core::optimization::CartesianMinimizerMap Class Reference

#include <CartesianMinimizerMap.hh>

Inheritance diagram for core::optimization::CartesianMinimizerMap:

Public Member Functions
	CartesianMinimizerMap ()
	~CartesianMinimizerMap () override
kinematics::DomainMap const &	domain_map () const override
void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent) override
	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...
void	add_atom (AtomID const &AtomID, DOF_ID const &dof_id) override
	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
bool	atom_is_moving (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...
	~MinimizerMapBase () override
	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

CartesianMinimizerMap()

core::optimization::CartesianMinimizerMap::CartesianMinimizerMap

(

)

Initialize atom_indices_ AtomID_Map default value to "0" with this sentinel value meaning that an atom is not moving.

References atom_indices_, and core::id::AtomID_Map< T >::default_value().

~CartesianMinimizerMap()

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

override

References moving_atoms_, moving_dofids_, and moving_torsionids_.

Member Function Documentation

add_atom()

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

overridevirtual

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.

add_torsion()

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

overridevirtual

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().

assign_rosetta_torsions_and_trim()

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

private

References atom_indices_, core::id::TorsionID::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().

atom_derivatives()

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

inline

References atom_derivatives_.

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

atom_is_moving()

bool core::optimization::CartesianMinimizerMap::atom_is_moving ( id::AtomID  x ) const

inline

References atom_indices_.

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

copy_dofs_from_pose()

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

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

Referenced by protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::cryst::ReportGradientsMover::compute(), protocols::md::CartesianMD::do_initialize(), protocols::md::CartesianMD::do_MD(), core::util::getMLweight_cart(), protocols::md::CartesianMD::report_MD(), and core::optimization::CartesianMinimizer::run().

copy_dofs_to_pose()

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

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

Referenced by core::optimization::cartesian_dfunc(), protocols::md::CartesianMD::do_MD(), core::optimization::CartesianMultifunc::dump(), protocols::md::CartesianMD::dump_poses(), core::optimization::CartesianMultifunc::operator()(), and protocols::md::CartesianMD::VelocityVerlet_Integrator().

domain_map()

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

inlineoverridevirtual

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

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

get_atom()

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

inline

References moving_atoms_.

Referenced by core::optimization::cart_numerical_derivative_check(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::cryst::ReportGradientsMover::compute(), protocols::md::CartesianMD::cst_on_pose_dynamic(), protocols::md::CartesianMD::do_initialize(), and protocols::md::Rattle::setup_constraint().

get_atom_index()

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

inline

References atom_indices_.

Referenced by core::optimization::cartesian_collect_torsional_deriv(), and protocols::md::Rattle::setup_constraint().

get_dof_id()

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

inline

References moving_dofids_.

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

get_TorsionID()

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

inline

References moving_torsionids_.

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

natoms()

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(), copy_dofs_to_pose(), protocols::md::CartesianMD::do_initialize(), protocols::md::Rattle::Rattle(), and protocols::md::Rattle::setup_constraint().

ndofs()

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(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::cryst::ReportGradientsMover::compute(), protocols::md::CartesianMD::do_initialize(), core::util::getMLweight_cart(), protocols::md::CartesianMD::report_MD(), and core::optimization::CartesianMinimizer::run().

ntorsions()

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

inline

References moving_dofids_.

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

reset()

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::size().

Referenced by setup().

setup()

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, assign_rosetta_torsions_and_trim(), atom_indices_, core::conformation::Conformation::atom_tree(), core::pose::Pose::atom_tree(), core::id::DOF_ID::BOGUS_DOF_ID(), core::pose::Pose::conformation(), domain_map_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::first_sidechain_hydrogen(), core::id::AtomID_Map< T >::get(), core::kinematics::MoveMap::get_atoms(), core::kinematics::MoveMap::get_bb(), core::kinematics::MoveMap::get_chi(), core::pose::initialize_atomid_map(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_virtual_residue(), moving_atoms_, core::id::AtomID_Map< T >::n_atom(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), reset(), core::pose::Pose::residue(), core::kinematics::AtomTree::root(), core::id::AtomID_Map< T >::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_branches(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_nu(), core::pose::setup_dof_mask_from_move_map(), core::pose::Pose::size(), and core::kinematics::AtomTree::update_domain_map().

Referenced by protocols::md::CartesianMD::apply(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::cryst::ReportGradientsMover::compute(), protocols::md::CartesianMD::do_initialize(), protocols::md::CartesianMD::do_MD(), protocols::md::CartesianMD::dump_poses(), core::util::getMLweight_cart(), and core::optimization::CartesianMinimizer::run().

zero_stored_derivs()

void core::optimization::CartesianMinimizerMap::zero_stored_derivs

(

)

References atom_derivatives_.

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

Member Data Documentation

atom_derivatives_

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

private

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

atom_indices_

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

private

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

domain_map_

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

private

Referenced by domain_map(), and setup().

moving_atoms_

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().

moving_dofids_

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().

moving_torsionids_

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

private

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

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

• src/core/optimization/CartesianMinimizerMap.hh
• src/core/optimization/CartesianMinimizerMap.cc