Rosetta 3.4
Public Types | Public Member Functions
core::conformation::Conformation Class Reference

A container of Residues and the kinematics to manage them. More...

#include <Conformation.hh>

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List of all members.

Public Types

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

Public Member Functions

 Conformation ()
 HIGHLY HIGHLY ILLEGAL ACCESS GRANTED TO CONFORMATION DATA. This function will be removed very very shortly.
virtual ~Conformation ()
 default destructor
 Conformation (Conformation const &src)
 copy constructor
virtual Conformationoperator= (Conformation const &src)
 operator
virtual ConformationOP clone () const
 clone the conformation
virtual bool same_type_as_me (Conformation const &other, bool recurse) const
bool sequence_matches (Conformation const &other) const
 do the names of all residues in this and src match?
Size size () const
 Returns the number of residues in the Conformation.
bool empty () const
 Returns true if this conformation does not have any residues.
Size chain_end (Size const chain) const
 Returns the position number of the last residue in <chain>
Size chain_begin (Size const chain) const
 Returns the position number of the first residue in <chain>
Size num_chains () const
 Returns the number of chains.
char secstruct (Size const seqpos) const
 Returns the secondary structure the position <seqpos>
virtual void set_secstruct (Size const seqpos, char const setting)
 Sets the secondary structure of the position <seqpos> to <setting>
virtual FoldTree const & fold_tree () const
 Returns the conformation's FoldTree.
AtomTree const & atom_tree () const
 Returns the conformation's AtomTree.
virtual void fold_tree (FoldTree const &fold_tree_in)
 Sets the FoldTree to <fold_tree_in>
utility::vector1< Size > const & chain_endings () const
 Returns the list of chain endings.
void chain_endings (utility::vector1< Size > const &endings)
 Sets the list of chain endings.
void insert_chain_ending (Size const seqpos)
 Marks <seqpos> as the end of a new chain.
void delete_chain_ending (Size const seqpos)
 Deletes <seqpos> from the list of chain endings.
void reset_chain_endings ()
 Resets chain data so that the Conformation is marked as a single chain.
void chains_from_termini ()
 Rederive the chains from the termini/polymer status.
chemical::AA const & aa (Size const seqpos) const
 Returns the AA enum for position <seqpos>
Residue const & residue (Size const seqpos) const
 access one of the residues; this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary.
chemical::ResidueType const & residue_type (Size const seqpos) const
 access one of the residue's types -- avoids coord/torsion update
virtual void append_residue_by_jump (conformation::Residue const &new_rsd, Size const anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool const start_new_chain=false)
 Append a new residue by a jump.
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="")
 Insert a new residue by jump.
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)
 Append a new residue by a bond.
void append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 glues to seqpos and perhaps also seqpos+1
void safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary
void prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 glues to seqpos and perhaps also seqpos-1
void safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary
virtual void replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone)
 replace residue
virtual void replace_residue (Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
 funtion to replace a residue based on superposition on
void delete_polymer_residue (Size const seqpos)
 Delete polymer residue at the given sequence position.
void delete_residue_slow (Size const seqpos)
 Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.
void delete_residue_range_slow (Size const range_begin, Size const range_end)
 Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.
void declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2)
 Declare that a chemical bond exists between two residues.
virtual void insert_conformation_by_jump (Conformation const &conf, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size const anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="")
 Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump.
void copy_segment (Size const size, Conformation const &src, Size const begin, Size const src_begin)
 copy a stretch of coordinates/torsions from another Conformation
void rebuild_polymer_bond_dependent_atoms (Size const seqpos)
 Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1.
void set_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt)
 Set the transform between two stubs -- only works if there's a jump between the two sets of stubatoms.
kinematics::RT get_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2) const
 get the transform between two stubs
void set_jump_atom_stub_id (id::StubID const &id)
kinematics::Stub stub_from_id (id::StubID const &id) const
void rebuild_residue_connection_dependent_atoms (Size const seqpos, Size const connid)
ResidueCAPs const_residues () const
 Inefficient -- constructs copy of residues_.
Real dof (DOF_ID const &id) const
 Returns the AtomTree degree of freedom (DOF) <id>
virtual void set_dof (DOF_ID const &id, Real const setting)
 Sets the AtomTree degree of freedom (DOF) <id> to <setting>
Real torsion (TorsionID const &id) const
 Returns the torsion angle <id>
virtual void set_torsion (TorsionID const &id, Real const setting)
 Sets the AtomTree DOF and the torsion in the corresponding Residue.
void insert_ideal_geometry_at_polymer_bond (Size const seqpos)
void insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)
virtual void set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting)
 Sets the torsion angle defined by <atom[1-4]> to <setting>
virtual void set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting)
 Sets the bond angle defined by <atom[1-3]> to <setting>
virtual void set_bond_length (AtomID const &atom1, AtomID const &atom2, Real const setting)
 Sets the cond length between <atom1> and <atom2> to <setting>
void insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)
Real torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const
 Returns the torsion angle defined by <atom[1-4]>
Real bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const
 Returns the bond angle defined by <atom[1-3]>
Real bond_length (AtomID const &atom1, AtomID const &atom2) const
 Returns the bond length between <atom1> and <atom2>
const Jumpjump (int const jump_number) const
 Returns the Jump with jump number <jump_number>
virtual void set_jump (int const jump_number, Jump const &new_jump)
 Sets the jump <jump_number> to <new_jump>
virtual void set_jump_now (int const jump_number, Jump const &new_jump)
 Sets a jump and forces immediate calculation of affected XYZ coords.
const Jumpjump (AtomID const &id) const
 access a jump
virtual void set_jump (AtomID const &id, Jump const &new_jump)
 set a jump
void set_polymeric_connection (Size res_id_lower, Size res_id_upper)
 identify polymeric connections
void update_polymeric_connection (Size const lower_seqpos)
 Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini.
void detect_bonds ()
void detect_pseudobonds ()
void detect_disulfides ()
 Detect existing disulfides from the protein structure.
void fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds)
 Assigns disulfide bonds based on a pre-determined list.
kinematics::Stub upstream_jump_stub (int const jump_number) const
 The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.
kinematics::Stub downstream_jump_stub (int const jump_number) const
 The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.
PointPosition const & xyz (AtomID const &id) const
 access xyz coordinates of an atom
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 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
 get four atoms which defined this torsion
void update_domain_map (DomainMap &domain_map) const
 Generate a domain_map from the current dof/xyz moved data.
bool structure_moved () const
 has the structure moved since the last call to reset_move_data or reset_structure_moved
void reset_structure_moved () const
 reset the structure_moved_ bool
void reset_move_data ()
 forget all the structure modifications
void clear ()
 clear data
void debug_residue_torsions (bool verbose=false) const
void show_residue_connections () const
 residue connections for debugging purposes
AtomID inter_residue_connection_partner (Size const seqpos, int const connection_index) const
 This returns the AtomID of the atom in the other residue to which the "connection_index"-th.
utility::vector1
< core::id::AtomID
bonded_neighbor_all_res (core::id::AtomID atomid, bool virt=false) const
 get all atoms bonded to another
void fill_missing_atoms (id::AtomID_Mask missing)
bool atom_is_backbone_norefold (Size const pos, Size const atomno) const
virtual utility::vector1< boolget_residue_mask () const
 returns a mask of residues to be used in scoring
virtual Real get_residue_weight (core::Size, core::Size) const
 returns a residue-pair weight
template<typename MemFn , typename Ptr >
utility::signals::Link attach_connection_obs (MemFn fn, Ptr ptr) const
 attach ConnectionEvent observer function
template<typename MemFn , typename Ptr >
bool detach_connection_obs (MemFn fn, Ptr ptr) const
 detach ConnectionEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link attach_general_obs (MemFn fn, Ptr ptr) const
 attach GeneralEvent observer function
template<typename MemFn , typename Ptr >
bool detach_general_obs (MemFn fn, Ptr ptr) const
 detach GeneralEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link attach_identity_obs (MemFn fn, Ptr ptr) const
 attach IdentityEvent observer function
template<typename MemFn , typename Ptr >
bool detach_identity_obs (MemFn fn, Ptr ptr) const
 detach IdentityEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link attach_length_obs (MemFn fn, Ptr ptr) const
 attach LengthEvent observer function
template<typename MemFn , typename Ptr >
bool detach_length_obs (MemFn fn, Ptr ptr) const
 detach LengthEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link attach_xyz_obs (MemFn fn, Ptr ptr) const
 attach XYZEvent observer function
template<typename MemFn , typename Ptr >
bool detach_xyz_obs (MemFn fn, Ptr ptr) const
 detach XYZEvent observer function
void clear_observers ()
 clear all observers
void receive_observers_from (Conformation const &src)
 fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation
void debug_pause (bool const flag) const
 wait for stdin after sending a GeneralEvent signal
bool debug_pause () const
 waiting for stdin after sending a GeneralEvent signal?
bool is_residue_typeset (std::string tag) const
 convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
bool is_fullatom () const
 convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
bool is_centroid () const
 convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
void buffer_signals ()
 block signals from being sent and buffer them to be sent after unblocking
void block_signals ()
 block signals from being sent
void unblock_signals ()
 allow signals to be sent
bool buffering_signals () const
 are signals being blocked and buffered?
bool blocking_signals () const
 are signals being blocked?

