#include <DOF_Node.hh>

Inheritance diagram for core::optimization::DOF_Node:

Collaboration diagram for core::optimization::DOF_Node:

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
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)

Private Attributes
Vector	F1_

Vector	F2_

int	depth_

DOF_ID	id

AtomIDs	atoms_

DOF_NodeOP	parent_

TorsionID	torsion_id_

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

Detailed Description

Definition at line 39 of file DOF_Node.hh.

Member Typedef Documentation

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

Definition at line 43 of file DOF_Node.hh.

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

Definition at line 44 of file DOF_Node.hh.

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

Definition at line 45 of file DOF_Node.hh.

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

Definition at line 47 of file DOF_Node.hh.

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

Definition at line 46 of file DOF_Node.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 157 of file DOF_Node.hh.

Member Function Documentation

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

inline

Definition at line 113 of file DOF_Node.hh.

References atoms_.

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

inline

Definition at line 77 of file DOF_Node.hh.

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

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

inline

Definition at line 73 of file DOF_Node.hh.

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

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

inline

Definition at line 92 of file DOF_Node.hh.

References atoms_.

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

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

inline

Definition at line 106 of file DOF_Node.hh.

References atoms_.

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

inline

Definition at line 205 of file DOF_Node.hh.

References depth_, and parent_.

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

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

inline

Definition at line 85 of file DOF_Node.hh.

References id.

Referenced by core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions(), core::optimization::MinimizerMap::assign_rosetta_torsions(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::SymMinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::symmetry::SymMinimizerMap::copy_dofs_to_pose(), core::optimization::MinimizerMap::copy_dofs_to_pose(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), and core::optimization::numerical_derivative_check().

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

inline

Definition at line 53 of file DOF_Node.hh.

References F1_.

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

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

inline

Definition at line 61 of file DOF_Node.hh.

References F1_.

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

inline

Definition at line 57 of file DOF_Node.hh.

References F2_.

Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), and core::optimization::torsional_derivative_from_cartesian_derivatives().

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

inline

Definition at line 65 of file DOF_Node.hh.

References F2_.

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

inline

sum derivative contributions down the tree

Definition at line 148 of file DOF_Node.hh.

References F1_, F2_, and parent_.

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

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

inline

Definition at line 99 of file DOF_Node.hh.

References parent_.

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

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

inline

Definition at line 69 of file DOF_Node.hh.

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

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

inline

Definition at line 171 of file DOF_Node.hh.

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

inline

Definition at line 176 of file DOF_Node.hh.

References parent_.

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

Definition at line 125 of file DOF_Node.hh.

References torsion_id_.

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

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

Definition at line 137 of file DOF_Node.hh.

References torsion_id_.

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

inline

Definition at line 81 of file DOF_Node.hh.

Friends And Related Function Documentation

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

friend

Definition at line 195 of file DOF_Node.hh.

Member Data Documentation

AtomIDs core::optimization::DOF_Node::atoms_

private

Definition at line 187 of file DOF_Node.hh.

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

int core::optimization::DOF_Node::depth_

mutableprivate

Definition at line 185 of file DOF_Node.hh.

Referenced by depth().

Vector core::optimization::DOF_Node::F1_

private

Definition at line 183 of file DOF_Node.hh.

Referenced by F1(), and link_vectors().

Vector core::optimization::DOF_Node::F2_

private

Definition at line 184 of file DOF_Node.hh.

Referenced by F2(), and link_vectors().

DOF_ID core::optimization::DOF_Node::id

private

Definition at line 186 of file DOF_Node.hh.

Referenced by dof_id().

DOF_NodeOP core::optimization::DOF_Node::parent_

private

Definition at line 188 of file DOF_Node.hh.

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

TorsionID core::optimization::DOF_Node::torsion_id_

private

Definition at line 189 of file DOF_Node.hh.

Referenced by torsion_id().

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

src/core/optimization/DOF_Node.hh

Public Types

Public Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation