Rosetta Protocols  2014.35
Public Member Functions | Private Types | Private Member Functions | Private Attributes | Friends | List of all members
protocols::environment::ProtectedConformation Class Reference

#include <ProtectedConformation.hh>

Public Member Functions

 ProtectedConformation (ProtectedConformation const &src)
 
virtual ~ProtectedConformation ()
 
EnvironmentCAP environment () const
 
void env_destruction ()
 
virtual bool is_protected () const
 
SequenceAnnotationCOP resolver () const
 
SequenceAnnotationCOP annotations () const
 
virtual
core::conformation::ConformationOP 
clone () const
 
virtual Conformationoperator= (Conformation const &src)
 
virtual void set_torsion (TorsionID const &id, core::Real const setting)
 
virtual void set_jump (AtomID const &, core::kinematics::Jump const &)
 
virtual void set_jump (int const, core::kinematics::Jump const &)
 
virtual void set_secstruct (Size const seqpos, char const setting)
 
virtual void replace_residue (Size const seqpos, core::conformation::Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
 
virtual void replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone)
 
virtual void set_stub_transform (core::id::StubID const &stub_id1, core::id::StubID const &stub_id2, core::kinematics::RT const &target_rt)
 
virtual void set_dof (DOF_ID const &id, core::Real const setting)
 
virtual void set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, core::Real const setting, bool quiet=false)
 
virtual void set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, core::Real const setting)
 
virtual void set_bond_length (AtomID const &atom1, AtomID const &atom2, core::Real const setting)
 
virtual void insert_fragment (core::id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)
 
virtual void fold_tree (FoldTree const &)
 
virtual void chain_endings (utility::vector1< Size > const &)
 
virtual void insert_chain_ending (Size const )
 
virtual void delete_chain_ending (Size const )
 
virtual void reset_chain_endings ()
 
virtual void chains_from_termini ()
 
virtual void append_residue_by_jump (core::conformation::Residue const &, Size const, std::string const &="", std::string const &="", bool const =false)
 
virtual void append_polymer_residue_after_seqpos (core::conformation::Residue const &, Size const, bool const )
 
virtual void safely_append_polymer_residue_after_seqpos (core::conformation::Residue const &, Size const, bool const )
 
virtual void prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, Size const, bool const )
 
virtual void safely_prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, Size const, bool const )
 
virtual void delete_polymer_residue (Size const )
 
virtual void delete_residue_slow (Size const )
 
virtual void delete_residue_range_slow (Size const range_begin, Size const range_end)
 
virtual void declare_chemical_bond (Size const, std::string const &, Size const, std::string const &)
 
virtual void insert_conformation_by_jump (Conformation const &, Size const, Size const, Size const, Size const, std::string const &="", std::string const &="")
 
virtual void rebuild_polymer_bond_dependent_atoms (Size const )
 
virtual void insert_ideal_geometry_at_polymer_bond (Size const seqpos)
 
virtual void insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)
 
virtual void set_polymeric_connection (Size, Size)
 
virtual void fix_disulfides (utility::vector1< std::pair< Size, Size > >)
 
virtual void set_xyz (AtomID const &id, core::PointPosition const &position)
 
virtual void batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< core::PointPosition > const &position)
 
virtual void reset_move_data ()
 
virtual void clear ()
 
virtual void fill_missing_atoms (core::id::AtomID_Mask missing)
 
virtual bool same_type_as_me (Conformation const &other, bool recurse) const
 
- Public Member Functions inherited from core::conformation::Conformation
 Conformation ()
 
virtual ~Conformation ()
 
 Conformation (Conformation const &src)
 
void clear ()
 
void debug_residue_torsions (bool verbose=false) const
 
void show_residue_connections () const
 
void show_residue_connections (std::ostream &os) const
 
bool sequence_matches (Conformation const &other) const
 
Size size () const
 
bool empty () const
 
bool is_residue_typeset (std::string tag) const
 
bool is_fullatom () const
 
bool is_centroid () const
 
bool is_membrane () const
 
bool contains_carbohydrate_residues () const
 
void contains_carbohydrate_residues (bool const setting)
 
