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core::kinematics::tree::BondedAtom Class Reference

an atom which are bonded to its parent, derived from Atom_ More...

#include <BondedAtom.hh>

Inheritance diagram for core::kinematics::tree::BondedAtom:
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Public Member Functions

 BondedAtom ()
 
void dfs (AtomDOFChangeSet &changeset, ResidueCoordinateChangeList &res_change_list, Size const start_atom_index) const override
 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. Will recurse on younger siblings if a phi on this atom has changed. More...
 
void update_xyz_coords () override
 The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded. Valid only if this atom is the maximal root of a subtree requiring coordinate updates – if any ancestor of this atom requires a coordinate update, then the Stub this atom generates for itself will be invalid. More...
 
void update_xyz_coords (Stub &stub) override
 update cartesian coordinates for this atom from its input stub and internal cooridnates More...
 
void update_internal_coords (std::deque< std::pair< Atom *, core::kinematics::Stub * > > *childlist, std::deque< core::kinematics::Stub > *stublist, Stub &stub) override
 update internal coordinates for this atom from its xyz position and input stub More...
 
void update_stub (Stub &stub) const override
 update the stub without actually updating coordinates More...
 
void set_dof (DOF_Type const type, core::Real const value) override
 set degrees of freedom (internal coordinates) More...
 
void set_dof (DOF_Type const type, core::Real const value, AtomDOFChangeSet &changeset) override
 set degrees of freedom (internal coordinates). For use in output-sensitive refold subroutine. More...
 
core::Real dof (DOF_Type const type) const override
 get degrees of freedom More...
 
Jump const & jump () const override
 abort if attempt to get jump for a bonded atom More...
 
void jump (Jump const &) override
 abort if attempt to set jump for a bonded atom More...
 
void jump (Jump const &, AtomDOFChangeSet &) override
 abort if attempt to set jump for a bonded atom More...
 
AtomOP clone (AtomAP parent_in, AtomPointer2D &atom_pointer) const override
 copy this atom More...
 
void setup_min_map (DOF_ID &last_torsion, DOF_ID_Mask const &allow_move, MinimizerMapBase &min_map) const override
 for minimizing,add DOF(PHI,THETA,D) for a BondedAtom into the MinimizerMap More...
 
void get_dof_axis_and_end_pos (Vector &axis, Position &end_pos, DOF_Type const type) const override
 get rotation axis and end_pos for a BondedAtom. More...
 
bool is_jump () const override
 bonded atom is a jump? of course not!!! More...
 
bool keep_1st_child_pos () const override
 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...
 
bool keep_dof_fixed (DOF_Type const type) const override
 whether a DOF for this atom should be fixed? More...
 
void copy_coords (Atom const &src) override
 copy DOFs, xyz's More...
 
AtomCOP stub_atom1 () const override
 stub_atom1 of a bonded atom More...
 
AtomCOP stub_atom2 () const override
 stub_atom2 of a bonded atom More...
 
AtomCOP stub_atom3 () const override
 stub_atom3 of a bonded atom More...
 
void steal_inversion (AtomOP steal_from) override
 
bool get_inversion ()
 
Atom const * raw_stub_atom1 () const override
 Rapid (increment-of-reference-count-avoiding) access to the fist stub atom. More...
 
Atom const * raw_stub_atom2 () const override
 Rapid (increment-of-reference-count-avoiding) access to the second stub atom. More...
 
Atom const * raw_stub_atom3 () const override
 Rapid (increment-of-reference-count-avoiding) access to the third stub atom. More...
 
- Public Member Functions inherited from core::kinematics::tree::Atom_
 ~Atom_ () override
 Destructor. More...
 
void update_internal_coords (bool const recursive) override
 update internal coords of this atom and its offspring atoms (if recursive) More...
 
void update_internal_coords (Stub &stub, bool const recursive=true) override
 Update internal coordinates for this atom and possibly all children. More...
 
Real dihedral_between_bonded_children (Atom const &child1, Atom const &child2) const override
 dihedral angle between two bonded children to this atom More...
 
void show () const override
 dump out AtomID for this atom, its parent and all its offspring More...
 
void show (int const &n_level) const override
 dump out AtomID for this atom, its parent and all its offspring up to n_level More...
 
void update_domain_map (int &current_color, int &biggest_color, DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &atom_moved) const override
 update domain map More...
 
Atoms_ConstIterator atoms_begin () const override
 starting const iterator of the children atom list More...
 
Atoms_ConstIterator atoms_end () const override
 ending const iterator of the children atom list More...
 
Atoms_Iterator atoms_begin () override
 starting iterator of the children atom list More...
 
Atoms_Iterator atoms_end () override
 ending iterator of the children atom list More...
 
Size n_atom () const override
 number of children atoms More...
 
void append_atom (AtomOP) override
 append an atom as this atom's child More...
 
void delete_atom (AtomOP) override
 remove an atom from this atom's children More...
 
void insert_atom (AtomOP) override
 insert an atom as this atom's child More...
 
void insert_atom (AtomOP, int const ) override
 tries to insert at the position specified by the second argument More...
 
void replace_atom (AtomOP const old_atom, AtomOP const new_atom) override
 replace the old atom by the new atom in the child atom list More...
 
AtomCOP get_nonjump_atom (Size const i) const override
 get non-jump atom by its index from the children atoms list More...
 
Size n_children () const override
 number of the child atoms More...
 
Size n_nonjump_children () const override
 number of the non-jump child atoms More...
 
AtomCOP child (Size const k) const override
 get a child atom by index (const method) More...
 
AtomOP child (Size const k) override
 get a child atom by index More...
 
Size child_index (AtomCOP child) const override
 the atom-index of this child More...
 
Size raw_child_index (Atom const *child) const override
 the atom-index of this child More...
 
bool downstream (AtomCOP atom1) const override
 whether atom1 is downstream of this atom. More...
 
AtomID const & id () const override
 Atom identifier. More...
 
void id (AtomID const &id_in) override
 AtomID assignment. More...
 
AtomID const & atom_id () const override
 Atom identifier. More...
 
Position const & position () const override
 Position. More...
 
void position (Position const &position_a) override
 Position assignment. More...
 
Position const & xyz () const override
 Position. More...
 
void xyz (Position const &position_a) override
 Position assignment. More...
 
Length const & x () const override
 x coordinate More...
 
Length const & y () const override
 y coordinate More...
 
Length const & z () const override
 z coordinate More...
 
Length distance (Atom const &atom) const override
 Distance to an Atom. More...
 
Length distance_squared (Atom const &atom) const override
 Distance squared to an Atom. More...
 
AtomOP parent () override
 Parent atom pointer. More...
 
AtomCOP parent () const override
 Parent atom pointer. More...
 
void parent (AtomAP parent_in) override
 parent assignment More...
 
Stub get_stub () const override
 stub centerd at this atom More...
 
Stub get_input_stub () const override
 stub used to build this atom More...
 
AtomID const & stub_atom1_id () const override
 stub atom1 's id More...
 
AtomID const & stub_atom2_id () const override
 stub atom2's id More...
 
AtomID const & stub_atom3_id () const override
 stub atom3's id More...
 
AtomCOP input_stub_atom0 () const override
 the center of the input stub for refolding this atom More...
 
AtomCOP input_stub_atom1 () const override
 the first atom to construct the input stub for refolding this atom More...
 
AtomCOP input_stub_atom2 () const override
 the second atom to construct the input stub for refolding this atom More...
 
AtomCOP input_stub_atom3 () const override
 the third atom to construct the input stub for refolding this atom More...
 
AtomID const & input_stub_atom0_id () const override
 input stub atom0's id More...
 
AtomID const & input_stub_atom1_id () const override
 input stub atom1's id More...
 
AtomID const & input_stub_atom2_id () const override
 input stub atom2's id More...
 
AtomID const & input_stub_atom3_id () const override
 input stub atom3's id More...
 
AtomCOP previous_sibling () const override
 routines for navigating the tree find the sibling atom before itself More...
 
AtomCOP previous_child (AtomCOP child) const override
 find the child atom before this child in the list More...
 
AtomOP next_child (AtomCOP child) override
 find the child atom after this child in the list More...
 
bool stub_defined () const override
 whether a Stub can be defined for this atom More...
 
Atom const * raw_parent () const override
 Rapid (increment-of-reference-count-avoiding) access to the parent atom pointer. More...
 
Atom const * raw_previous_sibling () const override
 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...
 