Detailed Description

A container of Residues and the kinematics to manage them.


Member Typedef Documentation


Constructor & Destructor Documentation

core::conformation::Conformation::Conformation ( )

HIGHLY HIGHLY ILLEGAL ACCESS GRANTED TO CONFORMATION DATA. This function will be removed very very shortly.

APL Removing accessor functions that voilate the data integrity guarantees of this class. Conformation forbids non-const access to its residues. Iterate from 1 to total_residue and request a Residue const & instead of iterating from res_begin to res_end. Returns a random-access iterator that points at the first residue in the Conformation. ResidueOPs::iterator res_begin() { return residues_.begin(); } Returns a random-access iterator that points just beyond the last residue in the Conformation. ResidueOPs::iterator res_end () { return residues_.end (); } constructor if you are using PyRosetta, you should NOT BE HERE!

Referenced by clone().

core::conformation::Conformation::~Conformation ( ) [virtual]

default destructor

core::conformation::Conformation::Conformation ( Conformation const &  src)

copy constructor

References size().


Member Function Documentation

chemical::AA const& core::conformation::Conformation::aa ( Size const  seqpos) const [inline]

Returns the AA enum for position <seqpos>

References size().

void core::conformation::Conformation::append_polymer_residue_after_seqpos ( Residue const &  new_rsd,
Size const  seqpos,
bool const  build_ideal_geometry 
)
void core::conformation::Conformation::append_residue_by_bond ( conformation::Residue const &  new_rsd,
bool const  build_ideal_geometry = false,
int  residue_connection_index = 0,
Size  anchor_pos = 0,
int  anchor_residue_connection_index = 0,
bool const  start_new_chain = false 
)

Append a new residue by a bond.