Size chain_end (Size const chain) const
 
Size chain_begin (Size const chain) const
 
Size num_chains () const
 
utility::vector1< Size > const & chain_endings () const
 
void chain_endings (utility::vector1< Size > const &endings)
 
void insert_chain_ending (Size const seqpos)
 
void delete_chain_ending (Size const seqpos)
 
void reset_chain_endings ()
 
void chains_from_termini ()
 
char secstruct (Size const seqpos) const
 
void set_membrane_info (membrane::MembraneInfoOP mem_info)
 
membrane::MembraneInfoOP membrane_info ()
 
membrane::MembraneInfoOP membrane_info () const
 
void update_membrane_position (Vector center, Vector normal)
 
void check_valid_membrane () const
 
virtual FoldTree const & fold_tree () const
 
AtomTree const & atom_tree () const
 
chemical::AA const & aa (Size const seqpos) const
 
Residue const & residue (Size const seqpos) const
 
chemical::ResidueType const & residue_type (Size const seqpos) const
 
ResidueCAPs const_residues () const
 
void insert_residue_by_jump (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false)
 
void insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false)
 
void append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false)
 
void append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 
void safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 
void prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 
void safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 
void delete_polymer_residue (Size const seqpos)
 
void delete_residue_slow (Size const seqpos)
 
void delete_residue_range_slow (Size const range_begin, Size const range_end)
 
virtual utility::vector1< boolget_residue_mask () const
 
virtual Real get_residue_weight (core::Size, core::Size) const
 
void detect_bonds ()
 
void detect_pseudobonds ()
 
void declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2)
 
void rebuild_polymer_bond_dependent_atoms_this_residue_only (Size const seqpos)
 
void rebuild_polymer_bond_dependent_atoms (Size const seqpos)
 
void rebuild_residue_connection_dependent_atoms (Size const seqpos, Size const connid)
 
AtomID inter_residue_connection_partner (Size const seqpos, int const connection_index) const
 
utility::vector1
< core::id::AtomID
bonded_neighbor_all_res (core::id::AtomID atomid, bool virt=false) const
 
void fill_missing_atoms (id::AtomID_Mask missing)
 
bool atom_is_backbone_norefold (Size const pos, Size const atomno) const
 
void set_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt)
 
kinematics::RT get_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2) const
 
void set_jump_atom_stub_id (id::StubID const &id)
 
kinematics::Stub stub_from_id (id::StubID const &id) const
 
kinematics::Stub upstream_jump_stub (int const jump_number) const
 
kinematics::Stub downstream_jump_stub (int const jump_number) const
 
void set_polymeric_connection (Size res_id_lower, Size res_id_upper)
 
void set_noncanonical_connection (Size res_id_lower, Size lr_conn_id, Size res_id_upper, Size ur_conn_id)
 
void update_polymeric_connection (Size const lower_seqpos, bool const update_connection_dep_atoms=false)
 
void update_noncanonical_connection (Size const lower_seqpos, Size const lr_conn_id, Size const upper_seqpos, Size const ur_conn_id)
 
virtual void detect_disulfides ()
 
void fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds)
 
void copy_segment (Size const size, Conformation const &src, Size const begin, Size const src_begin)
 
void insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)
 
Real dof (DOF_ID const &id) const
 
Real torsion (TorsionID const &id) const
 
Real torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const
 
Real bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const
 
Real bond_length (AtomID const &atom1, AtomID const &atom2) const
 
const Jumpjump (int const jump_number) const
 
const Jumpjump (AtomID const &id) const
 
PointPosition const & xyz (AtomID const &id) const
 
virtual void set_xyz (AtomID const &id, PointPosition const &position)
 
virtual void batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position)
 
virtual void batch_get_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const
 
void insert_ideal_geometry_at_polymer_bond (Size const seqpos)
 
void insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)
 
void update_actcoords ()
 
void update_actcoord (Size resid)
 
void update_orbital_coords (Residue &rsd) const
 
void update_orbital_coords (Size resid)
 
