#include <AtomTreeSCMinMinimizerMap.hh>

Inheritance diagram for core::pack::scmin::AtomTreeSCMinMinimizerMap:

Public Types
typedef optimization::DOF_Node	DOF_Node

typedef optimization::DOF_NodeOP	DOF_NodeOP

Public Types inherited from core::kinematics::MinimizerMapBase
typedef id::AtomID	AtomID

typedef id::DOF_ID	DOF_ID

typedef id::DOF_Type	DOF_Type

Public Member Functions
	AtomTreeSCMinMinimizerMap ()

	~AtomTreeSCMinMinimizerMap () override

void	set_total_residue (Size total_residue) override
	the AtomTreeSCMinMinimizerMap has to know how many residues are in the pose; this allows it to do O(1) updates to its DomainMap – this function costs O(N). More...

void	clear_active_dofs () override
	Disable the minimization for all residues. Ammortized O(1). More...

void	activate_residue_dofs (Size resindex) override
	Activate all the dofs for a particular residue. Ammortized O(1). More...

void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent) override
	Invoked during the depth-first traversal through the AtomTree. The AtomTree is indicating that a particular torsion is dependent on another torsion. Record that fact. More...

void	add_atom (AtomID const &atom_id, DOF_ID const &dof_id) override
	Invoked during the depth-first traversal through the AtomTree; the atom tree is indicating that a given atom is controlled by a particular DOF. Record that fact. More...

void	setup (AtomTreeCollectionOP trees) override
	Traverse the atom trees in preparation for minimization to tie together all the DOFs and the atoms they control. More...

Size	nactive_residues () const
	Accessors. More...

Size	active_residue (Size index) const

kinematics::DomainMap const &	domain_map () const override
	MinimizerMapBase class virtual accessor. More...

kinematics::DomainMap const &	dm () const
	Inline accessor. More...

Size	n_dof_nodes () const override

void	starting_dofs (optimization::Multivec &dofs) const override
	Initialize a multivec with the dofs reflected in the current residue(s) More...

void	assign_dofs_to_mobile_residues (optimization::Multivec const &dofs) override
	Assign the chi values to the residue(s) More...

optimization::DOF_Node &	dof_node (Size index) override

conformation::Residue const &	residue (Size seqpos) const override
	Convenience lookup – turns over the request to the AtomTreeCollection. More...

basic::datacache::BasicDataCache &	residue_data (Size seqpos) const override
	Convenience lookup – turns over the request to the AtomTreeCollection. More...

optimization::DOF_Node const &	dof_node_for_chi (Size resid, Size chiid) const override

id::TorsionID	tor_for_dof (id::DOF_ID const &dofid) const override

kinematics::tree::Atom const &	atom (AtomID const &atid) const override

void	zero_atom_derivative_vectors () override

void	link_torsion_vectors () override
	propagate f1/f2's up from children to parents More...

void	set_natoms_for_residue (Size resid, Size natoms) override

optimization::MultifuncOP	make_multifunc (pose::Pose &p, utility::vector1< conformation::ResidueCOP > const &bg_residues, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph) override

Public Member Functions inherited from core::pack::scmin::SCMinMinimizerMap
	SCMinMinimizerMap ()

	~SCMinMinimizerMap () override

Size	nactive_residues () const
	Accessors. More...

Size	active_residue (Size index) const

kinematics::DomainMap const &	domain_map () const override
	MinimizerMapBase class virtual accessor. More...

kinematics::DomainMap const &	dm () const
	Inline accessor. More...

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

void	set_nonideal (bool val_in)

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

	~MinimizerMapBase () override
	dstor More...

Protected Member Functions
void	reset_dof_nodes () override

Private Attributes
utility::vector1 < ResidueAtomTreeCollectionOP >	atcs_for_residues_

id::DOF_ID_Mask	dof_mask_

utility::vector1 < optimization::DOF_NodeOP >	dof_nodes_

Size	n_active_dof_nodes_

AtomTreeCollectionOP	atom_tree_collection_

utility::vector1< Size >	atoms_representing_chis_

utility::vector1< Size >	atoms_representing_ds_

utility::vector1< Size >	atoms_representing_thetas_

utility::vector1< Size >	chi_start_for_active_residue_

utility::vector1 < utility::vector1< Size > >	active_residue_atom_to_dofnode_index_

Size	dof_start_for_focused_residue_
	For parent_dof lookup: track which dofs a particular atom are responsible for. More...