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues. Otherwise the incoming coordinates of new_rsd are preserved. Fires a LengthEvent::RESIDUE_APPEND signal.

References core::conformation::atom_id_to_named_atom_id(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::id::AtomID::atomno(), core::id::BOGUS_NAMED_ATOM_ID, core::conformation::Residue::clone(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::lower_connect_atom(), core::chemical::ResidueType::lower_connect_id(), core::conformation::orient_residue_for_ideal_bond(), rebuild_polymer_bond_dependent_atoms(), core::conformation::Residue::residue_connection(), size(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ResidueType::upper_connect_id().

Referenced by protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), and core::conformation::is_ideal_position().

void core::conformation::Conformation::append_residue_by_jump ( conformation::Residue const &  new_rsd,
Size const  anchor_pos,
std::string const &  anchor_atom = "",
std::string const &  root_atom = "",
bool const  start_new_chain = false 
) [virtual]

Append a new residue by a jump.

add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. Fires a LengthEvent::RESIDUE_APPEND signal.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References core::id::BOGUS_NAMED_ATOM_ID, and size().

Referenced by protocols::comparative_modeling::ExtraThreadingMover::apply(), and core::conformation::symmetry::setup_symmetric_conformation().

bool core::conformation::Conformation::atom_is_backbone_norefold ( Size const  pos,
Size const  atomno 
) const
AtomTree const& core::conformation::Conformation::atom_tree ( ) const [inline]
template<typename MemFn , typename Ptr >
utility::signals::Link core::conformation::Conformation::attach_connection_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

attach ConnectionEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( ConnectionEvent const & )
ptrpointer to observer object
Returns:
Link that can be used to manage the connection
Remarks:
ConnectionEvent observers will only be notified upon a change in the state of the connection with the Conformation, e.g. if the Conformation is destroyed or if the connection is being transferred. SUGGESTION: Try to use the Link objects that are returned when attaching observers instead of attaching via this function and watching for ConnectionEvents, as it typically makes connection management easier.

Referenced by core::pose::PDBInfo::attach_to(), and core::scoring::constraints::ConstraintSet::attach_to_conformation().

template<typename MemFn , typename Ptr >
utility::signals::Link core::conformation::Conformation::attach_general_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

attach GeneralEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( GeneralEvent const & )
ptrpointer to observer object
Returns:
Link that can be used to manage the connection
Remarks:
GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.
template<typename MemFn , typename Ptr >
utility::signals::Link core::conformation::Conformation::attach_identity_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

attach IdentityEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( IdentityEvent const & )
ptrpointer to observer object
Returns:
Link that can be used to manage the connection

Referenced by core::pose::PDBInfo::attach_to().

template<typename MemFn , typename Ptr >
utility::signals::Link core::conformation::Conformation::attach_length_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

attach LengthEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( LengthEvent const & )
ptrpointer to observer object
Returns:
Link that can be used to manage the connection

Referenced by protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::attach_impl(), core::pose::datacache::SpecialSegmentsObserver::attach_impl(), core::pose::datacache::LengthEventCollector::attach_impl(), protocols::forge::build::BuildInstruction::attach_to(), core::pose::PDBInfo::attach_to(), and core::scoring::constraints::ConstraintSet::attach_to_conformation().

template<typename MemFn , typename Ptr >
utility::signals::Link core::conformation::Conformation::attach_xyz_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

attach XYZEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( XYZEvent const & )
ptrpointer to observer object
Returns:
Link that can be used to manage the connection
void core::conformation::Conformation::batch_get_xyz ( utility::vector1< AtomID > const &  id,
utility::vector1< PointPosition > &  position 
) const [virtual]

References xyz().

void core::conformation::Conformation::batch_set_xyz ( utility::vector1< AtomID > const &  id,
utility::vector1< PointPosition > const &  position 
) [virtual]
void core::conformation::Conformation::block_signals ( )

block signals from being sent

Warning:
for safety, ConnectionEvent are never blocked
for safety, ConnectionEvents are never blocked
bool core::conformation::Conformation::blocking_signals ( ) const

are signals being blocked?

Real core::conformation::Conformation::bond_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3 
) const

Returns the bond angle defined by <atom[1-3]>

Referenced by protocols::topology_broker::fix_mainchain_connect(), and core::fragment::BBTorsionAndAnglesSRFD::steal().

Real core::conformation::Conformation::bond_length ( AtomID const &  atom1,
AtomID const &  atom2 
) const

Returns the bond length between <atom1> and <atom2>

Referenced by protocols::topology_broker::fix_mainchain_connect().

utility::vector1< id::AtomID > core::conformation::Conformation::bonded_neighbor_all_res ( core::id::AtomID  atomid,
bool  virt = false 
) const
void core::conformation::Conformation::buffer_signals ( )

block signals from being sent and buffer them to be sent after unblocking

bool core::conformation::Conformation::buffering_signals ( ) const

are signals being blocked and buffered?

