP residue, core::kinematics::Stub transform);

    //@brief Returns a stub generated from the residue's orient atoms.
    //
    //Used in recapitulating residue orientations when the residue type is known.
    static core::kinematics::Stub residueStubOrientFrame(core::conformation::ResidueCOP const residue);

    //@brief Returns a stub generated from the residue's backbone and centroid location.
    //
    // Used in orienting residues of varying type in a generation direction of "interest".
    //
    // Transform aligns CA atom to <0, 0, 0>
    // CA->SC heavyatom centroid vector along <1,0,0>
    // CA->C vector on the XY plane (<CA->C> * <0,0,1> == 0)
    static core::kinematics::Stub residueStubCentroidFrame(core::conformation::ResidueCOP const residue);

    static Vector residueStubCentroid(core::conformation::ResidueCOP const residue);
  private:
    StubGenerator();
};

} // namespace hotspot_hashing
} // namespace protocols

#endif