Size	ndofs_added_for_focused_residue_

Additional Inherited Members
Protected Attributes inherited from core::pack::scmin::SCMinMinimizerMap
Size	focused_residue_

Size	nactive_residues_

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

utility::vector1< Size >	active_residue_index_for_res_

utility::vector1< Size >	active_residues_

kinematics::DomainMap	domain_map_

bool	nonideal_

Member Typedef Documentation

typedef optimization::DOF_Node core::pack::scmin::AtomTreeSCMinMinimizerMap::DOF_Node

typedef optimization::DOF_NodeOP core::pack::scmin::AtomTreeSCMinMinimizerMap::DOF_NodeOP

Constructor & Destructor Documentation

core::pack::scmin::AtomTreeSCMinMinimizerMap::AtomTreeSCMinMinimizerMap ( )

core::pack::scmin::AtomTreeSCMinMinimizerMap::~AtomTreeSCMinMinimizerMap ( )

overridedefault

Member Function Documentation

void core::pack::scmin::AtomTreeSCMinMinimizerMap::activate_residue_dofs ( Size resindex )

overridevirtual

Activate all the dofs for a particular residue. Ammortized O(1).

This should be called at most once per residue between calls to "clear_active_chi"

Implements core::pack::scmin::SCMinMinimizerMap.

References core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, core::pack::scmin::SCMinMinimizerMap::domain_map_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::active_residue ( Size index ) const

inline

References core::pack::scmin::SCMinMinimizerMap::active_residues_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

Referenced by setup().

void core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom	(	AtomID const &	atom_id,
		DOF_ID const &	dof_id
	)

overridevirtual

Invoked during the depth-first traversal through the AtomTree; the atom tree is indicating that a given atom is controlled by a particular DOF. Record that fact.

Implements core::pack::scmin::SCMinMinimizerMap.

References core::id::DOF_ID::atomno(), core::id::AtomID::atomno(), atoms_representing_chis_, atoms_representing_ds_, atoms_representing_thetas_, core::id::D, dof_nodes_, dof_start_for_focused_residue_, core::pack::scmin::SCMinMinimizerMap::focused_residue_, n_active_dof_nodes_, core::id::THETA, core::id::DOF_ID::type(), and core::id::DOF_ID::valid().

void core::pack::scmin::AtomTreeSCMinMinimizerMap::add_torsion	(	DOF_ID const &	new_torsion,
		DOF_ID const &	parent
	)

overridevirtual

Invoked during the depth-first traversal through the AtomTree. The AtomTree is indicating that a particular torsion is dependent on another torsion. Record that fact.

Implements core::pack::scmin::SCMinMinimizerMap.

References core::id::DOF_ID::atomno(), atoms_representing_chis_, atoms_representing_ds_, atoms_representing_thetas_, core::id::D, dof_nodes_, dof_start_for_focused_residue_, core::pack::scmin::SCMinMinimizerMap::focused_residue_, n_active_dof_nodes_, ndofs_added_for_focused_residue_, core::id::PHI, core::id::THETA, core::id::DOF_ID::type(), and core::id::DOF_ID::valid().

void core::pack::scmin::AtomTreeSCMinMinimizerMap::assign_dofs_to_mobile_residues ( optimization::Multivec const & dofs )

overridevirtual

Assign the chi values to the residue(s)

Implements core::pack::scmin::SCMinMinimizerMap.

References core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, core::optimization::DOF_Node::atomno(), core::id::D, dof_nodes_, n_active_dof_nodes_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, core::id::PHI, core::optimization::DOF_Node::rsd(), core::id::THETA, and core::optimization::DOF_Node::type().

kinematics::tree::Atom const & core::pack::scmin::AtomTreeSCMinMinimizerMap::atom ( AtomID const & atid ) const

overridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References atcs_for_residues_, core::id::AtomID::atomno(), and core::id::AtomID::rsd().

void core::pack::scmin::AtomTreeSCMinMinimizerMap::clear_active_dofs ( )

overridevirtual

Disable the minimization for all residues. Ammortized O(1).

