Rosetta 3.4
Public Member Functions
protocols::comparative_modeling::ThreadingMover Class Reference

#include <ThreadingMover.hh>

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List of all members.

Public Member Functions

 ThreadingMover (core::sequence::SequenceAlignment const &align, core::pose::Pose const &template_pose)
 align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model.
virtual ~ThreadingMover ()
core::Size query_index () const
 Returns the index of the query sequence in SequenceAlignment object.
core::Size template_index () const
 Returns the index of the template sequence in SequenceAlignment object.
core::sequence::SequenceAlignment alignment ()
 Returns the SequenceAlignment object used in threading.
void query_index (core::Size new_index)
 Sets the index of the query sequence in SequenceAlignment object.
void template_index (core::Size new_index)
 Sets the index of the template sequence in SequenceAlignment object.
void alignment (core::sequence::SequenceAlignment new_align)
 Sets the SequenceAlignment associated with this object.
void template_pose (core::pose::Pose template_pose)
void build_loops (bool setting)
void randomize_loop_coords (bool setting)
void repack_query (bool setting)
bool build_loops () const
bool repack_query () const
bool randomize_loop_coords ()
void min_loop_size (core::Size const new_size)
Size min_loop_size () const
utility::vector1
< core::fragment::FragSetOP
frag_libs () const
void frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)
core::id::SequenceMapping get_qt_mapping (core::pose::Pose const &query_pose) const
 Returns the SequenceMapping between query and template.
virtual void apply (core::pose::Pose &query_pose)
 Threads the given Pose onto the template_pose with the SequenceAlignment provided.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.

Constructor & Destructor Documentation

protocols::comparative_modeling::ThreadingMover::ThreadingMover ( core::sequence::SequenceAlignment const &  align,
core::pose::Pose const &  template_pose 
)

align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model.

virtual protocols::comparative_modeling::ThreadingMover::~ThreadingMover ( ) [inline, virtual]

Member Function Documentation

core::sequence::SequenceAlignment protocols::comparative_modeling::ThreadingMover::alignment ( )

Returns the SequenceAlignment object used in threading.

Referenced by protocols::comparative_modeling::PartialThreadingMover::parse_my_tag().

void protocols::comparative_modeling::ThreadingMover::alignment ( core::sequence::SequenceAlignment  new_align)

Sets the SequenceAlignment associated with this object.

void protocols::comparative_modeling::ThreadingMover::apply ( core::pose::Pose query_pose) [virtual]

Threads the given Pose onto the template_pose with the SequenceAlignment provided.

Implements protocols::moves::Mover.

Reimplemented in protocols::comparative_modeling::PartialThreadingMover.

References core::pose::add_score_line_string(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), build_loops(), core::chemical::CENTROID, core::conformation::Residue::clone(), core::pose::Pose::conformation(), protocols::loops::LoopMoverFactory::create_loop_mover(), frag_libs(), protocols::loops::LoopMoverFactory::get_instance(), get_qt_mapping(), core::scoring::getScoreFunction(), core::chemical::ResidueType::has(), core::conformation::idealize_hydrogens(), core::pose::initialize_atomid_map(), protocols::comparative_modeling::loops_from_alignment(), min_loop_size(), core::chemical::ResidueTypeSet::name(), core::conformation::Residue::name1(), core::conformation::Residue::natoms(), core::pack::optimize_H_and_notify(), core::pack::pack_missing_sidechains(), core::scoring::peptide_bond, randomize_loop_coords(), protocols::comparative_modeling::randomize_selected_atoms(), repack_query(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), core::pose::Pose::sequence(), core::pose::Pose::set_xyz(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and protocols::comparative_modeling::tr().

Referenced by protocols::domain_assembly::CombineChainsMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

void protocols::comparative_modeling::ThreadingMover::build_loops ( bool  setting)
bool protocols::comparative_modeling::ThreadingMover::build_loops ( ) const
void protocols::comparative_modeling::ThreadingMover::frag_libs ( utility::vector1< core::fragment::FragSetOP new_libs)
utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::ThreadingMover::frag_libs ( ) const

Referenced by apply().

std::string protocols::comparative_modeling::ThreadingMover::get_name ( ) const [virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::comparative_modeling::PartialThreadingMover.

core::id::SequenceMapping protocols::comparative_modeling::ThreadingMover::get_qt_mapping ( core::pose::Pose const &  query_pose) const
void protocols::comparative_modeling::ThreadingMover::min_loop_size ( core::Size const  new_size)
core::Size protocols::comparative_modeling::ThreadingMover::min_loop_size ( ) const

Referenced by apply().

void protocols::comparative_modeling::ThreadingMover::query_index ( core::Size  new_index)

Sets the index of the query sequence in SequenceAlignment object.

core::Size protocols::comparative_modeling::ThreadingMover::query_index ( ) const

Returns the index of the query sequence in SequenceAlignment object.

bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords ( )

Referenced by apply().

void protocols::comparative_modeling::ThreadingMover::randomize_loop_coords ( bool  setting)
bool protocols::comparative_modeling::ThreadingMover::repack_query ( ) const
void protocols::comparative_modeling::ThreadingMover::repack_query ( bool  setting)
void protocols::comparative_modeling::ThreadingMover::template_index ( core::Size  new_index)

Sets the index of the template sequence in SequenceAlignment object.

core::Size protocols::comparative_modeling::ThreadingMover::template_index ( ) const

Returns the index of the template sequence in SequenceAlignment object.

void protocols::comparative_modeling::ThreadingMover::template_pose ( core::pose::Pose  template_pose)

The documentation for this class was generated from the following files:
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