#include <CartesianMinimizerMap.hh>

Public Member Functions
	CartesianMinimizerMap ()

	~CartesianMinimizerMap ()

virtual kinematics::DomainMap const &	domain_map () const

virtual void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent)
	Allow the AtomTree to communicate to this class that a particular torsion (or angle or distance – a particular DOF) belongs in the minimization task to inform this class the parent DOF for that torsion. More...

virtual void	add_atom (AtomID const &AtomID, DOF_ID const &dof_id)
	Allow the AtomTree to inform this class that a particular atom belongs in the derivative calculation for a certain DOF. That certain DOF must have already been included in the minimization process through a prior invocation of the add_torsion method. More...

void	setup (pose::Pose &pose, kinematics::MoveMap const &move_map)

void	reset (pose::Pose const &pose)
	clears old data+dimensions dof_node_pointer using size data from the pose More...

void	copy_dofs_from_pose (pose::Pose const &pose, Multivec &dofs) const

void	copy_dofs_to_pose (pose::Pose &pose, Multivec const &dofs) const

int	ndofs () const

int	ntorsions () const

id::DOF_ID	get_dof_id (Size n) const

id::TorsionID	get_TorsionID (Size n) const

int	natoms () const

id::AtomID	get_atom (Size n) const

Size	get_atom_index (id::AtomID x) const

utility::vector1 < core::scoring::DerivVectorPair > &	atom_derivatives (Size resid)

void	zero_stored_derivs ()

Public Member Functions inherited from core::kinematics::MinimizerMapBase
	MinimizerMapBase ()
	default ctor; noop More...

virtual	~MinimizerMapBase ()
	dstor More...

Private Member Functions
void	assign_rosetta_torsions_and_trim (pose::Pose const &pose)

Private Attributes
id::AtomID_Map< core::Size >	atom_indices_

utility::vector1< id::AtomID >	moving_atoms_
	list of all the moving atoms More...

utility::vector1 < utility::vector1 < core::scoring::DerivVectorPair > >	atom_derivatives_

utility::vector1< id::DOF_ID >	moving_dofids_

utility::vector1< id::TorsionID >	moving_torsionids_

kinematics::DomainMap	domain_map_

Additional Inherited Members
Public Types inherited from core::kinematics::MinimizerMapBase
typedef id::AtomID	AtomID

typedef id::DOF_ID	DOF_ID

typedef id::DOF_Type	DOF_Type

Constructor & Destructor Documentation

core::optimization::CartesianMinimizerMap::CartesianMinimizerMap ( )

inline

core::optimization::CartesianMinimizerMap::~CartesianMinimizerMap ( )

References moving_atoms_, moving_dofids_, and moving_torsionids_.

Member Function Documentation

void core::optimization::CartesianMinimizerMap::add_atom	(	AtomID const &	atom_id,
		DOF_ID const &	dof_id
	)

virtual

Allow the AtomTree to inform this class that a particular atom belongs in the derivative calculation for a certain DOF. That certain DOF must have already been included in the minimization process through a prior invocation of the add_torsion method.

Implements core::kinematics::MinimizerMapBase.

void core::optimization::CartesianMinimizerMap::add_torsion	(	DOF_ID const &	new_torsion,
		DOF_ID const &	parent
	)

virtual

Allow the AtomTree to communicate to this class that a particular torsion (or angle or distance – a particular DOF) belongs in the minimization task to inform this class the parent DOF for that torsion.

Implements core::kinematics::MinimizerMapBase.

References moving_dofids_, core::id::PHI, and core::id::DOF_ID::type().

void core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim ( pose::Pose const & pose )

private

References atom_indices_, core::id::BOGUS_TORSION_ID, core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::id::AtomID_Map< T >::has(), moving_dofids_, moving_torsionids_, ndofs(), core::pose::setup_dof_to_torsion_map(), and core::id::TorsionID::valid().

Referenced by setup().

utility::vector1< core::scoring::DerivVectorPair >& core::optimization::CartesianMinimizerMap::atom_derivatives ( Size resid )

inline

References atom_derivatives_.

Referenced by core::optimization::cartesian_collect_atompairE_deriv().

void core::optimization::CartesianMinimizerMap::copy_dofs_from_pose	(	pose::Pose const &	pose,
		Multivec &	dofs
	)		const

References core::pose::Pose::batch_get_xyz(), moving_atoms_, natoms(), and runtime_assert.

Referenced by core::optimization::CartesianMinimizer::run().

void core::optimization::CartesianMinimizerMap::copy_dofs_to_pose	(	pose::Pose &	pose,
		Multivec const &	dofs
	)		const

References core::pose::Pose::batch_set_xyz(), moving_atoms_, natoms(), and runtime_assert.

