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Rosetta Core
2014.35
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Map from Atom identifiers to contained values class. More...
#include <AtomID_Map.hh>
Public Member Functions | |
AtomID_Map () | |
Default constructor with no arguments (PyRosetta workaround) More... | |
AtomID_Map (Value const &default_value_a) | |
Default constructor. More... | |
AtomID_Map (Size const n_res) | |
Number of residues constructor. More... | |
AtomID_Map (Size const n_res, Value const &default_value_a) | |
Number of residues constructor. More... | |
~AtomID_Map () | |
Destructor. More... | |
void | resize (Size const n_res) |
Resize to a given number of residues. More... | |
void | resize (Size const i_res, Size const n_atom) |
Resize the number of atoms of a residue and use the default fill value. More... | |
void | resize (Size const i_res, Size const n_atom, Value const &value) |
Resize the number of atoms of a residue and use a specified fill value. More... | |
void | fill () |
Fill the map with the default fill value. More... | |
void | fill_with (Value const &value) |
Fill the map with a specified fill value. More... | |
void | fill_with (Size const seqpos, Value const &value) |
Fill the map at position seqpos with a specified fill value. More... | |
ConstReference | get (AtomID const &id) const |
Get the value for an AtomID: Extend the map if necessary, filling with the default value Phil changing this to be a non-resizing function. More... | |
void | set (AtomID const &id, Value const &value) |
Set the value for an AtomID: Extend the map if necessary, filling with the default value. More... | |
void | finalize () |
Finalize after sizing all the vectors. More... | |
void | shrink () |
Shrink the vectors to remove unused capacity. More... | |
void | swap (AtomID_Map &s) |
swap( AtomID_Map ) More... | |
void | clear () |
Clear the map. More... | |
void | clear (Value const &default_value_a) |
Clear the map and set a new default value. More... | |
void | update_sequence_numbering (Size const new_size, utility::vector1< Size > const &old2new) |
Size | size () const |
Size. More... | |
Size | n_residue () const |
Number of residues (size) More... | |
Size | n_atom (Size const i_res) const |
Number of atoms in a residue. More... | |
bool | empty () const |
Empty? More... | |
Value const & | default_value () const |
Default value. More... | |
void | default_value (Value const &default_value_a) |
Set default value. More... | |
bool | has (AtomID const &id) const |
Is an element with this AtomID present? More... | |
ConstReference | operator[] (AtomID const &id) const |
AtomID_Map[ atom_id ] const. More... | |
Reference | operator[] (AtomID const &id) |
AtomID_Map[ atom_id ]. More... | |
ConstReference | operator() (AtomID const &id) const |
AtomID_Map( atom_id ) const. More... | |
Reference | operator() (AtomID const &id) |
AtomID_Map( atom_id ) More... | |
ConstReference | operator() (Size const i_res, Size const i_atom) const |
AtomID_Map( i_res, i_atom ) const. More... | |
Reference | operator() (Size const i_res, Size const i_atom) |
AtomID_Map( i_res, i_atom ) More... | |
AtomMap const & | operator[] (Size const i_res) const |
AtomID_Map[ i_res ] const. More... | |
AtomMap & | operator[] (Size const i_res) |
AtomID_Map[ i_res ]. More... | |
AtomMap const & | operator() (Size const i_res) const |
AtomID_Map( i_res ) const. More... | |
AtomMap & | operator() (Size const i_res) |
AtomID_Map( i_res ) More... | |
Private Attributes | |
Value | default_value_ |
Default value. More... | |
ResidueMap | res_map_ |
Map from Atom identifiers to values. More... | |
Friends | |
template<typename TF > | |
void | swap (AtomID_Map< TF > &a, AtomID_Map< TF > &b) |
swap( AtomID_Map, AtomID_Map ) More... | |
bool | operator== (AtomID_Map const &a, AtomID_Map const &b) |
AtomID_Map == AtomID_Map. More... | |
bool | operator!= (AtomID_Map const &a, AtomID_Map const &b) |
AtomID_Map != AtomID_Map. More... | |
Map from Atom identifiers to contained values class.
typedef utility::vector1< T > core::id::AtomID_Map< T >::AtomMap |
typedef AtomMap::const_reference core::id::AtomID_Map< T >::const_reference |
typedef AtomMap::ConstReference core::id::AtomID_Map< T >::ConstReference |
typedef AtomMap::reference core::id::AtomID_Map< T >::reference |
typedef AtomMap::Reference core::id::AtomID_Map< T >::Reference |
typedef utility::vector1< AtomMap > core::id::AtomID_Map< T >::ResidueMap |
typedef platform::Size core::id::AtomID_Map< T >::Size |
typedef AtomMap::size_type core::id::AtomID_Map< T >::size_type |
typedef T core::id::AtomID_Map< T >::Value |
typedef T core::id::AtomID_Map< T >::value_type |
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Default constructor with no arguments (PyRosetta workaround)
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Default constructor.
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Number of residues constructor.
