core::pose::copydofs Namespace Reference

Classes
class	CopyDofs

Typedefs
typedef utility::vector1 < std::pair< id::DOF_ID, core::Real > >	CopyDofsInfo
typedef utility::pointer::owning_ptr < CopyDofs >	CopyDofsOP
typedef utility::pointer::owning_ptr < CopyDofs const >	CopyDofsCOP

Functions
void	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, core::pose::ResMap const &res_map)
	A very useful function that copies degrees of freedom from one pose to another. More...
void	copy_dofs_match_atom_names (pose::Pose &pose, Pose const &scratch_pose)
void	copy_dofs_match_atom_names (pose::Pose &pose, MiniPose const &chunk_pose, core::pose::ResMap const &res_map)
void	copy_dofs (pose::Pose &pose, Pose const &scratch_pose)
void	copy_dofs (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map)
void	copy_dofs_match_atom_names (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map, bool const backbone_only, bool const side_chain_only, bool const ignore_virtual)
void	copy_dofs (pose::Pose &pose, Pose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)
void	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)
void	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map, std::map< id::AtomID, Size > const &atom_id_domain_map)
void	setup_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose)
void	setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &reference_pose, bool const backbone_only, bool const side_chain_only, bool const ignore_virtual)
void	setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, MiniPose const &chunk_pose)
void	apply_dofs (pose::Pose &pose, CopyDofsInfo const &copy_dofs_info, core::Real const dof_tolerance)
std::map< id::AtomID, Size >	blank_atom_id_domain_map (pose::Pose const &pose)

Typedef Documentation

typedef utility::pointer::owning_ptr< CopyDofs const > core::pose::copydofs::CopyDofsCOP

typedef utility::vector1< std::pair< id::DOF_ID, core::Real > > core::pose::copydofs::CopyDofsInfo

typedef utility::pointer::owning_ptr< CopyDofs > core::pose::copydofs::CopyDofsOP

Function Documentation

void core::pose::copydofs::apply_dofs	(	pose::Pose &	pose,
		CopyDofsInfo const &	copy_dofs_info,
		core::Real const	dof_tolerance
	)

References core::pose::Pose::dof(), and core::pose::Pose::set_dof().

Referenced by core::pose::copydofs::CopyDofs::apply().

std::map< id::AtomID, Size > core::pose::copydofs::blank_atom_id_domain_map

(

pose::Pose const &

pose

)

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by copy_dofs(), and core::pose::copydofs::CopyDofs::figure_out_atom_id_domain_map().

void core::pose::copydofs::copy_dofs	(	pose::Pose &	pose,
		MiniPose const &	scratch_pose,
		core::pose::ResMap const &	res_map
	)

A very useful function that copies degrees of freedom from one pose to another.

A very useful function that copies degrees of freedom from one pose to another. res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.

res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.

Author

rhiju, 2009.

rhiju, 2009.

References setup_atom_id_map().

Referenced by core::pose::rna::RNA_IdealCoord::apply_coords(), copy_dofs(), and copy_dofs_match_atom_names().

void core::pose::copydofs::copy_dofs	(	pose::Pose &	pose,
		Pose const &	scratch_pose
	)

References copy_dofs(), runtime_assert, and core::pose::Pose::total_residue().

void core::pose::copydofs::copy_dofs	(	pose::Pose &	pose,
		Pose const &	scratch_pose,
		core::pose::ResMap const &	res_map
	)

References copy_dofs(), and setup_atom_id_map().

void core::pose::copydofs::copy_dofs	(	pose::Pose &	pose,
		Pose const &	scratch_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_id_map
	)

References copy_dofs().

void core::pose::copydofs::copy_dofs	(	pose::Pose &	pose,
		MiniPose const &	scratch_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_id_map
	)

References blank_atom_id_domain_map(), and copy_dofs().

void core::pose::copydofs::copy_dofs	(	pose::Pose &	pose,
		MiniPose const &	scratch_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_id_map,
		std::map< id::AtomID, Size > const &	atom_id_domain_map
	)

References core::pose::copydofs::CopyDofs::apply(), and copy_dofs().

void core::pose::copydofs::copy_dofs_match_atom_names	(	pose::Pose &	pose,
		Pose const &	scratch_pose
	)

References runtime_assert, and core::pose::Pose::total_residue().

Referenced by core::pose::rna::RNA_IdealCoord::apply_coords().

void core::pose::copydofs::copy_dofs_match_atom_names	(	pose::Pose &	pose,
		MiniPose const &	chunk_pose,
		core::pose::ResMap const &	res_map
	)

References copy_dofs(), and setup_atom_id_map_match_atom_names().

void core::pose::copydofs::copy_dofs_match_atom_names	(	pose::Pose &	pose,
		Pose const &	scratch_pose,
		core::pose::ResMap const &	res_map,
		bool const	backbone_only,
		bool const	side_chain_only,
		bool const	ignore_virtual
	)

References copy_dofs(), and setup_atom_id_map_match_atom_names().

void core::pose::copydofs::setup_atom_id_map	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		ResMap const &	res_map,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::residue_type().

Referenced by copy_dofs().

void core::pose::copydofs::setup_atom_id_map_match_atom_names	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		ResMap const &	res_map,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	reference_pose,
		bool const	backbone_only,
		bool const	side_chain_only,
		bool const	ignore_virtual
	)

References core::pose::Pose::residue_type().

Referenced by copy_dofs_match_atom_names().

void core::pose::copydofs::setup_atom_id_map_match_atom_names	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		ResMap const &	res_map,
		core::pose::Pose const &	pose,
		MiniPose const &	chunk_pose
	)

References core::pose::MiniPose::atom_names_list(), and core::pose::Pose::residue_type().