Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::toolbox::AllowInsert Class Reference

#include <AllowInsert.hh>

Public Member Functions

 AllowInsert (core::pose::Pose const &pose)
 
virtual ~AllowInsert ()
 
AllowInsertoperator= (AllowInsert const &src)
 
 AllowInsert (AllowInsert const &src)
 
virtual AllowInsertOP clone () const
 
bool has_domain (core::id::AtomID const &atom_id) const
 
bool get (Size const &i) const
 
bool get (core::id::AtomID const &atom_id) const
 
bool get (core::id::TorsionID const &torsion_id, core::conformation::Conformation const &conformation) const
 
bool get_jump (Size const &jump_number, core::conformation::Conformation const &conformation) const
 
Size get_domain (Size const &i) const
 
Size get_domain (core::id::AtomID const &atom_id) const
 
Size get_domain (core::id::NamedAtomID const &named_atom_id, core::pose::Pose const &pose) const
 
void set_domain (Size const &i, Size const &setting)
 
void set_domain (core::id::AtomID const &atom_id, Size const &setting)
 
void set_domain (core::id::NamedAtomID const &atom_id, core::pose::Pose const &pose, Size const &setting)
 
void set_domain (Size const &setting)
 
void and_allow_insert (AllowInsertOP allow_insert_in)
 
core::Size nres () const
 
void set_phosphate_domain (core::Size const &i, core::pose::Pose const &pose, Size const &setting)
 
void set_phosphate (core::Size const &i, core::pose::Pose const &pose, bool const &setting)
 
void set (Size const &i, bool const &setting)
 
void set (core::id::NamedAtomID const &named_atom_id, core::pose::Pose const &pose, bool const &setting)
 
void set (core::id::AtomID const &atom_id, bool const &setting)
 
void set (bool const &setting)
 
void show ()
 
std::map< core::id::AtomID,
Size > const & 
calculated_atom_id_domain_map ()
 
std::map< core::id::AtomID,
Size > const & 
calculate_atom_id_domain_map (core::pose::Pose const &pose)
 
void renumber_after_variant_changes (core::pose::Pose const &pose)
 
void calculate_atom_id_map (core::pose::Pose const &pose, std::map< core::Size, core::Size > const &res_map, core::kinematics::FoldTree const &scratch_fold_tree, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)
 
void set_force_ideal_chainbreak (bool const &setting)
 
void append_residue (core::pose::Pose const &pose, Size const &i, bool const &setting)
 
void setup_movemap (core::kinematics::MoveMap &mm, core::pose::Pose const &pose)
 

Private Member Functions

void initialize (core::pose::Pose const &pose)
 

Private Attributes

std::map< core::id::AtomID, Sizeallow_insert_
 
std::map
< core::id::NamedAtomID,
core::id::AtomID
named_atom_id_map_
 
utility::vector1
< utility::vector1
< core::id::AtomID > > 
atom_ids_in_res_
 
std::map< core::id::AtomID, Sizecalculated_atom_id_domain_map_
 
std::map< core::id::AtomID,
core::id::AtomID
map_to_original_
 
core::Size nres_
 
bool force_ideal_chainbreak_
 

Constructor & Destructor Documentation

protocols::toolbox::AllowInsert::AllowInsert ( core::pose::Pose const &  pose)

References initialize().

Referenced by clone().

protocols::toolbox::AllowInsert::~AllowInsert ( )
virtual
protocols::toolbox::AllowInsert::AllowInsert ( AllowInsert const &  src)

Member Function Documentation

void protocols::toolbox::AllowInsert::and_allow_insert ( AllowInsertOP  allow_insert_in)

References allow_insert_.

void protocols::toolbox::AllowInsert::append_residue ( core::pose::Pose const &  pose,
Size const &  i,
bool const &  setting 
)
std::map< AtomID, Size > const & protocols::toolbox::AllowInsert::calculate_atom_id_domain_map ( core::pose::Pose const &  pose)
void protocols::toolbox::AllowInsert::calculate_atom_id_map ( core::pose::Pose const &  pose,
std::map< core::Size, core::Size > const &  res_map,
core::kinematics::FoldTree const &  scratch_fold_tree,
std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map 
)
std::map< AtomID, Size > const & protocols::toolbox::AllowInsert::calculated_atom_id_domain_map ( )
AllowInsertOP protocols::toolbox::AllowInsert::clone ( ) const
virtual

References AllowInsert().

bool protocols::toolbox::AllowInsert::get ( Size const &  i) const

References get_domain().