Implements core::pack::scmin::SCMinMinimizerMap.

References active_residue_atom_to_dofnode_index_, core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, chi_start_for_active_residue_, core::pack::scmin::SCMinMinimizerMap::domain_map_, core::sequence::end, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and reset_dof_nodes().

kinematics::DomainMap const& core::pack::scmin::AtomTreeSCMinMinimizerMap::dm ( ) const

inline

Inline accessor.

References core::pack::scmin::SCMinMinimizerMap::domain_map_.

optimization::DOF_Node& core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node ( Size index )

inlineoverridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References dof_nodes_, and n_active_dof_nodes_.

AtomTreeSCMinMinimizerMap::DOF_Node const & core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node_for_chi	(	Size	resid,
		Size	chiid
	)		const

overridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References active_residue_atom_to_dofnode_index_, core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, atcs_for_residues_, and dof_nodes_.

kinematics::DomainMap const& core::pack::scmin::AtomTreeSCMinMinimizerMap::domain_map ( ) const

inlineoverridevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

References core::pack::scmin::SCMinMinimizerMap::domain_map_.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::link_torsion_vectors ( )

overridevirtual

propagate f1/f2's up from children to parents

super simple – no need for a sort (nor is there a need in the optimization::MinimizerMap for that matter).

Implements core::pack::scmin::SCMinMinimizerMap.

References dof_nodes_, and n_active_dof_nodes_.

optimization::MultifuncOP core::pack::scmin::AtomTreeSCMinMinimizerMap::make_multifunc	(	pose::Pose &	p,
		utility::vector1< conformation::ResidueCOP > const &	bg_residues,
		scoring::ScoreFunction const &	sfxn,
		scoring::MinimizationGraph &	mingraph
	)

inlineoverridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::n_dof_nodes ( ) const

inlineoverridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References n_active_dof_nodes_.

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::nactive_residues ( ) const

inline

Accessors.

References core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::reset_dof_nodes ( )

overrideprotectedvirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References dof_nodes_, and n_active_dof_nodes_.

Referenced by clear_active_dofs(), set_total_residue(), and setup().

conformation::Residue const & core::pack::scmin::AtomTreeSCMinMinimizerMap::residue ( Size seqpos ) const

overridevirtual

Convenience lookup – turns over the request to the AtomTreeCollection.

Implements core::pack::scmin::SCMinMinimizerMap.

References atcs_for_residues_.

Referenced by tor_for_dof().

basic::datacache::BasicDataCache & core::pack::scmin::AtomTreeSCMinMinimizerMap::residue_data ( Size seqpos ) const

overridevirtual

Convenience lookup – turns over the request to the AtomTreeCollection.

Implements core::pack::scmin::SCMinMinimizerMap.

References atcs_for_residues_.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::set_natoms_for_residue	(	Size	resid,
		Size	natoms
	)

overridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References core::pack::scmin::SCMinMinimizerMap::atom_derivatives_.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::set_total_residue ( Size total_residue )

overridevirtual

the AtomTreeSCMinMinimizerMap has to know how many residues are in the pose; this allows it to do O(1) updates to its DomainMap – this function costs O(N).

Implements core::pack::scmin::SCMinMinimizerMap.

References active_residue_atom_to_dofnode_index_, core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, core::pack::scmin::SCMinMinimizerMap::atom_derivatives_, chi_start_for_active_residue_, dof_nodes_, core::pack::scmin::SCMinMinimizerMap::domain_map_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and reset_dof_nodes().

void core::pack::scmin::AtomTreeSCMinMinimizerMap::setup ( AtomTreeCollectionOP trees )

overridevirtual

Traverse the atom trees in preparation for minimization to tie together all the DOFs and the atoms they control.

Implements core::pack::scmin::SCMinMinimizerMap.