Size core::conformation::Conformation::chain_begin ( Size const  chain) const [inline]

Returns the position number of the first residue in <chain>

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::ligand_docking::append_ligand_RMSD(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::qsar::qsarMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TetherLigand::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::ligand_docking::HeavyAtomFilter::apply(), protocols::filters::HeavyAtomFilter::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::filters::CompleteConnectionsFilter::apply(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::TerminusDistanceFilter::compute(), protocols::protein_interface_design::HbondsToResidueFilter::compute(), protocols::protein_interface_design::ResidueBurialFilter::compute(), protocols::protein_interface_design::NeighborTypeFilter::compute(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::seeded_abinitio::define_movemap_chains(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::pack::task::operation::util::find_neighbors_within_CB_cutoff(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_residues(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::loops::loopfinder(), main(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), MinimizeInterface(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), core::scoring::constraints::SiteConstraint::setup_csts(), setup_pert_foldtree(), core::pose::Pose::split_by_chain(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), protocols::protein_interface_design::transform_pose(), and protocols::fldsgn::CircularPermutation::which_chain().

Size core::conformation::Conformation::chain_end ( Size const  chain) const [inline]

Returns the position number of the last residue in <chain>

References size().

Referenced by protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::ligand_docking::append_ligand_RMSD(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::ligand_docking::HeavyAtomFilter::apply(), protocols::filters::HeavyAtomFilter::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::filters::CompleteConnectionsFilter::apply(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::TerminusDistanceFilter::compute(), protocols::protein_interface_design::ResidueBurialFilter::compute(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::seeded_abinitio::define_movemap_chains(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::pack::task::operation::util::find_neighbors_within_CB_cutoff(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::rosetta_scripts::foreach_movemap_tag(), core::pose::get_chain_residues(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), insert_conformation_by_jump(), protocols::loops::loopfinder(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), MinimizeInterface(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), core::scoring::constraints::SiteConstraint::setup_csts(), setup_pert_foldtree(), core::pose::Pose::split_by_chain(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), protocols::protein_interface_design::transform_pose(), and protocols::fldsgn::CircularPermutation::which_chain().

void core::conformation::Conformation::chain_endings ( utility::vector1< Size > const &  endings)

Sets the list of chain endings.

Remarks:
All positions must be strictly less than the number of residues in the Conformation, otherwise the routine will fail fast. Note that the last residue position is not counted as a chain end.

References size().

utility::vector1< Size > const & core::conformation::Conformation::chain_endings ( ) const
void core::conformation::Conformation::chains_from_termini ( )

Rederive the chains from the termini/polymer status.

References size().

void core::conformation::Conformation::clear ( )
void core::conformation::Conformation::clear_observers ( )

clear all observers

Remarks:
ConnectionEvent::DISCONNECT will be sent to all observers

References core::conformation::signals::ConnectionEvent::DISCONNECT.

ConformationOP core::conformation::Conformation::clone ( ) const [virtual]

clone the conformation

make a copy of this conformation( allocate actual memory for it )

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References Conformation().

ResidueCAPs core::conformation::Conformation::const_residues ( ) const

Inefficient -- constructs copy of residues_.

References size().

Referenced by insert_residue_by_jump(), and replace_residue().

void core::conformation::Conformation::copy_segment ( Size const  size,
Conformation const &  src,
Size const  begin,
Size const  src_begin 
)

copy a stretch of coordinates/torsions from another Conformation

copy a stretch of coordinates/torsions from another pose Fires IdentityEvent signals as residues are replaced.

References replace_residue(), residue(), and size().

void core::conformation::Conformation::debug_pause ( bool const  flag) const

wait for stdin after sending a GeneralEvent signal

bool core::conformation::Conformation::debug_pause ( ) const

waiting for stdin after sending a GeneralEvent signal?

void core::conformation::Conformation::debug_residue_torsions ( bool  verbose = false) const
void core::conformation::Conformation::declare_chemical_bond ( Size const  seqpos1,
std::string const &  atom_name1,
Size const  seqpos2,
std::string const &  atom_name2 
)
void core::conformation::Conformation::delete_chain_ending ( Size const  seqpos)

Deletes <seqpos> from the list of chain endings.

Remarks:
The last residue position is not counted as a chain ending.

Referenced by protocols::forge::build::SegmentRebuild::modify_impl().

void core::conformation::Conformation::delete_polymer_residue ( Size const  seqpos)

Delete polymer residue at the given sequence position.

delete a polymer residues Fires a LengthEvent::RESIDUE_DELETE signal.

References core::conformation::signals::LengthEvent::RESIDUE_DELETE, and size().

void core::conformation::Conformation::delete_residue_range_slow ( Size const  range_begin,
Size const  range_end 
)
void core::conformation::Conformation::delete_residue_slow ( Size const  seqpos)

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.

Delete a residue from the Conformation the slow way -- triggers a rebuild of the atomtree Fires a LengthEvent::RESIDUE_DELETE signal.

Note:
Could be upstream and/or downstream of a jump or chemical edge, or the root of the tree
Not well-tested. Expect funny behavior in new or different situations (email pbradley@fhcrc.org)

LOGIC: uses fold_tree.delete_seqpos to handle shifting the topology around if necessary, then calls setup_atom_tree

References core::conformation::signals::LengthEvent::RESIDUE_DELETE, and size().

Referenced by protocols::match::MatcherMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::relax::delete_virtual_residues(), core::pose::remove_ligand_canonical_residues(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), core::pose::remove_virtual_residues(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), and protocols::nonlocal::StarTreeBuilder::tear_down().

template<typename MemFn , typename Ptr >
bool core::conformation::Conformation::detach_connection_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

detach ConnectionEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( ConnectionEvent const & )
ptrpointer to observer object
Returns:
true if disconnect successful, false if connection does not exist
Remarks:
ConnectionEvent observers will only be notified upon a change in the state of the connection with the Conformation, e.g. if the Conformation is destroyed or if the connection is being transferred. SUGGESTION: Try to use the Link objects that are returned when attaching observers instead of attaching via this function and watching for ConnectionEvents, as it typically makes connection management easier.

