core::pose::copydofs Namespace Reference

Classes
class	CopyDofs
class	CopyDofsInfo

Typedefs
typedef utility::pointer::shared_ptr< CopyDofs >	CopyDofsOP
typedef utility::pointer::shared_ptr< CopyDofs const >	CopyDofsCOP
typedef utility::pointer::shared_ptr< CopyDofsInfo >	CopyDofsInfoOP
typedef utility::pointer::shared_ptr< CopyDofsInfo const >	CopyDofsInfoCOP

Functions
Size const	FIXED_DOMAIN (999)
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	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map, Size const default_domain)
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)

Variables
core::Size const	FIXED_DOMAIN

Typedef Documentation

CopyDofsCOP

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

CopyDofsInfoCOP

typedef utility::pointer::shared_ptr< CopyDofsInfo const > core::pose::copydofs::CopyDofsInfoCOP

CopyDofsInfoOP

typedef utility::pointer::shared_ptr< CopyDofsInfo > core::pose::copydofs::CopyDofsInfoOP

CopyDofsOP

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

Function Documentation

apply_dofs()

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

References core::pose::copydofs::CopyDofsInfo::apply_dofs().

Referenced by protocols::simple_moves::CopyDofMover::apply(), and core::pose::copydofs::CopyDofs::apply().

copy_dofs() [1/7]

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 protocols::simple_moves::CopyDofMover::apply(), core::pose::rna::RNA_IdealCoord::apply_coords(), protocols::stepwise::modeler::rna::contain_residue_at_seq_num(), copy_dofs(), copy_dofs_match_atom_names(), protocols::stepwise::modeler::rna::create_strand_list(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_full_rigid_body_sampler(), core::import_pose::libraries::ChunkSet::insert_chunk_into_pose(), protocols::rna::denovo::coarse::CoarseRNA_Fragments::insert_fragment(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), and protocols::stepwise::modeler::rna::sort_copy_dofs().

copy_dofs() [2/7]

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

References copy_dofs().

copy_dofs() [3/7]

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

References copy_dofs().

copy_dofs() [4/7]

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 copy_dofs().

copy_dofs() [5/7]

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

References copy_dofs(), and core::pose::Pose::size().

copy_dofs() [6/7]

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().

copy_dofs() [7/7]

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().

copy_dofs_match_atom_names() [1/3]

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().

copy_dofs_match_atom_names() [2/3]

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

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

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), core::pose::rna::RNA_IdealCoord::apply_coords(), protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::apply_current_pose_segment(), protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

copy_dofs_match_atom_names() [3/3]

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().

Referenced by protocols::stepwise::modeler::merge_two_poses(), and protocols::stepwise::modeler::slice().

FIXED_DOMAIN()

Size const core::pose::copydofs::FIXED_DOMAIN

(

999

)

setup_atom_id_map()

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

Referenced by copy_dofs().

setup_atom_id_map_match_atom_names() [1/2]

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::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::first_sidechain_hydrogen(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_virtual(), core::chemical::ResidueType::last_backbone_atom(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), and core::pose::Pose::residue_type().

Referenced by core::fragment::rna::analyze_for_homology(), protocols::simple_moves::CopyDofMover::apply(), and copy_dofs_match_atom_names().

setup_atom_id_map_match_atom_names() [2/2]

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::chemical::ResidueType::atom_name(), core::pose::MiniPose::atom_names_list(), core::chemical::ResidueType::natoms(), and core::pose::Pose::residue_type().

Variable Documentation

FIXED_DOMAIN

core::Size const core::pose::copydofs::FIXED_DOMAIN

extern

Referenced by core::pose::copydofs::CopyDofs::check_domain_map(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag(), core::pose::toolbox::AtomLevelDomainMap::get(), core::pose::toolbox::AtomLevelDomainMap::get_domain(), core::pose::toolbox::AtomLevelDomainMap::set(), core::pose::toolbox::AtomLevelDomainMap::set_fixed_if_moving(), core::pose::toolbox::AtomLevelDomainMap::set_phosphate(), core::pose::toolbox::AtomLevelDomainMap::set_sugar(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_full_model_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_full_model_info(), and core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_o2prime().