References active_residue(), active_residue_atom_to_dofnode_index_, core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, atom_tree_collection_, atoms_representing_chis_, atoms_representing_ds_, atoms_representing_thetas_, core::conformation::Residue::chi_atoms(), core::id::D, dof_mask_, dof_start_for_focused_residue_, core::pack::scmin::SCMinMinimizerMap::focused_residue_, n_active_dof_nodes_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), ndofs_added_for_focused_residue_, core::pack::scmin::SCMinMinimizerMap::nonideal_, core::id::PHI, reset_dof_nodes(), and core::id::THETA.

void core::pack::scmin::AtomTreeSCMinMinimizerMap::starting_dofs ( optimization::Multivec & dofs ) const

overridevirtual

Initialize a multivec with the dofs reflected in the current residue(s)

Implements core::pack::scmin::SCMinMinimizerMap.

References atcs_for_residues_, core::optimization::DOF_Node::atomno(), core::id::D, dof_nodes_, n_active_dof_nodes_, core::id::PHI, core::optimization::DOF_Node::rsd(), core::id::THETA, and core::optimization::DOF_Node::type().

id::TorsionID core::pack::scmin::AtomTreeSCMinMinimizerMap::tor_for_dof ( id::DOF_ID const & dofid ) const

overridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References core::id::DOF_ID::atomno(), core::id::TorsionID::BOGUS_TORSION_ID(), core::id::CHI, core::id::PHI, residue(), core::id::DOF_ID::rsd(), and core::id::DOF_ID::type().

void core::pack::scmin::AtomTreeSCMinMinimizerMap::zero_atom_derivative_vectors ( )

overridevirtual

Implements core::pack::scmin::SCMinMinimizerMap.

References core::pack::scmin::SCMinMinimizerMap::active_residues_, core::pack::scmin::SCMinMinimizerMap::atom_derivatives_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

Member Data Documentation

utility::vector1< utility::vector1< Size > > core::pack::scmin::AtomTreeSCMinMinimizerMap::active_residue_atom_to_dofnode_index_

private

Referenced by clear_active_dofs(), dof_node_for_chi(), set_total_residue(), and setup().

utility::vector1< ResidueAtomTreeCollectionOP > core::pack::scmin::AtomTreeSCMinMinimizerMap::atcs_for_residues_

private

Referenced by assign_dofs_to_mobile_residues(), atom(), clear_active_dofs(), dof_node_for_chi(), residue(), residue_data(), set_total_residue(), setup(), and starting_dofs().

AtomTreeCollectionOP core::pack::scmin::AtomTreeSCMinMinimizerMap::atom_tree_collection_

private

Referenced by setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::atoms_representing_chis_

private

Referenced by add_atom(), add_torsion(), and setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::atoms_representing_ds_

private

Referenced by add_atom(), add_torsion(), and setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::atoms_representing_thetas_

private

Referenced by add_atom(), add_torsion(), and setup().

utility::vector1< Size > core::pack::scmin::AtomTreeSCMinMinimizerMap::chi_start_for_active_residue_

private

Referenced by clear_active_dofs(), and set_total_residue().

id::DOF_ID_Mask core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_mask_

private

Referenced by setup().

utility::vector1< optimization::DOF_NodeOP > core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_nodes_

private

Referenced by add_atom(), add_torsion(), assign_dofs_to_mobile_residues(), dof_node(), dof_node_for_chi(), link_torsion_vectors(), reset_dof_nodes(), set_total_residue(), and starting_dofs().

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_start_for_focused_residue_

private

For parent_dof lookup: track which dofs a particular atom are responsible for.

Referenced by add_atom(), add_torsion(), and setup().

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::n_active_dof_nodes_

private

Referenced by add_atom(), add_torsion(), assign_dofs_to_mobile_residues(), dof_node(), link_torsion_vectors(), n_dof_nodes(), reset_dof_nodes(), setup(), and starting_dofs().

Size core::pack::scmin::AtomTreeSCMinMinimizerMap::ndofs_added_for_focused_residue_

private

Referenced by add_torsion(), and setup().

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

src/core/pack/scmin/AtomTreeSCMinMinimizerMap.hh
src/core/pack/scmin/AtomTreeSCMinMinimizerMap.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation