RB_geometry.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:
//
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/// @file RB_moves - rigid body geometry
/// @brief functions that set up the geometry required for rigid body moves
/// @author Monica Berrondo
/// edited 8.05.08 by G.Lemmon.  I changed jump_ids from int to core::Size.
/// I also added 3 methods to get downstream and upstream centroids so we can avoid "dummy" centroids


#ifndef INCLUDED_protocols_rigid_RB_geometry_hh
#define INCLUDED_protocols_rigid_RB_geometry_hh


// Package headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <numeric/xyzMatrix.fwd.hh>

// C++ Headers
// AUTO-REMOVED #include <utility>

#include <utility/vector1.hh>


namespace protocols {
namespace geometry {

numeric::xyzMatrix_double
random_reorientation_matrix(const double phi_range= 360.0, const double psi_range= 360.0);

void
centroids_by_jump(
  core::pose::Pose const & pose,
  core::Size const jump_id,
  core::Vector & upstream_ctrd, //< output
  core::Vector & downstream_ctrd //< output
);

void
centroids_by_jump(
  core::pose::Pose const & pose,
  core::Size const jump_id,
  core::Vector & upstream_ctrd, //< output
  core::Vector & downstream_ctrd, //< output
  utility::vector1< bool > ok_for_centroid_calculation
);


std::pair < core::Vector, core::Vector > centroid_pair_by_jump(
  core::pose::Pose const & pose,
  core::Size jump_id
);

core::Vector downstream_centroid_by_jump(
  core::pose::Pose const & pose,
  core::Size jump_id
);

core::Vector upstream_centroid_by_jump(
  core::pose::Pose const & pose,
  core::Size jump_id
);

void
centroids_by_jump_int(
  core::pose::Pose const & pose,
  core::Size jump_id,
  core::Vector & upstream_ctrd,
  core::Vector & downstream_ctrd
);

numeric::xyzVector< core::Real>
center_of_mass(
  core::pose::Pose const & pose,
  int const start,
  int const stop
);

int
residue_center_of_mass(
  core::pose::Pose const & pose,
  int const start,
  int const stop
);

/* int
residue_center_of_mass(
  core::pose::Pose & pose,
  core::Vector const positions
); */

int
return_nearest_residue(
  core::pose::Pose const & pose,
  int const begin,
  int const end,
  core::Vector center
);
} // geometry
} // core

#endif