Referenced by core::pose::PDBInfo::detach_from(), and core::scoring::constraints::ConstraintSet::detach_from_conformation().

template<typename MemFn , typename Ptr >
bool core::conformation::Conformation::detach_general_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

detach GeneralEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( GeneralEvent const & )
ptrpointer to observer object
Returns:
true if disconnect successful, false if connection does not exist
Remarks:
GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.
template<typename MemFn , typename Ptr >
bool core::conformation::Conformation::detach_identity_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

detach IdentityEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( IdentityEvent const & )
ptrpointer to observer object
Returns:
true if disconnect successful, false if connection does not exist

Referenced by core::pose::PDBInfo::detach_from().

template<typename MemFn , typename Ptr >
bool core::conformation::Conformation::detach_length_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

detach LengthEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( LengthEvent const & )
ptrpointer to observer object
Returns:
true if disconnect successful, false if connection does not exist

Referenced by core::pose::PDBInfo::detach_from(), and core::scoring::constraints::ConstraintSet::detach_from_conformation().

template<typename MemFn , typename Ptr >
bool core::conformation::Conformation::detach_xyz_obs ( MemFn  fn,
Ptr  ptr 
) const [inline]

detach XYZEvent observer function

Parameters:
fnpointer to observer's unary member function with signature void( XYZEvent const & )
ptrpointer to observer object
Returns:
true if disconnect successful, false if connection does not exist
void core::conformation::Conformation::detect_bonds ( )
void core::conformation::Conformation::detect_disulfides ( )

Detect existing disulfides from the protein structure.

Note:
Assumes full atom

looks at SG-SG distance. If the SG-SG are about 2.02 A apart, calls it a disulfide bond.

For full atom confomations, looks at SG-SG distance. If the SG-SG are about 2.02 A apart, calls it a disulfide bond. For centroid and other conformations, the less accurate CB-CB distance is used instead. In this case a CB-CB distance of 3.72 A is optimal.

References core::conformation::Residue::aa(), core::chemical::aa_cys, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atoms(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::chemical::FA_STANDARD, core::conformation::find_neighbors(), core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::has_variant_type(), make_table_of_pilot_apps::name, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_type(), size(), core::conformation::TR(), core::conformation::Residue::type(), xyz(), and core::conformation::Atom::xyz().

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::initialize_disulfide_bonds(), protocols::abinitio::AbrelaxApplication::relax(), protocols::forge::methods::restore_residues(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::protein_interface_design::transform_pose().

void core::conformation::Conformation::detect_pseudobonds ( )
Real core::conformation::Conformation::dof ( DOF_ID const &  id) const

Returns the AtomTree degree of freedom (DOF) <id>

Referenced by core::conformation::symmetry::SymmetricConformation::set_dof().

id::DOF_ID core::conformation::Conformation::dof_id_from_torsion_id ( TorsionID const &  id) const
kinematics::Stub core::conformation::Conformation::downstream_jump_stub ( int const  jump_number) const
bool core::conformation::Conformation::empty ( ) const [inline]

Returns true if this conformation does not have any residues.

void core::conformation::Conformation::fill_missing_atoms ( id::AtomID_Mask  missing)
void core::conformation::Conformation::fix_disulfides ( utility::vector1< std::pair< Size, Size > >  disulf_bonds)
void core::conformation::Conformation::fold_tree ( FoldTree const &  fold_tree_in) [virtual]

Sets the FoldTree to <fold_tree_in>

setup atom tree as well from the fold tree

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References core::kinematics::FoldTree::nres(), and size().

virtual FoldTree const& core::conformation::Conformation::fold_tree ( ) const [inline, virtual]

Returns the conformation's FoldTree.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

Referenced by protocols::comparative_modeling::hybridize::InsertChunkMover::change_anchor(), core::conformation::symmetry::SymmetryInfo::dependent_dofs(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight(), core::conformation::idealize_position(), protocols::comparative_modeling::hybridize::HybridizeFoldtreeDynamic::initialize(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::is_ideal_position(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::fibril::reorient_extended_fibril(), protocols::simple_filters::AlaScan::report(), protocols::protein_interface_design::AlaScan::report(), protocols::comparative_modeling::hybridize::HybridizeFoldtreeDynamic::reset(), core::conformation::symmetry::set_asymm_unit_fold_tree(), core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::symmetrize_fold_tree().

utility::vector1< bool > core::conformation::Conformation::get_residue_mask ( ) const [virtual]

returns a mask of residues to be used in scoring

Returns a mask of residues over which scoring is restricted. Only these residues will be used in constructing the neighbor list.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

Referenced by core::scoring::NeighborList::setup().

Real core::conformation::Conformation::get_residue_weight ( core::Size  ,
core::Size   
) const [virtual]

returns a residue-pair weight

Returns a weight to be used when scoring this residue.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

Referenced by core::scoring::NeighborList::setup().

kinematics::RT core::conformation::Conformation::get_stub_transform ( id::StubID const &  stub_id1,
id::StubID const &  stub_id2 
) const

get the transform between two stubs

Referenced by protocols::forge::build::ConnectRight::extract_rt(), and core::fragment::DownJumpSRFD::steal().

bool core::conformation::Conformation::get_torsion_angle_atom_ids ( TorsionID const &  tor_id,
AtomID id1,
AtomID id2,
AtomID id3,
AtomID id4 
) const
void core::conformation::Conformation::insert_chain_ending ( Size const  seqpos)

Marks <seqpos> as the end of a new chain.

