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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

typedef utility::pointer::shared_ptr< CopyDofs const > core::pose::copydofs::CopyDofsCOP
typedef utility::pointer::shared_ptr< CopyDofsInfo const > core::pose::copydofs::CopyDofsInfoCOP
typedef utility::pointer::shared_ptr< CopyDofsInfo > core::pose::copydofs::CopyDofsInfoOP
typedef utility::pointer::shared_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 
)
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(), 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(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

void core::pose::copydofs::copy_dofs ( pose::Pose pose,
Pose const &  scratch_pose 
)
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 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 
)
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 
)
void core::pose::copydofs::copy_dofs_match_atom_names ( pose::Pose pose,
Pose const &  scratch_pose 
)
void core::pose::copydofs::copy_dofs_match_atom_names ( pose::Pose pose,
MiniPose const &  chunk_pose,
core::pose::ResMap const &  res_map 
)
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 
)
Size const core::pose::copydofs::FIXED_DOMAIN ( 999  )
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 
)
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 
)

Variable Documentation

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