DOF_ID dof_id_from_torsion_id (TorsionID const &id) const
 
id::AtomID jump_atom_id (int const jump_number) const
 
bool get_torsion_angle_atom_ids (TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
 
bool get_jump_atom_ids (core::Size const jump_number, AtomID &upstream_id, AtomID &downstream_id) const
 
void update_domain_map (DomainMap &domain_map) const
 
bool structure_moved () const
 
void reset_structure_moved () const
 
void reset_move_data ()
 
utility::signals::Link attach_connection_obs (MemFn fn, Ptr ptr) const
 
bool detach_connection_obs (MemFn fn, Ptr ptr) const
 
utility::signals::Link attach_general_obs (MemFn fn, Ptr ptr) const
 
bool detach_general_obs (MemFn fn, Ptr ptr) const
 
utility::signals::Link attach_identity_obs (MemFn fn, Ptr ptr) const
 
bool detach_identity_obs (MemFn fn, Ptr ptr) const
 
utility::signals::Link attach_length_obs (MemFn fn, Ptr ptr) const
 
bool detach_length_obs (MemFn fn, Ptr ptr) const
 
utility::signals::Link attach_xyz_obs (MemFn fn, Ptr ptr) const
 
bool detach_xyz_obs (MemFn fn, Ptr ptr) const
 
void clear_observers ()
 
void receive_observers_from (Conformation const &src)
 
void debug_pause (bool const flag) const
 
bool debug_pause () const
 
void buffer_signals ()
 
void block_signals ()
 
void unblock_signals ()
 
bool buffering_signals () const
 
bool blocking_signals () const
 

Private Types

typedef
core::conformation::Conformation 
Parent
 
typedef
core::environment::SequenceAnnotationCOP 
SequenceAnnotationCOP
 

Private Member Functions

 ProtectedConformation (EnvironmentCAP, core::conformation::Conformation const &)
 
bool verify (core::id::TorsionID const &)
 
bool verify (core::id::DOF_ID const &)
 
bool verify_jump (core::id::AtomID const &)
 
bool verify_backbone (Size const &seqpos)
 
void fail_verification (std::string const &str)
 
template<typename Param >
void replace_residue_sandbox (Size const seqpos, Residue const &new_rsd, Param)
 
void push_passport (core::environment::DofPassportCOP)
 
core::environment::DofPassportCOP pop_passport ()
 
bool has_passport () const
 
void set_environment (EnvironmentCAP)
 
void attach_annotation (SequenceAnnotationCOP)
 

Private Attributes

std::stack
< core::environment::DofPassportCOP
unlocks_
 
SequenceAnnotationCOP annotations_
 
EnvironmentCAP env_
 
bool environment_exists_
 

Friends

class DofUnlock
 
class Environment
 
class EnvClaimBroker
 

Additional Inherited Members

- Public Types inherited from core::conformation::Conformation
typedef kinematics::Jump Jump
 
typedef kinematics::FoldTree FoldTree
 
typedef kinematics::FoldTreeOP FoldTreeOP
 
typedef kinematics::AtomTree AtomTree
 
typedef kinematics::AtomTreeOP AtomTreeOP
 
typedef id::AtomID AtomID
 
typedef id::AtomID_Mask AtomID_Mask
 
typedef id::DOF_ID DOF_ID
 
typedef id::TorsionID TorsionID
 
typedef kinematics::DomainMap DomainMap
 
typedef
core::conformation::signals::ConnectionEvent 
ConnectionEvent
 
typedef
core::conformation::signals::GeneralEvent 
GeneralEvent
 
typedef
core::conformation::signals::IdentityEvent 
IdentityEvent
 
typedef
core::conformation::signals::LengthEvent 
LengthEvent
 
typedef
core::conformation::signals::XYZEvent 
XYZEvent
 
typedef std::map< id::AtomID,
Vector
FragXYZ
 
typedef std::map< id::StubID,
kinematics::RT
FragRT
 
- Protected Attributes inherited from core::conformation::Conformation
ResidueOPs residues_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::environment::ProtectedConformation::ProtectedConformation ( ProtectedConformation const &  src)

References environment().

Referenced by clone().

protocols::environment::ProtectedConformation::~ProtectedConformation ( )
virtual
protocols::environment::ProtectedConformation::ProtectedConformation ( EnvironmentCAP  env,
core::conformation::Conformation const &  src 
)
private

References environment().

Member Function Documentation

SequenceAnnotationCOP protocols::environment::ProtectedConformation::annotations ( ) const
inline
void protocols::environment::ProtectedConformation::append_polymer_residue_after_seqpos ( core::conformation::Residue const &  ,
Size const  ,
bool const   
)
virtual
void protocols::environment::ProtectedConformation::append_residue_by_jump ( core::conformation::Residue const &  ,
Size const  ,
std::string const &  = "",
std::string const &  = "",
bool const  = false 
)
virtual

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::attach_annotation ( SequenceAnnotationCOP  annotations)
private
void protocols::environment::ProtectedConformation::batch_set_xyz ( utility::vector1< AtomID > const &  id,
utility::vector1< core::PointPosition > const &  position 
)
virtual
void protocols::environment::ProtectedConformation::chain_endings ( utility::vector1< Size > const &  )
virtual
void protocols::environment::ProtectedConformation::chains_from_termini ( )
virtual
void protocols::environment::ProtectedConformation::clear ( )
virtual
core::conformation::ConformationOP protocols::environment::ProtectedConformation::clone ( ) const
virtual
void protocols::environment::ProtectedConformation::declare_chemical_bond ( Size const  ,
std::string const &  ,
Size const  ,
std::string const &   
)
virtual
void protocols::environment::ProtectedConformation::delete_chain_ending ( Size const  )
virtual
void protocols::environment::ProtectedConformation::delete_polymer_residue ( Size const  )
virtual
void protocols::environment::ProtectedConformation::delete_residue_range_slow ( Size const  range_begin,
Size const  range_end 
)
virtual
void protocols::environment::ProtectedConformation::delete_residue_slow ( Size const  )
virtual
void protocols::environment::ProtectedConformation::env_destruction ( )
inline
EnvironmentCAP protocols::environment::ProtectedConformation::environment ( ) const
void protocols::environment::ProtectedConformation::fail_verification ( std::string const &  str)
inlineprivate
void protocols::environment::ProtectedConformation::fill_missing_atoms ( core::id::AtomID_Mask  missing)
virtual
void protocols::environment::ProtectedConformation::fix_disulfides ( utility::vector1< std::pair< Size, Size > >  )
virtual
void protocols::environment::ProtectedConformation::fold_tree ( FoldTree const &  )
virtual

Reimplemented from core::conformation::Conformation.

bool protocols::environment::ProtectedConformation::has_passport ( ) const
privatevirtual

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::insert_chain_ending ( Size const  )
virtual
void protocols::environment::ProtectedConformation::insert_conformation_by_jump ( Conformation const &  ,
Size const  ,
Size const  ,
Size const  ,
Size const  ,
std::string const &  = "",
std::string const &  = "" 
)
virtual

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::insert_fragment ( core::id::StubID const &  instub_id,
FragRT const &  outstub_transforms,
FragXYZ const &  frag_xyz 
)
virtual

References runtime_assert.

void protocols::environment::ProtectedConformation::insert_ideal_geometry_at_polymer_bond ( Size const  seqpos)
virtual
void protocols::environment::ProtectedConformation::insert_ideal_geometry_at_residue_connection ( Size const  pos1,
Size const  connid1 
)
virtual
virtual bool protocols::environment::ProtectedConformation::is_protected ( ) const
inlinevirtual

Reimplemented from core::conformation::Conformation.

Conformation & protocols::environment::ProtectedConformation::operator= ( Conformation const &  src)
virtual
DofPassportCOP protocols::environment::ProtectedConformation::pop_passport ( )
privatevirtual

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::prepend_polymer_residue_before_seqpos ( core::conformation::Residue const &  ,
Size const  ,
bool const   
)
virtual
void protocols::environment::ProtectedConformation::push_passport ( core::environment::DofPassportCOP  passport)
privatevirtual

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::rebuild_polymer_bond_dependent_atoms ( Size const  )
virtual
void protocols::environment::ProtectedConformation::replace_residue ( Size const  seqpos,
core::conformation::Residue const &  new_rsd,
utility::vector1< std::pair< std::string, std::string > > const &  atom_pairs 
)
virtual

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::replace_residue ( Size const  seqpos,
Residue const &  new_rsd,
bool const  orient_backbone 
)
virtual

Reimplemented from core::conformation::Conformation.

template<typename Param >
void protocols::environment::ProtectedConformation::replace_residue_sandbox ( Size const  seqpos,
Residue const &  new_rsd,
Param  p 
)
private
void protocols::environment::ProtectedConformation::reset_chain_endings ( )
virtual
void protocols::environment::ProtectedConformation::reset_move_data ( )
virtual
SequenceAnnotationCOP protocols::environment::ProtectedConformation::resolver ( ) const
void protocols::environment::ProtectedConformation::safely_append_polymer_residue_after_seqpos ( core::conformation::Residue const &  ,
Size const  ,
bool const   
)
virtual
void protocols::environment::ProtectedConformation::safely_prepend_polymer_residue_before_seqpos ( core::conformation::Residue const &  ,
Size const  ,
bool const   
)
virtual
bool protocols::environment::ProtectedConformation::same_type_as_me ( Conformation const &  other,
bool  recurse 
) const
virtual
void protocols::environment::ProtectedConformation::set_bond_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
core::Real const  setting 
)
virtual
void protocols::environment::ProtectedConformation::set_bond_length ( AtomID const &  atom1,
AtomID const &  atom2,
core::Real const  setting 
)
virtual
void protocols::environment::ProtectedConformation::set_dof ( DOF_ID const &  id,
core::Real const  setting 
)
virtual
void protocols::environment::ProtectedConformation::set_environment ( EnvironmentCAP  env)
private
void protocols::environment::ProtectedConformation::set_jump ( AtomID const &  id,
core::kinematics::Jump const &  new_jump 
)
virtual
void protocols::environment::ProtectedConformation::set_jump ( int const  jump_number,
core::kinematics::Jump const &  new_jump 
)
virtual
void protocols::environment::ProtectedConformation::set_polymeric_connection ( Size  ,
Size   
)
virtual
void protocols::environment::ProtectedConformation::set_secstruct ( Size const  seqpos,
char const  setting 
)
virtual
void protocols::environment::ProtectedConformation::set_stub_transform ( core::id::StubID const &  stub_id1,
core::id::StubID const &  stub_id2,
core::kinematics::RT const &  target_rt 
)
virtual

References utility::to_string().

void protocols::environment::ProtectedConformation::set_torsion ( TorsionID const &  id,
core::Real const  setting 
)
virtual
void protocols::environment::ProtectedConformation::set_torsion_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
AtomID const &  atom4,
core::Real const  setting,
bool  quiet = false 
)
virtual
void protocols::environment::ProtectedConformation::set_xyz ( AtomID const &  id,
core::PointPosition const &  position 
)
virtual
bool protocols::environment::ProtectedConformation::verify ( core::id::TorsionID const &  id)
inlineprivate

References core::id::DOF_ID::valid().

Referenced by set_torsion().

bool protocols::environment::ProtectedConformation::verify ( core::id::DOF_ID const &  id)
inlineprivate
bool protocols::environment::ProtectedConformation::verify_backbone ( Size const &  seqpos)
inlineprivate
bool protocols::environment::ProtectedConformation::verify_jump ( core::id::AtomID const &  a_id)
inlineprivate

References core::id::RB1, and core::id::RB6.

Referenced by set_jump().

Friends And Related Function Documentation

friend class DofUnlock
friend
friend class EnvClaimBroker
friend
friend class Environment
friend

Member Data Documentation

SequenceAnnotationCOP protocols::environment::ProtectedConformation::annotations_
private

Referenced by operator=().

EnvironmentCAP protocols::environment::ProtectedConformation::env_
private

Referenced by environment(), and operator=().

bool protocols::environment::ProtectedConformation::environment_exists_
private
std::stack<core::environment::DofPassportCOP> protocols::environment::ProtectedConformation::unlocks_
private

Referenced by operator=().


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