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Rosetta
2021.16
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Rosetta
2021.16
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The AtomTree is responsible for informing the conformation of which residues have had either internal (DOF) or external (xyz) coordinate changes so that the Conformation may shuttle O(k) – output sensitive – data from the AtomTree to the Residue objects it manages. More...
#include <ResidueCoordinateChangeList.hh>
Public Member Functions | |
| ResidueCoordinateChangeList () | |
| ~ResidueCoordinateChangeList () override | |
| ResidueCoordinateChangeList & | operator= (ResidueCoordinateChangeList const &rhs) |
| void | total_residue (Size total_residue) |
| Set the number of residues in the conformation being tracked. More... | |
| Size | total_residue () const |
| Return the number of. More... | |
| bool | empty () const |
| Is the list of the changed residues empty? More... | |
| void | clear () |
| Reset the list of those residues that have moved. O(k). More... | |
| void | mark_residue_moved (id::AtomID atid) |
| Mark a residue as having changed by passing in an AtomId for one atom in that residue. More... | |
| void | mark_residue_moved (Size resid) |
| Mark a residue as having changed by passing in the index of that residue. More... | |
| ResidueListIterator | residues_moved_begin () const |
| returns an iterator to the beginning of the (unordered) list of residues that have moved. More... | |
| ResidueListIterator | residues_moved_end () const |
| returns an iterator to the end of the (unordered) list of residues that have moved. More... | |
Private Member Functions | |
| bool | no_residues_with_nonzero_change_id () const |
| O(N) – used in assert statements in debug mode. More... | |
Private Attributes | |
| ResidueIndexList | changed_residues_ |
| utility::vector1< Size > | residue_change_id_ |
| The reverse mapping from residue index to its position in the list of residues that have changed. Size total_residue_. More... | |
| Size | total_residue_ |
The AtomTree is responsible for informing the conformation of which residues have had either internal (DOF) or external (xyz) coordinate changes so that the Conformation may shuttle O(k) – output sensitive – data from the AtomTree to the Residue objects it manages.
| core::kinematics::ResidueCoordinateChangeList::ResidueCoordinateChangeList | ( | ) |
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overridedefault |
| void core::kinematics::ResidueCoordinateChangeList::clear | ( | ) |
Reset the list of those residues that have moved. O(k).
– reset the residue_change_id_ for those residues which had previously changed
References changed_residues_, and residue_change_id_.
Referenced by operator=().
| bool core::kinematics::ResidueCoordinateChangeList::empty | ( | ) | const |
Is the list of the changed residues empty?
Is the list of the changed residues empty? bool.
References changed_residues_.
Referenced by total_residue().
| void core::kinematics::ResidueCoordinateChangeList::mark_residue_moved | ( | id::AtomID | atid | ) |
Mark a residue as having changed by passing in an AtomId for one atom in that residue.
References core::id::AtomID::rsd().
Referenced by core::kinematics::tree::Atom_::dfs(), and core::kinematics::tree::Atom_::transform_Ax_plus_b_recursive().
| void core::kinematics::ResidueCoordinateChangeList::mark_residue_moved | ( | Size | resid | ) |
Mark a residue as having changed by passing in the index of that residue.
References changed_residues_, residue_change_id_, total_residue_, and core::kinematics::tr().
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private |
O(N) – used in assert statements in debug mode.
References residue_change_id_, and total_residue_.
Referenced by total_residue().
| ResidueCoordinateChangeList & core::kinematics::ResidueCoordinateChangeList::operator= | ( | ResidueCoordinateChangeList const & | rhs | ) |
References changed_residues_, clear(), residue_change_id_, and total_residue_.
| ResidueListIterator core::kinematics::ResidueCoordinateChangeList::residues_moved_begin | ( | ) | const |
returns an iterator to the beginning of the (unordered) list of residues that have moved.
References changed_residues_.
| ResidueListIterator core::kinematics::ResidueCoordinateChangeList::residues_moved_end | ( | ) | const |
returns an iterator to the end of the (unordered) list of residues that have moved.
References changed_residues_.
| void core::kinematics::ResidueCoordinateChangeList::total_residue | ( | Size | total_residue | ) |
Set the number of residues in the conformation being tracked.
adding and deleting residues repeatedly should be O(1) so use the stl resize-with-argument command when resizing residue_change_id_. That way, if residue_change_id_ has reserved space of at least total_residue, then the resize will initialize exactly the number of new residues that have been added. In debug mode, this operation is O( total_residue ).
References changed_residues_, empty(), no_residues_with_nonzero_change_id(), residue_change_id_, total_residue(), and total_residue_.
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inline |
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private |
Referenced by clear(), empty(), mark_residue_moved(), operator=(), residues_moved_begin(), residues_moved_end(), and total_residue().
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private |
The reverse mapping from residue index to its position in the list of residues that have changed. Size total_residue_.
Referenced by clear(), mark_residue_moved(), no_residues_with_nonzero_change_id(), operator=(), and total_residue().
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private |
Referenced by mark_residue_moved(), no_residues_with_nonzero_change_id(), operator=(), and total_residue().
1.8.7