Remarks:
The last residue position is not counted as a chain ending. Also increases the chain ID number by 1 for all residues upstream from seqpos.

References size().

Referenced by core::io::pdb::build_pose_as_is1(), core::pose::create_subpose(), core::fragment::make_pose_from_frags(), core::io::serialization::read_binary(), and protocols::fldsgn::CircularPermutation::split_chains().

void core::conformation::Conformation::insert_conformation_by_jump ( Conformation const &  conf,
Size const  insert_seqpos,
Size const  insert_jumppos,
Size const  anchor_pos,
Size const  anchor_jump_number = 0,
std::string const &  anchor_atom = "",
std::string const &  root_atom = "" 
) [virtual]

Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump.

Insert one conformation into another. Some tricky issues: (1) residue connections: assume all residue connections within conf carry over, after renumbering residues positions (2) jump numbers: see FoldTree::insert_fold_tree_by_jump (3) chains: chain endings are inserted before insert_seqpos, and after insert_seqpos+conf.size()-1 ie. at the beginning and ending of the inserted conformation; all internal chain endings from conf are used (4) atom_tree: setup_atom_tree is called to rebuild from scratch using the fold_tree

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References chain_end(), core::id::AtomID_Map< T >::clear(), core::conformation::Residue::clone(), fold_tree(), num_chains(), residue(), core::id::AtomID_Map< T >::resize(), and size().

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

void core::conformation::Conformation::insert_fragment ( id::StubID const &  instub_id,
FragRT const &  outstub_transforms,
FragXYZ const &  frag_xyz 
)
void core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond ( Size const  seqpos)
void core::conformation::Conformation::insert_ideal_geometry_at_residue_connection ( Size const  pos1,
Size const  connid1 
)

Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS -- NOT EVEN OMEGA IF ITS A PROTEIN

References rebuild_residue_connection_dependent_atoms(), set_bond_angle(), and set_bond_length().

void core::conformation::Conformation::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 = "" 
)
AtomID core::conformation::Conformation::inter_residue_connection_partner ( Size const  seqpos,
int const  connection_index 
) const [inline]

This returns the AtomID of the atom in the other residue to which the "connection_index"-th.

connection of residue seqpos is connected to.

References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::residue_connection(), and core::conformation::Residue::residue_connection_partner().

Referenced by core::chemical::ICoorAtomID::atom_id().

bool core::conformation::Conformation::is_centroid ( ) const

convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )

this is not a good test --Doug

References core::chemical::CENTROID, and is_residue_typeset().

bool core::conformation::Conformation::is_fullatom ( ) const

convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )

this is not a good test --Doug

References core::chemical::FA_STANDARD, and is_residue_typeset().

Referenced by core::conformation::form_disulfide().

bool core::conformation::Conformation::is_residue_typeset ( std::string  tag) const

convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )

this is nt a good test --Doug

References core::chemical::ResidueTypeSet::name(), residue_type(), core::chemical::ResidueType::residue_type_set(), and size().

Referenced by is_centroid(), and is_fullatom().

Conformation::Jump const & core::conformation::Conformation::jump ( int const  jump_number) const

Returns the Jump with jump number <jump_number>

References jump_atom_id().

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

Conformation::Jump const & core::conformation::Conformation::jump ( AtomID const &  id) const

access a jump

id::AtomID core::conformation::Conformation::jump_atom_id ( int const  jump_number) const
Size core::conformation::Conformation::num_chains ( ) const [inline]

Returns the number of chains.

Referenced by protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::EnergyPerResidueFilter::apply(), protocols::enzdes::LigInterfaceEnergyFilter::apply(), protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::ResidueBurialFilter::compute(), core::pose::conf2pdb_chain(), protocols::seeded_abinitio::define_movemap_chains(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), core::pose::get_chain_ids_from_chain(), core::pose::has_chain(), insert_conformation_by_jump(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), and protocols::fldsgn::CircularPermutation::which_chain().

Conformation & core::conformation::Conformation::operator= ( Conformation const &  src) [virtual]

operator

operator= implementation. If lengths & sequence of source and target are different, will fire a LengthEvent::INVALIDATE signal and then an IdentityEvent::INVALIDATE signal.

References clear(), core::conformation::signals::IdentityEvent::INVALIDATE, core::conformation::signals::LengthEvent::INVALIDATE, sequence_matches(), and size().

void core::conformation::Conformation::prepend_polymer_residue_before_seqpos ( Residue const &  new_rsd,
Size const  seqpos,
bool const  build_ideal_geometry 
)
void core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms ( Size const  seqpos)

Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1.

rebuilds the atoms that are dependent on the bond between seqpos an seqpos+1 for their torsion offset

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), and prepend_polymer_residue_before_seqpos().

void core::conformation::Conformation::rebuild_residue_connection_dependent_atoms ( Size const  seqpos,
Size const  connid 
)
Note:
This could be rewritten to avoid a refold using set_bond_angle, etc might be safer since by-xyz ignores possibility of propagating dependencies from the moving atoms...

References core::chemical::AtomICoor::build(), core::chemical::AtomICoor::depends_on_residue_connection(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), and set_xyz().

