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core::optimization::DOF_Node Class Reference

#include <DOF_Node.hh>

Inheritance diagram for core::optimization::DOF_Node:
Inheritance graph
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Public Types

typedef id::AtomID AtomID
 
typedef utility::vector1< AtomID > AtomIDs
 
typedef id::DOF_ID DOF_ID
 
typedef id::TorsionID TorsionID
 
typedef id::DOF_Type DOF_Type
 

Public Member Functions

std::string to_string () const
 
Vector & F1 ()
 
Vector & F2 ()
 
Vector const & F1 () const
 
Vector const & F2 () const
 
int rsd () const
 
int atomno () const
 
AtomID const & atom_id () const
 
DOF_Type type () const
 
DOF_ID const & dof_id () const
 
int depth () const
 
AtomIDs const & atoms () const
 
DOF_NodeCOP parent () const
 
void clear_atoms ()
 
void add_atom (AtomID const &atom)
 
TorsionID const & torsion_id () const
 get the rosetta torsion id for this DOF More...
 
void torsion_id (id::TorsionID const &id_in)
 set the rosetta torsion id for this DOF More...
 
void link_vectors ()
 sum derivative contributions down the tree More...
 
 DOF_Node (DOF_ID const &id_in, DOF_NodeOP parent_in)
 
void set_id (DOF_ID const &setting)
 
void set_parent (DOF_NodeOP setting)
 
bool dependent () const
 
void dependent (bool const setting)
 

Private Attributes

Vector F1_
 
Vector F2_
 
int depth_
 
DOF_ID id
 
AtomIDs atoms_
 
DOF_NodeOP parent_
 
TorsionID torsion_id_
 
bool dependent_
 

Friends

bool operator< (DOF_Node const &t1, DOF_Node const &t2)
 

Member Typedef Documentation

◆ AtomID

typedef id::AtomID core::optimization::DOF_Node::AtomID

◆ AtomIDs

typedef utility::vector1< AtomID > core::optimization::DOF_Node::AtomIDs

◆ DOF_ID

typedef id::DOF_ID core::optimization::DOF_Node::DOF_ID

◆ DOF_Type

typedef id::DOF_Type core::optimization::DOF_Node::DOF_Type

◆ TorsionID

typedef id::TorsionID core::optimization::DOF_Node::TorsionID

Constructor & Destructor Documentation

◆ DOF_Node()

core::optimization::DOF_Node::DOF_Node ( DOF_ID const &  id_in,
DOF_NodeOP  parent_in 
)
inline

Member Function Documentation

◆ add_atom()

void core::optimization::DOF_Node::add_atom ( AtomID const &  atom)
inline

References atoms_.

◆ atom_id()

AtomID const& core::optimization::DOF_Node::atom_id ( ) const
inline

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::optimization::MinimizerMap::reset_jump_rb_deltas(), and core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas().

◆ atomno()

int core::optimization::DOF_Node::atomno ( ) const
inline

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::assign_dofs_to_mobile_residues(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::numerical_derivative_check(), core::optimization::symmetry::numerical_derivative_check(), and core::pack::scmin::AtomTreeSCMinMinimizerMap::starting_dofs().

◆ atoms()

AtomIDs const& core::optimization::DOF_Node::atoms ( ) const
inline

References atoms_.

Referenced by core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::optimization::numerical_derivative_check(), and core::optimization::symmetry::numerical_derivative_check().

◆ clear_atoms()

void core::optimization::DOF_Node::clear_atoms ( )
inline

References atoms_.

◆ dependent() [1/2]

bool core::optimization::DOF_Node::dependent ( ) const
inline

References dependent_.

Referenced by core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::SymMinimizerMap::copy_dofs_from_pose(), core::optimization::symmetry::SymMinimizerMap::copy_dofs_to_pose(), core::optimization::numerical_derivative_check(), core::optimization::symmetry::numerical_derivative_check(), and core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas().

◆ dependent() [2/2]

void core::optimization::DOF_Node::dependent ( bool const  setting)
inline

References dependent_.

◆ depth()

int core::optimization::DOF_Node::depth ( ) const
inline

References depth_, and parent_.

Referenced by core::optimization::MinimizerMap::link_torsion_vectors(), and core::optimization::symmetry::SymMinimizerMap::link_torsion_vectors().

◆ dof_id()

DOF_ID const& core::optimization::DOF_Node::dof_id ( ) const
inline

References id.

Referenced by core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions(), core::optimization::MinimizerMap::assign_rosetta_torsions(), core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::symmetry::SymMinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::copy_dofs_to_pose(), core::optimization::symmetry::SymMinimizerMap::copy_dofs_to_pose(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), and core::optimization::numerical_derivative_check().

◆ F1() [1/2]

Vector& core::optimization::DOF_Node::F1 ( )
inline

References F1_.

Referenced by core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), and core::optimization::torsional_derivative_from_cartesian_derivatives().

◆ F1() [2/2]

Vector const& core::optimization::DOF_Node::F1 ( ) const
inline

References F1_.

◆ F2() [1/2]

Vector& core::optimization::DOF_Node::F2 ( )
inline

References F2_.

Referenced by core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), and core::optimization::torsional_derivative_from_cartesian_derivatives().

◆ F2() [2/2]

Vector const& core::optimization::DOF_Node::F2 ( ) const
inline

References F2_.

◆ link_vectors()

void core::optimization::DOF_Node::link_vectors ( )
inline

sum derivative contributions down the tree

References F1_, F2_, and parent_.

Referenced by core::optimization::MinimizerMap::link_torsion_vectors(), and core::optimization::symmetry::SymMinimizerMap::link_torsion_vectors().

◆ parent()

DOF_NodeCOP core::optimization::DOF_Node::parent ( ) const
inline

References parent_.

Referenced by core::optimization::numerical_derivative_check(), and core::optimization::symmetry::numerical_derivative_check().

◆ rsd()

int core::optimization::DOF_Node::rsd ( ) const
inline

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::assign_dofs_to_mobile_residues(), core::pack::scmin::SCMinMultifunc::dfunc(), core::optimization::numerical_derivative_check(), core::optimization::symmetry::numerical_derivative_check(), and core::pack::scmin::AtomTreeSCMinMinimizerMap::starting_dofs().

◆ set_id()

void core::optimization::DOF_Node::set_id ( DOF_ID const &  setting)
inline

◆ set_parent()

void core::optimization::DOF_Node::set_parent ( DOF_NodeOP  setting)
inline

References parent_.

◆ to_string()

std::string core::optimization::DOF_Node::to_string ( ) const
inline

References F1_, and F2_.

◆ torsion_id() [1/2]

TorsionID const& core::optimization::DOF_Node::torsion_id ( ) const
inline

get the rosetta torsion id for this DOF

This may not exist, of course. But it's useful to know what it is when calculating derivatives of terms like rama/dunbrack/paa

References torsion_id_.

Referenced by core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions(), core::optimization::MinimizerMap::assign_rosetta_torsions(), core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), and protocols::cartesian::MolecularDynamics::getCartesianDerivatives().

◆ torsion_id() [2/2]

void core::optimization::DOF_Node::torsion_id ( id::TorsionID const &  id_in)
inline

set the rosetta torsion id for this DOF

This may not exist, of course. But it's useful to know what it is when calculating derivatives of terms like rama/dunbrack/paa

References torsion_id_.

◆ type()

DOF_Type core::optimization::DOF_Node::type ( ) const
inline

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::assign_dofs_to_mobile_residues(), core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions(), core::optimization::MinimizerMap::assign_rosetta_torsions(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::optimization::numerical_derivative_check(), core::optimization::symmetry::numerical_derivative_check(), core::optimization::MinimizerMap::reset_jump_rb_deltas(), core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas(), core::pack::scmin::SCMinMultifunc::scmin_numerical_derivative_check(), core::pack::scmin::AtomTreeSCMinMinimizerMap::starting_dofs(), core::optimization::symmetry::SymMinimizerMap::torsion_scale_factor(), core::optimization::MinimizerMap::torsion_scale_factor(), and core::optimization::torsional_derivative_from_cartesian_derivatives().

Friends And Related Function Documentation

◆ operator<

bool operator< ( DOF_Node const &  t1,
DOF_Node const &  t2 
)
friend

Member Data Documentation

◆ atoms_

AtomIDs core::optimization::DOF_Node::atoms_
private

Referenced by add_atom(), atoms(), and clear_atoms().

◆ dependent_

bool core::optimization::DOF_Node::dependent_
private

Referenced by dependent().

◆ depth_

int core::optimization::DOF_Node::depth_
mutableprivate

Referenced by depth().

◆ F1_

Vector core::optimization::DOF_Node::F1_
private

Referenced by F1(), link_vectors(), and to_string().

◆ F2_

Vector core::optimization::DOF_Node::F2_
private

Referenced by F2(), link_vectors(), and to_string().

◆ id

DOF_ID core::optimization::DOF_Node::id
private

Referenced by dof_id().

◆ parent_

DOF_NodeOP core::optimization::DOF_Node::parent_
private

Referenced by depth(), link_vectors(), parent(), and set_parent().

◆ torsion_id_

TorsionID core::optimization::DOF_Node::torsion_id_
private

Referenced by torsion_id().

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