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Number of residues constructor.
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Destructor.
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Clear the map.
Referenced by core::conformation::build_tree(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::conformation::Conformation::clear(), core::kinematics::AtomTree::clear(), core::scoring::sasa::SasaCalc::init(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Conformation::insert_conformation_by_jump(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), and core::kinematics::AtomTree::replace_residue_subtree().
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Clear the map and set a new default value.
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Default value.
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Set default value.
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Empty?
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Fill the map with the default fill value.
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Fill the map with a specified fill value.
Referenced by core::conformation::Conformation::reset_move_data().
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Fill the map at position seqpos with a specified fill value.
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Finalize after sizing all the vectors.
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Get the value for an AtomID: Extend the map if necessary, filling with the default value Phil changing this to be a non-resizing function.
Referenced by core::pack::figure_out_repackable_residues(), core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing(), and core::scoring::methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing().
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Is an element with this AtomID present?
Referenced by core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::eval_atom_derivative(), and core::kinematics::AtomTree::has().
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Number of atoms in a residue.
Referenced by core::scoring::calc_per_atom_sasa_sc(), and core::scoring::packing::initialize_AtomID_Map().
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Number of residues (size)
Referenced by core::scoring::calc_per_atom_sasa_sc(), core::scoring::sasa::get_sc_bb_sasa(), and core::scoring::sasa::get_sc_bb_sasa_per_res().
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AtomID_Map( atom_id ) const.
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AtomID_Map( atom_id )
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AtomID_Map( i_res, i_atom ) const.
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AtomID_Map( i_res, i_atom )
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AtomID_Map( i_res ) const.
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AtomID_Map( i_res )
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AtomID_Map[ atom_id ] const.
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AtomID_Map[ atom_id ].
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AtomID_Map[ i_res ] const.
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AtomID_Map[ i_res ].
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Resize to a given number of residues.
Referenced by core::conformation::build_tree(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::kinematics::AtomTree::delete_seqpos(), core::scoring::packing::initialize_AtomID_Map(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Conformation::insert_conformation_by_jump(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), and core::conformation::Conformation::residues_append().
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Resize the number of atoms of a residue and use the default fill value.
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Resize the number of atoms of a residue and use a specified fill value.
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Set the value for an AtomID: Extend the map if necessary, filling with the default value.
Referenced by core::sequence::calpha_superimpose_with_mapping(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), core::pose::convert_from_std_map(), core::conformation::setup_corresponding_atoms(), core::scoring::methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::scoring::methods::DipolarCouplingEnergy::setup_for_minimizing(), and core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::setup_for_minimizing().
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Shrink the vectors to remove unused capacity.
Referenced by core::id::AtomID_Map< Real >::finalize().
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Size.
Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::kinematics::AtomTree::AtomTree(), core::kinematics::AtomTree::find_root_from_atom_pointer(), core::scoring::packing::initialize_AtomID_Map(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::kinematics::AtomTree::replace_tree(), core::kinematics::AtomTree::size(), core::kinematics::AtomTree::update_atom_ids_from_atom_pointer(), and core::id::AtomID_Map< Real >::update_sequence_numbering().
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swap( AtomID_Map )
Referenced by core::id::AtomID_Map< Real >::update_sequence_numbering().
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Should move to .cc? if old2new[pos] == 0 , that position's mapping is lost if old2new[1...old_size] doesnt cover all of [1...new_size], the missed positions will have res_map_[pos].empty()
Referenced by core::kinematics::AtomTree::update_sequence_numbering(), and core::conformation::Conformation::update_sequence_numbering().
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AtomID_Map != AtomID_Map.
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AtomID_Map == AtomID_Map.
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swap( AtomID_Map, AtomID_Map )
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Default value.
Referenced by core::id::AtomID_Map< Real >::clear(), core::id::AtomID_Map< Real >::default_value(), core::id::AtomID_Map< Real >::fill(), core::id::AtomID_Map< Real >::get(), core::id::AtomID_Map< Real >::resize(), core::id::AtomID_Map< Real >::set(), and core::id::AtomID_Map< Real >::update_sequence_numbering().
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Map from Atom identifiers to values.
Referenced by core::id::AtomID_Map< Real >::clear(), core::id::AtomID_Map< Real >::empty(), core::id::AtomID_Map< Real >::fill(), core::id::AtomID_Map< Real >::fill_with(), core::id::AtomID_Map< Real >::get(), core::id::AtomID_Map< Real >::has(), core::id::AtomID_Map< Real >::n_atom(), core::id::AtomID_Map< Real >::n_residue(), core::id::AtomID_Map< Real >::operator()(), core::id::AtomID_Map< Real >::operator[](), core::id::AtomID_Map< Real >::resize(), core::id::AtomID_Map< Real >::set(), core::id::AtomID_Map< Real >::shrink(), core::id::AtomID_Map< Real >::size(), core::id::AtomID_Map< Real >::swap(), and core::id::AtomID_Map< Real >::update_sequence_numbering().