Referenced by insert_ideal_geometry_at_residue_connection().

void core::conformation::Conformation::receive_observers_from ( Conformation const &  src)

fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation

Parameters:
srcTake observers from this source Conformation.
Remarks:
Only observers that properly honor the TRANSFER event by re-attaching themselves to 'this' Conformation will be transferred.

References core::conformation::signals::ConnectionEvent::TRANSFER.

void core::conformation::Conformation::replace_residue ( Size const  seqpos,
Residue const &  new_rsd,
utility::vector1< std::pair< std::string, std::string > > const &  atom_pairs 
) [virtual]

funtion to replace a residue based on superposition on

function to replace a residue based on superposition on the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works Fires an IdentityEvent signal.

the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References core::conformation::Residue::orient_onto_residue(), and replace_residue().

void core::conformation::Conformation::replace_residue ( Size const  seqpos,
Residue const &  new_rsd_in,
bool const  orient_backbone 
) [virtual]
void core::conformation::Conformation::reset_chain_endings ( )

Resets chain data so that the Conformation is marked as a single chain.

Referenced by protocols::fldsgn::CircularPermutation::apply(), and protocols::domain_assembly::AssembleLinkerMover::apply().

void core::conformation::Conformation::reset_move_data ( )

forget all the structure modifications

called after domain map information is transferred to the Energies class

References core::id::AtomID_Map< T >::fill_with().

void core::conformation::Conformation::reset_structure_moved ( ) const [inline]

reset the structure_moved_ bool

Residue const& core::conformation::Conformation::residue ( Size const  seqpos) const [inline]

access one of the residues; this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary.

update coordinates and torsions for this and all other residues before allowing read access

References size().

Referenced by core::conformation::add_variant_type_to_conformation_residue(), core::conformation::annotated_atom_graph_from_conformation(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), core::conformation::atom_graph_from_conformation(), bonded_neighbor_all_res(), core::conformation::change_cys_state(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::ResidueDistanceFilter::compute(), protocols::protein_interface_design::ResidueBurialFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::star::copy_residues(), copy_segment(), debug_residue_torsions(), detect_bonds(), detect_disulfides(), detect_pseudobonds(), core::scoring::constraints::AtomPairConstraint::dist(), core::conformation::disulfide_bonds(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_residue_kinemage(), protocols::viewer::dump_structure_kinemage(), fix_disulfides(), core::conformation::form_disulfide(), protocols::pockets::PocketGrid::getRelaxResidues(), core::conformation::idealize_position(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::is_disulfide_bond(), core::conformation::is_ideal_position(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), protocols::pockets::PocketConstraint::PocketConstraint(), core::conformation::print_atom(), protocols::viewer::print_node(), core::conformation::symmetry::recenter(), core::conformation::remove_variant_type_from_conformation_residue(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), core::scoring::constraints::ConformationXYZ::residue(), core::conformation::symmetry::residue_center_of_mass(), core::conformation::residue_point_graph_from_conformation(), core::conformation::symmetry::return_nearest_residue(), protocols::pockets::PlaidFingerprint::rmsd(), sequence_matches(), protocols::pockets::PocketConstraint::set_target_res(), protocols::pockets::PocketConstraint::set_target_res_pdb(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::protein_interface_design::filters::RelativePoseFilter::thread_seq(), torsion(), and core::conformation::ConformationKinWriter::write_coords().

chemical::ResidueType const& core::conformation::Conformation::residue_type ( Size const  seqpos) const [inline]
void core::conformation::Conformation::safely_append_polymer_residue_after_seqpos ( Residue const &  new_rsd,
Size const  seqpos,
bool const  build_ideal_geometry 
)
void core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos ( Residue const &  new_rsd,
Size const  seqpos,
bool const  build_ideal_geometry 
)
bool core::conformation::Conformation::same_type_as_me ( Conformation const &  other,
bool  recurse 
) const [virtual]
char core::conformation::Conformation::secstruct ( Size const  seqpos) const [inline]

Returns the secondary structure the position <seqpos>

Returns:
character representing secondary structure; returns 'L' if the requested sequence position is larger than the length in the secondary structure array

Referenced by protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::methods::EnvEnergy::residue_energy(), and core::scoring::methods::CenPairEnergy::residue_pair_energy().

bool core::conformation::Conformation::sequence_matches ( Conformation const &  other) const

do the names of all residues in this and src match?

Am I composed of the same sequence of ResidueType objects as other? DANGER! Fails, unexpectedly, if a histidine pair has a different tautomerization. tex, 9/12/08 The above comment points out that this method isn't a clearly defined idea, because there are many ways that someone could imagine comparing the a sequence, including:

  • cutpoint variants
  • tautomers
  • disulfides For some applications, it's probably to get strings of the one-letter names of the sequence and compare those instead.

References residue(), size(), and core::conformation::Residue::type().

Referenced by operator=().

void core::conformation::Conformation::set_bond_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
Real const  setting 
) [virtual]
void core::conformation::Conformation::set_bond_length ( AtomID const &  atom1,
AtomID const &  atom2,
Real const  setting 
) [virtual]
void core::conformation::Conformation::set_dof ( DOF_ID const &  id,
Real const  setting 
) [virtual]

Sets the AtomTree degree of freedom (DOF) <id> to <setting>

Reimplemented in core::conformation::symmetry::SymmetricConformation.