Referenced by core::optimization::cartesian_dfunc(), core::optimization::CartesianMultifunc::dump(), and core::optimization::CartesianMultifunc::operator()().

virtual kinematics::DomainMap const& core::optimization::CartesianMinimizerMap::domain_map ( ) const

inlinevirtual

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

Referenced by core::optimization::cartesian_collect_atompairE_deriv(), and core::optimization::CartesianMinimizer::run().

id::AtomID core::optimization::CartesianMinimizerMap::get_atom ( Size n ) const

inline

References moving_atoms_.

Referenced by core::optimization::cart_numerical_derivative_check(), and core::optimization::cartesian_collect_atompairE_deriv().

Size core::optimization::CartesianMinimizerMap::get_atom_index ( id::AtomID x ) const

inline

References atom_indices_.

Referenced by core::optimization::cartesian_collect_torsional_deriv().

id::DOF_ID core::optimization::CartesianMinimizerMap::get_dof_id ( Size n ) const

inline

References moving_dofids_.

Referenced by core::optimization::cartesian_collect_torsional_deriv().

id::TorsionID core::optimization::CartesianMinimizerMap::get_TorsionID ( Size n ) const

inline

References moving_torsionids_.

Referenced by core::optimization::cartesian_collect_torsional_deriv().

int core::optimization::CartesianMinimizerMap::natoms ( ) const

inline

References moving_atoms_.

Referenced by core::optimization::cart_numerical_derivative_check(), core::optimization::cartesian_collect_atompairE_deriv(), copy_dofs_from_pose(), and copy_dofs_to_pose().

int core::optimization::CartesianMinimizerMap::ndofs ( ) const

inline

References moving_atoms_.

Referenced by assign_rosetta_torsions_and_trim(), core::optimization::cart_numerical_derivative_check(), core::optimization::cartesian_dfunc(), and core::optimization::CartesianMinimizer::run().

int core::optimization::CartesianMinimizerMap::ntorsions ( ) const

inline

References moving_dofids_.

Referenced by core::optimization::cartesian_collect_torsional_deriv().

void core::optimization::CartesianMinimizerMap::reset ( pose::Pose const & pose )

clears old data+dimensions dof_node_pointer using size data from the pose

References atom_derivatives_, moving_atoms_, moving_dofids_, moving_torsionids_, core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by setup().

void core::optimization::CartesianMinimizerMap::setup	(	pose::Pose &	pose,
		kinematics::MoveMap const &	move_map
	)

References core::chemical::aa_vrt, assign_rosetta_torsions_and_trim(), atom_indices_, core::pose::Pose::atom_tree(), core::conformation::Conformation::atom_tree(), bb_move, core::id::BOGUS_DOF_ID, chi_move, core::pose::Pose::conformation(), core::kinematics::MoveMap::dof_id_begin(), core::kinematics::MoveMap::dof_id_end(), domain_map_, core::kinematics::MoveMap::get_bb(), core::kinematics::MoveMap::get_chi(), core::pose::initialize_atomid_map(), j, moving_atoms_, core::pose::Pose::n_residue(), core::id::RB1, reset(), core::pose::Pose::residue(), core::kinematics::AtomTree::root(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::pose::setup_dof_mask_from_move_map(), core::pose::Pose::total_residue(), and core::kinematics::AtomTree::update_domain_map().

Referenced by core::util::getMLweight_cart(), and core::optimization::CartesianMinimizer::run().

void core::optimization::CartesianMinimizerMap::zero_stored_derivs ( )

References atom_derivatives_.

Referenced by core::optimization::cartesian_dfunc().

Member Data Documentation

utility::vector1< utility::vector1< core::scoring::DerivVectorPair > > core::optimization::CartesianMinimizerMap::atom_derivatives_

private

Referenced by atom_derivatives(), reset(), and zero_stored_derivs().

id::AtomID_Map< core::Size > core::optimization::CartesianMinimizerMap::atom_indices_

private

Referenced by assign_rosetta_torsions_and_trim(), get_atom_index(), and setup().

kinematics::DomainMap core::optimization::CartesianMinimizerMap::domain_map_

private

Referenced by domain_map(), and setup().

utility::vector1<id::AtomID> core::optimization::CartesianMinimizerMap::moving_atoms_

private

list of all the moving atoms

Referenced by copy_dofs_from_pose(), copy_dofs_to_pose(), get_atom(), natoms(), ndofs(), reset(), setup(), and ~CartesianMinimizerMap().

utility::vector1<id::DOF_ID> core::optimization::CartesianMinimizerMap::moving_dofids_

private

list of all moving torsions: dof ids and torsion ids we don't need all the info from dof_node, just this

Referenced by add_torsion(), assign_rosetta_torsions_and_trim(), get_dof_id(), ntorsions(), reset(), and ~CartesianMinimizerMap().

utility::vector1<id::TorsionID> core::optimization::CartesianMinimizerMap::moving_torsionids_

private

Referenced by assign_rosetta_torsions_and_trim(), get_TorsionID(), reset(), and ~CartesianMinimizerMap().

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

symlinks/rosetta/src/core/optimization/CartesianMinimizerMap.hh
symlinks/rosetta/src/core/optimization/CartesianMinimizerMap.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation