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core::kinematics::tree::Atom Class Referenceabstract

Kinematics Atom interface class. More...

#include <Atom.hh>

Inheritance diagram for core::kinematics::tree::Atom:
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Public Types

typedef PointPosition Position
 
typedef utility::vector0< AtomOPAtoms
 
typedef Atoms::ConstIterator Atoms_ConstIterator
 
typedef Atoms::Iterator Atoms_Iterator
 
typedef numeric::xyzMatrix< RealMatrix
 
typedef id::DOF_Type DOF_Type
 
typedef id::DOF_ID DOF_ID
 
typedef id::AtomID AtomID
 
typedef id::AtomID_Mask AtomID_Mask
 
typedef id::DOF_ID_Mask DOF_ID_Mask
 
typedef void iterator_category
 
typedef void difference_type
 

Public Member Functions

AtomCOP get_self_ptr () const
 
AtomOP get_self_ptr ()
 
AtomCAP get_self_weak_ptr () const
 
AtomAP get_self_weak_ptr ()
 
virtual void dfs (AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const =0
 Perform a depth-first traversal of the tree that would be effected by a DOF change from this atom. Stop at atoms that have already been traversed. More...
 
virtual void update_xyz_coords ()=0
 The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded. More...
 
virtual void update_xyz_coords (Stub &stub)=0
 update xyz coords from stub and internal coords and More...
 
virtual void update_internal_coords (Stub &stub, bool const recursive=true)=0
 update internal coords from stub and xyz coords More...
 
virtual void update_internal_coords (bool const recursive)=0
 calculate my input_stub from the current xyz's and use that input_stub to update my torsions More...
 
virtual void update_stub (Stub &stub) const =0
 update the stub without actually updating coordinates More...
 
virtual void copy_coords (Atom const &src)=0
 copy DOFs and xyz coords from src Atom More...
 
virtual Real dof (DOF_Type const type) const =0
 get dof More...
 
virtual void set_dof (DOF_Type const type, Real const value)=0
 set dof, use "set_" syntax since we have multiple dof's More...
 
virtual void set_dof (DOF_Type const type, Real const value, AtomDOFChangeSet &set)=0
 set dof, use "set_" syntax since we have multiple dof's – for use in output-sensitive refold routine More...
 
virtual Jump const & jump () const =0
 get Jump More...
 
virtual void jump (Jump const &jump_in)=0
 set Jump More...
 
virtual void jump (Jump const &jump_in, AtomDOFChangeSet &set)=0
 set Jump – for use in output-sensitive refolding More...
 
virtual AtomOP clone (AtomAP parent_in, AtomPointer2D &atom_pointer) const =0
 copy atom with new memory allocation More...
 
virtual void setup_min_map (DOF_ID &last_torsion, DOF_ID_Mask const &move_map, MinimizerMapBase &min_map) const =0
 
virtual void get_dof_axis_and_end_pos (Vector &axis, Position &end_pos, DOF_Type const type) const =0
 
virtual bool is_jump () const =0
 atom is a jump atom? More...
 
virtual bool keep_1st_child_pos () const =0
 when other atoms are inserted insert after 1st child if available. –> this enables us to keep a stub of Downstream Jump atoms inside a single residue More...
 
virtual bool keep_dof_fixed (DOF_Type const ) const
 DoF should be fixed for this atom? More...
 
virtual void show () const =0
 dump out AtomID for this atom, its parent and all its offspring More...
 
virtual void show (int const &) const =0
 dump out AtomID for this atom, its parent and all its offspring up to n_level More...
 
virtual Real dihedral_between_bonded_children (Atom const &child1, Atom const &child2) const =0
 dihedral angle between two bonded children to this atom More...
 
virtual void update_domain_map (int &current_color, int &biggest_color, DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &atom_moved) const =0
 
virtual Atoms_ConstIterator atoms_begin () const =0
 
virtual Atoms_ConstIterator atoms_end () const =0
 
virtual Atoms_Iterator atoms_begin ()=0
 
virtual Atoms_Iterator atoms_end ()=0
 
virtual Size n_atom () const =0
 
virtual void append_atom (AtomOP)=0
 
virtual void delete_atom (AtomOP)=0
 
virtual void insert_atom (AtomOP)=0
 
virtual void insert_atom (AtomOP, int const )=0
 
virtual void replace_atom (AtomOP const old_atom, AtomOP const new_atom)=0
 
virtual AtomCOP get_nonjump_atom (Size const i) const =0
 
virtual Size n_children () const =0
 
virtual Size n_nonjump_children () const =0
 
virtual AtomCOP child (Size const k) const =0
 
virtual AtomOP child (Size const k)=0
 
virtual Size child_index (AtomCOP child) const =0
 the atom-index of this child More...
 