Atom const * raw_previous_child (Atom const *child) const override
 Rapid (increment-of-reference-count-avoiding) access to the previous child pointer;. More...
 
Atom const * raw_input_stub_atom0 () const override
 Rapid (increment-of-reference-count-avoiding) access to the 0th input stub atom;. More...
 
Atom const * raw_input_stub_atom1 () const override
 Rapid (increment-of-reference-count-avoiding) access to the 1st input stub atom;. More...
 
Atom const * raw_input_stub_atom2 () const override
 Rapid (increment-of-reference-count-avoiding) access to the 2nd input stub atom;. More...
 
Atom const * raw_input_stub_atom3 () const override
 Rapid (increment-of-reference-count-avoiding) access to the 3rd input stub atom;. More...
 
Atom const * raw_get_nonjump_atom (Size const i) const override
 Rapid (increment-of-reference-count-avoiding) access to the ith non-jump atom in this atom's list of children. More...
 
- Public Member Functions inherited from core::kinematics::tree::Atom
AtomCOP get_self_ptr () const
 
AtomOP get_self_ptr ()
 
AtomCAP get_self_weak_ptr () const
 
AtomAP get_self_weak_ptr ()
 

Private Types

typedef Atom_ Super
 

Private Attributes

Real phi_
 DOF properties of a bonded atom. More...
 
Real theta_
 
Real d_
 
bool dof_change_propagates_to_younger_siblings_
 Track whether a dof change from this node (since the last update_xyz) induces a coordinate change for this node's younger siblings. More...
 
bool inverted_frame_
 Stores whether or not this atom is folding in an inverted coordinate system. More...
 

Additional Inherited Members

- Public Types inherited from core::kinematics::tree::Atom
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
 
- Protected Member Functions inherited from core::kinematics::tree::Atom_
 Atom_ ()
 Default constructor. More...
 
 Atom_ (Atom_ const &atom)
 Copy constructor. More...
 
Atom_operator= (Atom_ const &atom)
 Copy assignment. More...
 
void update_child_torsions (AtomOP const child) override
 when subtrees have changed their coordinates More...
 
Atoms_ConstIterator nonjump_atoms_begin () const override
 constant iterator of the first non-jump (bonded) atom in the vector of children atoms. More...
 
Atoms_Iterator nonjump_atoms_begin () override
 iterator of the first non-jump (bonded) atom in the vector of children atoms. More...
 
void abort_bad_call () const
 helper function to abort if something is wrong in atom tree More...
 
void transform_Ax_plus_b_recursive (Matrix const &A, Vector const &b, ResidueCoordinateChangeList &res_change_list) override
 Transform atom and children by linear transformation. More...
 
void get_path_from_root (utility::vector1< AtomCAP > &path) const override
 
bool atom_is_on_path_from_root (AtomCOP atm) const override
 
void note_dof_change (AtomDOFChangeSet &changset)
 Records this atom as having a changed DOF in the input list of Atoms with changed DOFs. For use in output-sensitive refold subroutine. More...
 
void note_xyz_uptodate ()
 To ensure proper function of the output-senstive refold subroutine, derived classes must invoke this function during their update_xyz_coord subroutines. More...
 
Size dof_refold_index () const
 read access for derived classes More...
 
- Protected Member Functions inherited from core::kinematics::tree::Atom
 Atom ()=default
 Default constructor. More...
 
Atomoperator= (Atom const &)=default
 Copy assignment. More...
 
- Protected Attributes inherited from core::kinematics::tree::Atom_
AtomID atom_id_
 Atom ID. More...
 
AtomAP parent_
 Associated conformation Atom. More...
 
Atomraw_parent_
 Workaround copy of the parent pointer for use in functions where locking and unlocking the parent_ pointer would be prohibitively slow. More...
 
PointPosition position_
 xyz More...
 
Atoms atoms_
 Children atom pointers. More...
 

Detailed Description

an atom which are bonded to its parent, derived from Atom_

See AtomTree overview and concepts for details.

Member Typedef Documentation

Constructor & Destructor Documentation

core::kinematics::tree::BondedAtom::BondedAtom ( )
inline

Referenced by clone().

Member Function Documentation

AtomOP core::kinematics::tree::BondedAtom::clone ( AtomAP  parent_in,
AtomPointer2D atom_pointer 
) const
overridevirtual
void core::kinematics::tree::BondedAtom::copy_coords ( Atom const &  src)
overridevirtual
void core::kinematics::tree::BondedAtom::dfs ( AtomDOFChangeSet changeset,
ResidueCoordinateChangeList res_change_list,
Size const  start_atom_index 
) const
overridevirtual

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. Will recurse on younger siblings if a phi on this atom has changed.

Invokes Atom_ dfs function before, optionally recursing to younger siblings should those younger siblings be effected by a DOF change on this node (e.g. phi_ change).

Reimplemented from core::kinematics::tree::Atom_.

References core::kinematics::tree::Atom_::dfs(), dof_change_propagates_to_younger_siblings_, core::kinematics::tree::Atom_::dof_refold_index(), core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::parent_.

Real core::kinematics::tree::BondedAtom::dof ( DOF_Type const  type) const
overridevirtual

get degrees of freedom

Implements core::kinematics::tree::Atom.

References core::id::D, d_, core::chemical::rings::PHI, phi_, core::chemical::rings::THETA, and theta_.

Referenced by clone().

void core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos ( Vector axis,
Position end_pos,
DOF_Type const  type 
) const
overridevirtual

get rotation axis and end_pos for a BondedAtom.

  • axis is the unit vector along the rotation axis for that DOF(Eab).
  • end_pos is the ending point of this unit vector(Vb).

consider simple case like, A->B->C->D and we want to know the change of D position with respect to the rotation along B->C bond( dr/dphi). In this case, Eab is the unit vector along B->C, end_positon is C, and dr/dphi is given as Eab x (D-C).
For B->C bond rotation is the DOF(PHI) of Atom D, so end_pos is input_stub.v which is the position of Atom C and axis is input_stub.M.col(1) which is the unit vector pointing from B to C.
For DOF(THETA) of Atom D, it is a rotation around a unit vector (ending at C) which is perpendicular to B->C->D plane. So the end_pos is the position of Atom C and the axix is the my_stub.M.col(3). For DOF(D) of Atom D, it is a translation along C->D axis and that is my_stub.M.col(1)

Implements core::kinematics::tree::Atom.

References core::id::D, core::kinematics::tree::Atom_::get_input_stub(), core::kinematics::tree::Atom_::get_stub(), inverted_frame_, core::kinematics::Stub::M, core::chemical::rings::PHI, core::chemical::rings::THETA, and core::kinematics::Stub::v.

bool core::kinematics::tree::BondedAtom::get_inversion ( )
inline

References inverted_frame_.

Referenced by steal_inversion().

bool core::kinematics::tree::BondedAtom::is_jump ( ) const
inlineoverridevirtual

bonded atom is a jump? of course not!!!

Implements core::kinematics::tree::Atom.

Jump const& core::kinematics::tree::BondedAtom::jump ( ) const
inlineoverridevirtual

abort if attempt to get jump for a bonded atom

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::abort_bad_call(), and core::kinematics::tree::BOGUS_JUMP.

void core::kinematics::tree::BondedAtom::jump ( Jump const &  )
inlineoverridevirtual

abort if attempt to set jump for a bonded atom

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::abort_bad_call().

void core::kinematics::tree::BondedAtom::jump ( Jump const &  ,
AtomDOFChangeSet  
)
inlineoverridevirtual

abort if attempt to set jump for a bonded atom

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::abort_bad_call().

bool core::kinematics::tree::BondedAtom::keep_1st_child_pos ( ) const
inlineoverridevirtual

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

Implements core::kinematics::tree::Atom.

bool core::kinematics::tree::BondedAtom::keep_dof_fixed ( DOF_Type const  type) const
overridevirtual

whether a DOF for this atom should be fixed?

  • bond distance D can always be flexible
  • bond angle THETA is not meaningful if it is defined by A-B-A in some special cases, for example N-CA-C in which CA is a jump atom, then THETA of the N atom is defined by N-CA-N.
  • torsion angle PHI is not meaningful if it is defined by A-B-A-D or A-B-D-A or A-D-B-A in some special cases.

Reimplemented from core::kinematics::tree::Atom_.

References core::id::D, core::kinematics::tree::Atom_::id(), core::kinematics::tree::Atom_::parent(), core::kinematics::tree::Atom_::parent_, core::chemical::rings::PHI, core::chemical::rings::THETA, and core::kinematics::tree::TR().

Referenced by setup_min_map(), update_internal_coords(), and update_xyz_coords().

Atom const * core::kinematics::tree::BondedAtom::raw_stub_atom1 ( ) const
overridevirtual

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

Implements core::kinematics::tree::Atom.

Atom const * core::kinematics::tree::BondedAtom::raw_stub_atom2 ( ) const
overridevirtual

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

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::raw_parent().

Atom const * core::kinematics::tree::BondedAtom::raw_stub_atom3 ( ) const
overridevirtual
void core::kinematics::tree::BondedAtom::set_dof ( DOF_Type const  type,
core::Real const  value 
)
overridevirtual

set degrees of freedom (internal coordinates)

Implements core::kinematics::tree::Atom.

References core::id::D, d_, core::id::PHI, phi_, core::id::THETA, and theta_.

Referenced by set_dof().

void core::kinematics::tree::BondedAtom::set_dof ( DOF_Type const  type,
core::Real const  value,
AtomDOFChangeSet set 
)
overridevirtual

set degrees of freedom (internal coordinates). For use in output-sensitive refold subroutine.

calls set_dof non-polymorphically: assumption is that BondedAtom is not subclassed, or, that if it is, that the derived class implements this overloaded set_dof function.

Implements core::kinematics::tree::Atom.

References dof_change_propagates_to_younger_siblings_, core::kinematics::tree::Atom_::note_dof_change(), core::id::PHI, and set_dof().

void core::kinematics::tree::BondedAtom::setup_min_map ( DOF_ID last_torsion,
DOF_ID_Mask const &  allow_move,
MinimizerMapBase min_map 
) const
overridevirtual

for minimizing,add DOF(PHI,THETA,D) for a BondedAtom into the MinimizerMap

last torsion is the torsion( Phi for BondedAtom and RB for JumpAtom) of the parent atom or previous bonded sibling. Since BondedAtom's PHI is dependent on its previous sibling BondedAtom,this may modify last_torsion, if our bond torsion angle is changing and this atom has other sibling atoms after itself. recursively done all its offspring

Implements core::kinematics::tree::Atom.

References core::kinematics::MinimizerMapBase::add_atom(), core::kinematics::MinimizerMapBase::add_torsion(), core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), core::id::D, keep_dof_fixed(), core::chemical::rings::PHI, core::id::phi_torsion(), and core::chemical::rings::THETA.

void core::kinematics::tree::BondedAtom::steal_inversion ( AtomOP  steal_from)
overridevirtual
AtomCOP core::kinematics::tree::BondedAtom::stub_atom1 ( ) const
inlineoverridevirtual

stub_atom1 of a bonded atom

it is itself

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom::get_self_ptr().

AtomCOP core::kinematics::tree::BondedAtom::stub_atom2 ( ) const
inlineoverridevirtual

stub_atom2 of a bonded atom

it is its parent

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::parent().

AtomCOP core::kinematics::tree::BondedAtom::stub_atom3 ( ) const
inlineoverridevirtual

stub_atom3 of a bonded atom

  • if this atom's parent is a bonded_atom it is this atom's parent's parent.
  • if this atom's parent is a jump atom, it is this atom's first non-jump sibling or its second non-jump sibling (if it itself is the first) or its first non-jump child (if it does not have any sibling)

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom::get_self_ptr(), core::kinematics::tree::is_collinear(), and core::kinematics::tree::Atom_::parent().

void core::kinematics::tree::BondedAtom::update_internal_coords ( std::deque< std::pair< Atom *, core::kinematics::Stub * > > *  childlist,
std::deque< core::kinematics::Stub > *  stublist,
Stub stub 
)
overridevirtual

update internal coordinates for this atom from its xyz position and input stub

If childlist and stublist are not nullptr, childlist has pairs of (child atom, this stub), and stublist stores unique stubs. (Multiple pointers in childlist can point to the same stub, since that stub ultimately gets updated during the update of the coordinate.) appended so that children may subsequently be updated.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

starting from the input stub, calculate the internal coordinates d_, theta_ and phi_ for this atom. If childlist and stublist are not nullptr, childlist has pairs of (child atom, this stub), and stublist stores unique stubs. (Multiple pointers in childlist can point to the same stub, since that stub ultimately gets updated during the update of the coordinate.) appended so that children may subsequently be updated.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), d_, inverted_frame_, core::kinematics::Stub::is_orthogonal(), keep_dof_fixed(), core::kinematics::Stub::M, phi_, core::kinematics::tree::Atom_::position(), core::chemical::rings::THETA, theta_, core::id::to_string(), core::kinematics::Stub::v, core::kinematics::tree::Atom_::x(), core::kinematics::tree::Atom_::y(), and core::kinematics::tree::Atom_::z().

void core::kinematics::tree::BondedAtom::update_stub ( Stub stub) const
overridevirtual

update the stub without actually updating coordinates

pass out the stub we would pass out if we were actually updating coords or DOFs, which is rotate the stub around its x axis by phi_.

Implements core::kinematics::tree::Atom.

References core::kinematics::Stub::M, and phi_.

void core::kinematics::tree::BondedAtom::update_xyz_coords ( )
overridevirtual

The atom must retrieve an appropriate stub from its parent; it is the root of the subtree being refolded. Valid only if this atom is the maximal root of a subtree requiring coordinate updates – if any ancestor of this atom requires a coordinate update, then the Stub this atom generates for itself will be invalid.

Relies on get_input_stub, which will use the coordinates of this atom's ancestors to build a stub. If this function has been invoked by AtomTree update_xyz_coords(), then these coordinates are guaranteed correct, since this atom is the root of a tree which needs to be refolded. Ergo, nothing in the tree above this atom needs to be refolded.

Reimplemented from core::kinematics::tree::Atom_.

References dof_change_propagates_to_younger_siblings_, core::kinematics::tree::Atom_::get_input_stub(), inverted_frame_, core::kinematics::Stub::M, core::kinematics::Jump::mirror_z_transform, core::kinematics::tree::Atom_::parent(), and core::kinematics::tree::Atom_::parent_.

void core::kinematics::tree::BondedAtom::update_xyz_coords ( Stub stub)
overridevirtual

update cartesian coordinates for this atom from its input stub and internal cooridnates

starting from the input stub, calculate xyz position of this atom from its internal coordinates d_, theta_ and phi_. If recursive is true, obtain the new stub centered at this atom and pass the new stub to all its children atoms to update their xyz positions recursively.

Note
stub passed in is modified by rotating phi_ around x in the stub frame

Implements core::kinematics::tree::Atom.

References core::kinematics::tree::Atom_::atoms_begin(), core::kinematics::tree::Atom_::atoms_end(), d_, dof_change_propagates_to_younger_siblings_, inverted_frame_, core::kinematics::Stub::is_orthogonal(), keep_dof_fixed(), core::kinematics::Stub::M, core::kinematics::tree::Atom_::note_xyz_uptodate(), phi_, core::kinematics::tree::Atom_::position(), core::chemical::rings::THETA, theta_, and core::kinematics::Stub::v.

Member Data Documentation

Real core::kinematics::tree::BondedAtom::d_
private
bool core::kinematics::tree::BondedAtom::dof_change_propagates_to_younger_siblings_
private

Track whether a dof change from this node (since the last update_xyz) induces a coordinate change for this node's younger siblings.

Referenced by clone(), dfs(), set_dof(), and update_xyz_coords().

bool core::kinematics::tree::BondedAtom::inverted_frame_
private

Stores whether or not this atom is folding in an inverted coordinate system.

Referenced by clone(), get_dof_axis_and_end_pos(), get_inversion(), steal_inversion(), update_internal_coords(), and update_xyz_coords().

Real core::kinematics::tree::BondedAtom::phi_
private

DOF properties of a bonded atom.

  • a bonded atom is an atom who connects to its parent by a "bond" (covalent or virtual) and therefore its position is defined by three internal coordinates: d_, theta_, and phi_.
  • d_ is the bond distance between this atom and its parent.
  • theta_ is the bond angle between this atom(A), its parent's stub_atom1(B) and its parent's stub_atom2(C), i.e., angle in between B->A ^ C->B.
  • phi_ is either the torsion angle defined by A, B, C and D (C's parents), or the improper angle defined by A, B, C and D (B's child and A's previous sibling).

Referenced by copy_coords(), dof(), set_dof(), update_internal_coords(), update_stub(), and update_xyz_coords().

Real core::kinematics::tree::BondedAtom::theta_
private

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