superimpose.hh File Reference

header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) More...

#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.fwd.hh>
#include <numeric/xyzVector.fwd.hh>
#include <ObjexxFCL/FArray2.fwd.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::toolbox

Typedefs
typedef numeric::xyzMatrix < core::Real >	protocols::toolbox::Matrix
typedef numeric::xyzVector < core::Real >	protocols::toolbox::Vector

Functions
void	protocols::toolbox::CA_superimpose (ObjexxFCL::FArray1_double const &weights, core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)
void	protocols::toolbox::CA_superimpose (core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)
void	protocols::toolbox::superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, Matrix &rotation, Vector &to_init_center, Vector &to_fit_center)
void	protocols::toolbox::superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, utility::vector1< core::Real > &coord_weights, Matrix &rotation, Vector &to_init_center, Vector &to_fit_center)
void	protocols::toolbox::apply_superposition_transform_to_jump (core::pose::Pose &pose, core::Size jump_id, Matrix rotation, Vector to_init_center, Vector to_fit_center)
void	protocols::toolbox::apply_superposition_transform (core::pose::Pose &pose, Matrix rotation, Vector to_init_center, Vector to_fit_center)
template<typename T >
void	protocols::toolbox::vector_vector_to_FArray2 (utility::vector1< numeric::xyzVector< T > > &from, ObjexxFCL::FArray2D< T > &to)
void	protocols::toolbox::superposition_transform (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, Matrix &R, Vector &toCenter, Vector &toFitCenter)
void	protocols::toolbox::fit_centered_coords (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double const &ref_coords, ObjexxFCL::FArray2_double &coords, Matrix &R)
void	protocols::toolbox::reset_x (core::Size n, ObjexxFCL::FArray2_double &x, ObjexxFCL::FArray1_double const &wts, ObjexxFCL::FArray1_double &transvec)
void	protocols::toolbox::dump_as_pdb (std::string filename, core::Size n, ObjexxFCL::FArray2_double &coords, ObjexxFCL::FArray1D_double transvec=ObjexxFCL::FArray1D_double(3, 0.0))
	write a CA ALA pdb More...
void	protocols::toolbox::fill_CA_coords (core::pose::Pose const &pose, core::Size natoms, ObjexxFCL::FArray2_double &coords)
void	protocols::toolbox::fill_CA_coords (core::pose::Pose const &pose, ObjexxFCL::FArray2_double &coords)

Detailed Description

header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh)

Author

Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om