Referenced by protocols::farna::moveable_jump().

bool protocols::toolbox::AllowInsert::get ( core::id::AtomID const &  atom_id) const

References get_domain().

bool protocols::toolbox::AllowInsert::get ( core::id::TorsionID const &  torsion_id,
core::conformation::Conformation const &  conformation 
) const
Size protocols::toolbox::AllowInsert::get_domain ( Size const &  i) const
Size protocols::toolbox::AllowInsert::get_domain ( core::id::AtomID const &  atom_id) const
Size protocols::toolbox::AllowInsert::get_domain ( core::id::NamedAtomID const &  named_atom_id,
core::pose::Pose const &  pose 
) const
bool protocols::toolbox::AllowInsert::get_jump ( Size const &  jump_number,
core::conformation::Conformation const &  conformation 
) const
bool protocols::toolbox::AllowInsert::has_domain ( core::id::AtomID const &  atom_id) const

References map_to_original_.

void protocols::toolbox::AllowInsert::initialize ( core::pose::Pose const &  pose)
private
core::Size protocols::toolbox::AllowInsert::nres ( ) const
inline

References nres_.

Referenced by setup_movemap().

AllowInsert & protocols::toolbox::AllowInsert::operator= ( AllowInsert const &  src)
void protocols::toolbox::AllowInsert::renumber_after_variant_changes ( core::pose::Pose const &  pose)
void protocols::toolbox::AllowInsert::set ( Size const &  i,
bool const &  setting 
)

References set_domain().

void protocols::toolbox::AllowInsert::set ( core::id::NamedAtomID const &  named_atom_id,
core::pose::Pose const &  pose,
bool const &  setting 
)
void protocols::toolbox::AllowInsert::set ( core::id::AtomID const &  atom_id,
bool const &  setting 
)

References set_domain().

void protocols::toolbox::AllowInsert::set ( bool const &  setting)

References set_domain().

void protocols::toolbox::AllowInsert::set_domain ( Size const &  i,
Size const &  setting 
)

References atom_ids_in_res_.

Referenced by set(), set_domain(), and set_phosphate_domain().

void protocols::toolbox::AllowInsert::set_domain ( core::id::AtomID const &  atom_id,
Size const &  setting 
)
void protocols::toolbox::AllowInsert::set_domain ( core::id::NamedAtomID const &  atom_id,
core::pose::Pose const &  pose,
Size const &  setting 
)
void protocols::toolbox::AllowInsert::set_domain ( Size const &  setting)

References allow_insert_.

void protocols::toolbox::AllowInsert::set_force_ideal_chainbreak ( bool const &  setting)
inline
void protocols::toolbox::AllowInsert::set_phosphate ( core::Size const &  i,
core::pose::Pose const &  pose,
bool const &  setting 
)
void protocols::toolbox::AllowInsert::set_phosphate_domain ( core::Size const &  i,
core::pose::Pose const &  pose,
Size const &  setting 
)
void protocols::toolbox::AllowInsert::setup_movemap ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose 
)
void protocols::toolbox::AllowInsert::show ( )

References allow_insert_, atom_ids_in_res_, I, and nres_.

Member Data Documentation

std::map< core::id::AtomID, Size > protocols::toolbox::AllowInsert::allow_insert_
private
utility::vector1< utility::vector1< core::id::AtomID > > protocols::toolbox::AllowInsert::atom_ids_in_res_
private
std::map< core::id::AtomID, Size > protocols::toolbox::AllowInsert::calculated_atom_id_domain_map_
private
bool protocols::toolbox::AllowInsert::force_ideal_chainbreak_
private
std::map< core::id::AtomID, core::id::AtomID > protocols::toolbox::AllowInsert::map_to_original_
private
std::map< core::id::NamedAtomID, core::id::AtomID > protocols::toolbox::AllowInsert::named_atom_id_map_
private
core::Size protocols::toolbox::AllowInsert::nres_
private

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