virtual Size raw_child_index (Atom const *child) const =0
 the atom-index of this child More...
 
virtual bool downstream (AtomCOP atom1) const =0
 
virtual void steal_inversion (AtomOP)=0
 
virtual AtomID const & id () const =0
 Atom identifier. More...
 
virtual void id (AtomID const &id_in)=0
 AtomID assignment. More...
 
virtual AtomID const & atom_id () const =0
 Atom identifier. More...
 
virtual Position const & position () const =0
 Position. More...
 
virtual void position (Position const &position_a)=0
 Position assignment. More...
 
virtual Position const & xyz () const =0
 Position. More...
 
virtual void xyz (Position const &position_a)=0
 Position assignment. More...
 
virtual Length const & x () const =0
 x coordinate More...
 
virtual Length const & y () const =0
 y coordinate More...
 
virtual Length const & z () const =0
 z coordinate More...
 
virtual Length distance (Atom const &atom) const =0
 Distance to an Atom. More...
 
virtual Length distance_squared (Atom const &atom) const =0
 Distance squared to an Atom. More...
 
virtual void transform_Ax_plus_b_recursive (Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list)=0
 Transform atom and children by linear transformation. More...
 
virtual AtomCOP parent () const =0
 Parent atom pointer, NULL for root atom. More...
 
virtual void get_path_from_root (utility::vector1< AtomCAP > &path) const =0
 
virtual bool atom_is_on_path_from_root (AtomCOP atm) const =0
 
virtual void parent (AtomAP parent_in)=0
 parent assignment More...
 
virtual AtomOP parent ()=0
 Parent atom pointer, NULL for root atom. More...
 
virtual Stub get_stub () const =0
 Get stub information. More...
 
virtual Stub get_input_stub () const =0
 
virtual AtomCOP stub_atom1 () const =0
 
virtual AtomCOP stub_atom2 () const =0
 
virtual AtomCOP stub_atom3 () const =0
 
virtual AtomID const & stub_atom1_id () const =0
 
virtual AtomID const & stub_atom2_id () const =0
 
virtual AtomID const & stub_atom3_id () const =0
 
virtual AtomCOP input_stub_atom0 () const =0
 
virtual AtomCOP input_stub_atom1 () const =0
 
virtual AtomCOP input_stub_atom2 () const =0
 
virtual AtomCOP input_stub_atom3 () const =0
 
virtual AtomID const & input_stub_atom0_id () const =0
 
virtual AtomID const & input_stub_atom1_id () const =0
 
virtual AtomID const & input_stub_atom2_id () const =0
 
virtual AtomID const & input_stub_atom3_id () const =0
 
virtual AtomCOP previous_sibling () const =0
 
virtual AtomCOP previous_child (AtomCOP child) const =0
 
virtual AtomOP next_child (AtomCOP child)=0
 
virtual Atom const * raw_parent () const =0
 Rapid (increment-of-reference-count-avoiding) access to the parent atom pointer. More...
 
virtual Atom const * raw_previous_sibling () const =0
 Rapid (increment-of-reference-count-avoiding) access to the previous sibling pointer, i.e. the first child in the parent's children list to precede this atom. More...
 
virtual Atom const * raw_previous_child (Atom const *child) const =0
 Rapid (increment-of-reference-count-avoiding) access to the previous child pointer;. More...
 
virtual Atom const * raw_stub_atom1 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the fist stub atom. More...
 
virtual Atom const * raw_stub_atom2 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the second stub atom. More...
 
virtual Atom const * raw_stub_atom3 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the third stub atom. More...
 
virtual Atom const * raw_input_stub_atom0 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the 0th input stub atom;. More...
 
virtual Atom const * raw_input_stub_atom1 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the 1st input stub atom;. More...
 
virtual Atom const * raw_input_stub_atom2 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the 2nd input stub atom;. More...
 
virtual Atom const * raw_input_stub_atom3 () const =0
 Rapid (increment-of-reference-count-avoiding) access to the 3rd input stub atom;. More...
 
virtual Atom const * raw_get_nonjump_atom (Size const i) const =0
 Rapid (increment-of-reference-count-avoiding) access to the ith non-jump atom in this atom's list of children. More...
 
virtual bool stub_defined () const =0
 

Protected Member Functions

 Atom ()=default
 Default constructor. More...
 
Atomoperator= (Atom const &)=default
 Copy assignment. More...
 
virtual void update_child_torsions (AtomOP const child)=0
 
virtual Atoms_ConstIterator nonjump_atoms_begin () const =0
 
virtual Atoms_Iterator nonjump_atoms_begin ()=0
 

Friends

Length distance (Atom const &atom1, Atom const &atom2)
 Distance between two Atoms. More...
 
Length distance_squared (Atom const &atom1, Atom const &atom2)
 Distance squared between two Atoms. More...
 

Detailed Description

Kinematics Atom interface class.

Member Typedef Documentation

typedef utility::vector0< AtomOP > core::kinematics::tree::Atom::Atoms
typedef numeric::xyzMatrix< Real > core::kinematics::tree::Atom::Matrix

Constructor & Destructor Documentation

core::kinematics::tree::Atom::Atom ( )
inlineprotecteddefault

Default constructor.

Member Function Documentation

virtual void core::kinematics::tree::Atom::append_atom ( AtomOP  )
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::atom_id ( ) const
pure virtual
virtual bool core::kinematics::tree::Atom::atom_is_on_path_from_root ( AtomCOP  atm) const
pure virtual
virtual Atoms_ConstIterator core::kinematics::tree::Atom::atoms_begin ( ) const
pure virtual
virtual Atoms_Iterator core::kinematics::tree::Atom::atoms_begin ( )
pure virtual
virtual Atoms_ConstIterator core::kinematics::tree::Atom::atoms_end ( ) const
pure virtual
virtual Atoms_Iterator core::kinematics::tree::Atom::atoms_end ( )
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::child ( Size const  k) const
pure virtual
virtual AtomOP core::kinematics::tree::Atom::child ( Size const  k)
pure virtual
virtual Size core::kinematics::tree::Atom::child_index ( AtomCOP  child) const
pure virtual

the atom-index of this child

Implemented in core::kinematics::tree::Atom_.

virtual AtomOP core::kinematics::tree::Atom::clone ( AtomAP  parent_in,
AtomPointer2D atom_pointer 
) const
pure virtual

copy atom with new memory allocation

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::copy_coords ( Atom const &  src)
pure virtual

copy DOFs and xyz coords from src Atom

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::delete_atom ( AtomOP  )
pure virtual
virtual void core::kinematics::tree::Atom::dfs ( AtomDOFChangeSet changeset,
ResidueCoordinateChangeList res_change_list,
Size const  start_atom_index 
) const
pure virtual

Perform a depth-first traversal of the tree that would be effected by a DOF change from this atom. Stop at atoms that have already been traversed.

Implemented in core::kinematics::tree::Atom_, core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual Real core::kinematics::tree::Atom::dihedral_between_bonded_children ( Atom const &  child1,
Atom const &  child2 
) const
pure virtual

dihedral angle between two bonded children to this atom

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Length core::kinematics::tree::Atom::distance ( Atom const &  atom) const
pure virtual
virtual Length core::kinematics::tree::Atom::distance_squared ( Atom const &  atom) const
pure virtual

Distance squared to an Atom.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::distance_squared().

virtual Real core::kinematics::tree::Atom::dof ( DOF_Type const  type) const
pure virtual
virtual bool core::kinematics::tree::Atom::downstream ( AtomCOP  atom1) const
pure virtual
virtual void core::kinematics::tree::Atom::get_dof_axis_and_end_pos ( Vector axis,
Position end_pos,
DOF_Type const  type 
) const
pure virtual
virtual Stub core::kinematics::tree::Atom::get_input_stub ( ) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::get_nonjump_atom ( Size const  i) const
pure virtual
virtual void core::kinematics::tree::Atom::get_path_from_root ( utility::vector1< AtomCAP > &  path) const
pure virtual
AtomCOP core::kinematics::tree::Atom::get_self_ptr ( ) const
inline
AtomOP core::kinematics::tree::Atom::get_self_ptr ( )
inline
AtomCAP core::kinematics::tree::Atom::get_self_weak_ptr ( ) const
inline
AtomAP core::kinematics::tree::Atom::get_self_weak_ptr ( )
inline
virtual Stub core::kinematics::tree::Atom::get_stub ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::id ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::id ( AtomID const &  id_in)
pure virtual

AtomID assignment.

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom0 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom0_id ( ) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom1 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom1_id ( ) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom2 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom2_id ( ) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::input_stub_atom3 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::input_stub_atom3_id ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::insert_atom ( AtomOP  )
pure virtual
virtual void core::kinematics::tree::Atom::insert_atom ( AtomOP  ,
int  const 
)
pure virtual
virtual bool core::kinematics::tree::Atom::is_jump ( ) const
pure virtual
virtual Jump const& core::kinematics::tree::Atom::jump ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::jump ( Jump const &  jump_in)
pure virtual
virtual void core::kinematics::tree::Atom::jump ( Jump const &  jump_in,
AtomDOFChangeSet set 
)
pure virtual

set Jump – for use in output-sensitive refolding

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual bool core::kinematics::tree::Atom::keep_1st_child_pos ( ) const
pure virtual

when other atoms are inserted insert after 1st child if available. –> this enables us to keep a stub of Downstream Jump atoms inside a single residue

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual bool core::kinematics::tree::Atom::keep_dof_fixed ( DOF_Type  const) const
inlinevirtual

DoF should be fixed for this atom?

for DoFs that must be kept fixed due to topology of tree e.g., phi of stub_atoms for jump_atoms

Reimplemented in core::kinematics::tree::BondedAtom, core::kinematics::tree::JumpAtom, and core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Size core::kinematics::tree::Atom::n_atom ( ) const
pure virtual
virtual Size core::kinematics::tree::Atom::n_children ( ) const
pure virtual
virtual Size core::kinematics::tree::Atom::n_nonjump_children ( ) const
pure virtual
virtual AtomOP core::kinematics::tree::Atom::next_child ( AtomCOP  child)
pure virtual
virtual Atoms_ConstIterator core::kinematics::tree::Atom::nonjump_atoms_begin ( ) const
protectedpure virtual
virtual Atoms_Iterator core::kinematics::tree::Atom::nonjump_atoms_begin ( )
protectedpure virtual
Atom& core::kinematics::tree::Atom::operator= ( Atom const &  )
inlineprotecteddefault

Copy assignment.

virtual AtomCOP core::kinematics::tree::Atom::parent ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::parent ( AtomAP  parent_in)
pure virtual

parent assignment

Implemented in core::kinematics::tree::Atom_.

virtual AtomOP core::kinematics::tree::Atom::parent ( )
pure virtual

Parent atom pointer, NULL for root atom.

Implemented in core::kinematics::tree::Atom_.

virtual Position const& core::kinematics::tree::Atom::position ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::position ( Position const &  position_a)
pure virtual

Position assignment.

Implemented in core::kinematics::tree::Atom_.

virtual AtomCOP core::kinematics::tree::Atom::previous_child ( AtomCOP  child) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::previous_sibling ( ) const
pure virtual
virtual Size core::kinematics::tree::Atom::raw_child_index ( Atom const *  child) const
pure virtual

the atom-index of this child

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_get_nonjump_atom ( Size const  i) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the ith non-jump atom in this atom's list of children.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::JumpAtom::raw_stub_atom3(), and core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom0 ( ) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 0th input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom1 ( ) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 1st input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom2 ( ) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 2nd input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_input_stub_atom3 ( ) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the 3rd input stub atom;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::AtomTree::torsion_angle_dof_id().

virtual Atom const* core::kinematics::tree::Atom::raw_parent ( ) const
pure virtual
virtual Atom const* core::kinematics::tree::Atom::raw_previous_child ( Atom const *  child) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the previous child pointer;.

Implemented in core::kinematics::tree::Atom_.

Referenced by core::kinematics::tree::Atom_::raw_previous_sibling().

virtual Atom const* core::kinematics::tree::Atom::raw_previous_sibling ( ) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the previous sibling pointer, i.e. the first child in the parent's children list to precede this atom.

Implemented in core::kinematics::tree::Atom_.

virtual Atom const* core::kinematics::tree::Atom::raw_stub_atom1 ( ) const
pure virtual

Rapid (increment-of-reference-count-avoiding) access to the fist stub atom.