Referenced by protocols::topology_broker::fix_internal_coords_of_siblings().

void core::conformation::Conformation::set_jump ( int const  jump_number,
Jump const &  new_jump 
) [virtual]

Sets the jump <jump_number> to <new_jump>

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References jump_atom_id(), and core::kinematics::Jump::ortho_check().

void core::conformation::Conformation::set_jump ( AtomID const &  id,
Jump const &  new_jump 
) [virtual]
void core::conformation::Conformation::set_jump_atom_stub_id ( id::StubID const &  id)
void core::conformation::Conformation::set_jump_now ( int const  jump_number,
Jump const &  new_jump 
) [virtual]

Sets a jump and forces immediate calculation of affected XYZ coords.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References jump_atom_id(), and core::kinematics::Jump::ortho_check().

void core::conformation::Conformation::set_polymeric_connection ( Size  res_id_lower,
Size  res_id_upper 
)

identify polymeric connections

identify polymeric connections The lower residue connects to the upper residue through its upper_connect connection The upper residue connects to the lower residue through its lower_connect connection

Referenced by update_polymeric_connection().

virtual void core::conformation::Conformation::set_secstruct ( Size const  seqpos,
char const  setting 
) [inline, virtual]

Sets the secondary structure of the position <seqpos> to <setting>

Sets secondary structure character of a sequence position. Will resize the secondary structure array if the requested sequence position is larger than the length of the array.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

void core::conformation::Conformation::set_stub_transform ( id::StubID const &  stub_id1,
id::StubID const &  stub_id2,
kinematics::RT const &  target_rt 
)
void core::conformation::Conformation::set_torsion ( TorsionID const &  id,
Real const  setting 
) [virtual]
void core::conformation::Conformation::set_torsion_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
AtomID const &  atom4,
Real const  setting 
) [virtual]
void core::conformation::Conformation::set_xyz ( AtomID const &  id,
PointPosition const &  position 
) [virtual]
void core::conformation::Conformation::show_residue_connections ( ) const
Size core::conformation::Conformation::size ( ) const [inline]

Returns the number of residues in the Conformation.

Referenced by aa(), core::conformation::annotated_atom_graph_from_conformation(), append_polymer_residue_after_seqpos(), append_residue_by_bond(), append_residue_by_jump(), core::conformation::atom_graph_from_conformation(), protocols::idealize::basic_idealize(), chain_end(), chain_endings(), chains_from_termini(), protocols::comparative_modeling::hybridize::InsertChunkMover::change_anchor(), Conformation(), const_residues(), copy_segment(), debug_residue_torsions(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), detect_bonds(), detect_disulfides(), detect_pseudobonds(), core::conformation::disulfide_bonds(), protocols::viewer::dump_residue_kinemage(), protocols::viewer::dump_structure_kinemage(), core::conformation::Residue::fill_missing_atoms(), fill_missing_atoms(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), fix_disulfides(), fold_tree(), core::conformation::idealize_position(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), insert_chain_ending(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), insert_residue_by_jump(), core::conformation::is_ideal_position(), is_residue_typeset(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), operator=(), prepend_polymer_residue_before_seqpos(), core::conformation::symmetry::recenter(), protocols::fibril::reorient_extended_fibril(), residue(), core::conformation::residue_point_graph_from_conformation(), residue_type(), sequence_matches(), core::conformation::symmetry::set_fold_tree_from_symm_data(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_scoring(), core::conformation::symmetry::setup_symmetric_conformation(), show_residue_connections(), core::conformation::symmetry::symmetrize_fold_tree(), update_actcoords(), update_domain_map(), update_polymeric_connection(), core::conformation::ConformationKinWriter::write_coords(), and core::chemical::ICoorAtomID::xyz().

bool core::conformation::Conformation::structure_moved ( ) const [inline]
kinematics::Stub core::conformation::Conformation::stub_from_id ( id::StubID const &  id) const
Real core::conformation::Conformation::torsion ( TorsionID const &  id) const
Real core::conformation::Conformation::torsion_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
AtomID const &  atom4 
) const

Returns the torsion angle defined by <atom[1-4]>

Referenced by protocols::topology_broker::fix_mainchain_connect().

void core::conformation::Conformation::unblock_signals ( )

allow signals to be sent

If unblocking after buffering, buffered/held signals will be sent.

void core::conformation::Conformation::update_actcoord ( Size  resid)
void core::conformation::Conformation::update_actcoords ( )

References size().

void core::conformation::Conformation::update_domain_map ( DomainMap domain_map) const

Generate a domain_map from the current dof/xyz moved data.

References size().

void core::conformation::Conformation::update_orbital_coords ( Residue rsd) const
void core::conformation::Conformation::update_orbital_coords ( Size  resid)
void core::conformation::Conformation::update_polymeric_connection ( Size const  lower_seqpos)

Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini.

work in progress void insert_chemical_chainbreak_between_polymer_residues( Size const lower_seqpos ) { ResidueOP lower_rsd( residues_[ lower_seqpos ] );

the type of the desired variant residue ResidueTypeSet const & rsd_set( lower_rsd->residue_type_set() );

ResidueType const & new_lower_rsd_type ( rsd_set.get_residue_type_with_variant_removed( lower_rsd.type(), UPPER_TERMINUS ) ); ResidueOP new_lower_rsd( ResidueFactory::create_residue( new_lower_rsd_type ) );

}

References core::conformation::Residue::chain(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), set_polymeric_connection(), and size().

Referenced by protocols::protein_interface_design::movers::copy_hotspot_to_pose(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs().

kinematics::Stub core::conformation::Conformation::upstream_jump_stub ( int const  jump_number) const
PointPosition const & core::conformation::Conformation::xyz ( AtomID const &  id) const

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