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

Referenced by core::kinematics::tree::Atom_::raw_input_stub_atom1(), and core::kinematics::tree::Atom_::raw_input_stub_atom3().

virtual Atom const* core::kinematics::tree::Atom::raw_stub_atom2 ( ) const
pure virtual
virtual Atom const* core::kinematics::tree::Atom::raw_stub_atom3 ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::replace_atom ( AtomOP const  old_atom,
AtomOP const  new_atom 
)
pure virtual
virtual void core::kinematics::tree::Atom::set_dof ( DOF_Type const  type,
Real const  value 
)
pure virtual

set dof, use "set_" syntax since we have multiple dof's

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::set_dof ( DOF_Type const  type,
Real const  value,
AtomDOFChangeSet set 
)
pure virtual

set dof, use "set_" syntax since we have multiple dof's – for use in output-sensitive refold routine

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::setup_min_map ( DOF_ID last_torsion,
DOF_ID_Mask const &  move_map,
MinimizerMapBase min_map 
) const
pure virtual
virtual void core::kinematics::tree::Atom::show ( ) const
pure virtual

dump out AtomID for this atom, its parent and all its offspring

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::show ( int const &  ) const
pure virtual

dump out AtomID for this atom, its parent and all its offspring up to n_level

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::steal_inversion ( AtomOP  )
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::stub_atom1 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::stub_atom1_id ( ) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::stub_atom2 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::stub_atom2_id ( ) const
pure virtual
virtual AtomCOP core::kinematics::tree::Atom::stub_atom3 ( ) const
pure virtual
virtual AtomID const& core::kinematics::tree::Atom::stub_atom3_id ( ) const
pure virtual
virtual bool core::kinematics::tree::Atom::stub_defined ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::transform_Ax_plus_b_recursive ( Matrix const &  A,
Vector const &  b,
ResidueCoordinateChangeList res_change_list 
)
pure virtual

Transform atom and children by linear transformation.

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::update_child_torsions ( AtomOP const  child)
protectedpure virtual
virtual void core::kinematics::tree::Atom::update_domain_map ( int &  current_color,
int &  biggest_color,
DomainMap domain_map,
AtomID_Mask const &  dof_moved,
AtomID_Mask const &  atom_moved 
) const
pure virtual
virtual void core::kinematics::tree::Atom::update_internal_coords ( Stub stub,
bool const  recursive = true 
)
pure virtual

update internal coords from stub and xyz coords

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::update_internal_coords ( bool const  recursive)
pure virtual

calculate my input_stub from the current xyz's and use that input_stub to update my torsions

Implemented in core::kinematics::tree::Atom_.

virtual void core::kinematics::tree::Atom::update_stub ( Stub stub) const
pure virtual

update the stub without actually updating coordinates

Implemented in core::kinematics::tree::JumpAtom, and core::kinematics::tree::BondedAtom.

virtual void core::kinematics::tree::Atom::update_xyz_coords ( )
pure virtual

The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded.

Implemented in core::kinematics::tree::Atom_, core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual void core::kinematics::tree::Atom::update_xyz_coords ( Stub stub)
pure virtual

update xyz coords from stub and internal coords and

Implemented in core::kinematics::tree::BondedAtom, and core::kinematics::tree::JumpAtom.

virtual Length const& core::kinematics::tree::Atom::x ( ) const
pure virtual

x coordinate

Implemented in core::kinematics::tree::Atom_.

virtual Position const& core::kinematics::tree::Atom::xyz ( ) const
pure virtual
virtual void core::kinematics::tree::Atom::xyz ( Position const &  position_a)
pure virtual

Position assignment.

Implemented in core::kinematics::tree::Atom_.

virtual Length const& core::kinematics::tree::Atom::y ( ) const
pure virtual

y coordinate

Implemented in core::kinematics::tree::Atom_.

virtual Length const& core::kinematics::tree::Atom::z ( ) const
pure virtual

z coordinate

Implemented in core::kinematics::tree::Atom_.

Friends And Related Function Documentation

Length distance ( Atom const &  atom1,
Atom const &  atom2 
)
friend

Distance between two Atoms.

Length distance_squared ( Atom const &  atom1,
Atom const &  atom2 
)
friend

Distance squared between two Atoms.


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