core::pack::scmin::CartSCMinMinimizerMap Class Reference

#include <CartSCMinMinimizerMap.hh>

Inheritance diagram for core::pack::scmin::CartSCMinMinimizerMap:

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
	CartSCMinMinimizerMap ()
	~CartSCMinMinimizerMap () override
void	set_total_residue (Size total_residue) override
	the CartSCMinMinimizerMap 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
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
Size	get_atom_index (id::AtomID const &atm)
id::AtomID const &	get_atom (Size idx)
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< utility::vector1< id::AtomID > >	moving_atoms_
utility::vector1< core::Size >	nactive_moving_atoms_
core::Size	nactive_moving_atoms_total_
utility::vector1< id::AtomID >	dofid_to_atoms_
utility::vector1< utility::vector1< Size > >	atoms_to_dofid_
utility::vector1< core::Vector >	residue_coord_workspace_
AtomTreeCollectionOP	atom_tree_collection_
utility::vector1< ResidueAtomTreeCollectionOP >	atcs_for_residues_
kinematics::DomainMap	domain_map_

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

DOF_Node

typedef optimization::DOF_Node core::pack::scmin::CartSCMinMinimizerMap::DOF_Node

DOF_NodeOP

typedef optimization::DOF_NodeOP core::pack::scmin::CartSCMinMinimizerMap::DOF_NodeOP

Constructor & Destructor Documentation

CartSCMinMinimizerMap()

core::pack::scmin::CartSCMinMinimizerMap::CartSCMinMinimizerMap

(

)

References residue_coord_workspace_.

~CartSCMinMinimizerMap()

core::pack::scmin::CartSCMinMinimizerMap::~CartSCMinMinimizerMap ( )

overridedefault

Member Function Documentation

activate_residue_dofs()

void core::pack::scmin::CartSCMinMinimizerMap::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_, domain_map_, and core::pack::scmin::SCMinMinimizerMap::nactive_residues_.

active_residue()

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

inline

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

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), setup(), and starting_dofs().

add_atom()

void core::pack::scmin::CartSCMinMinimizerMap::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.

add_torsion()

void core::pack::scmin::CartSCMinMinimizerMap::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.

assign_dofs_to_mobile_residues()

void core::pack::scmin::CartSCMinMinimizerMap::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_, moving_atoms_, nactive_moving_atoms_total_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and residue_coord_workspace_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

atom()

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

overridevirtual

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

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

clear_active_dofs()

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

overridevirtual

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

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

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

dm()

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

inline

Inline accessor.

References domain_map_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

dof_node()

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

overridevirtual

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

References core::pack::scmin::dummy_nodeop.

dof_node_for_chi()

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

overridevirtual

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

References core::pack::scmin::dummy_nodeop.

domain_map()

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

inlineoverridevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

get_atom()

id::AtomID const& core::pack::scmin::CartSCMinMinimizerMap::get_atom ( Size  idx )

inline

References dofid_to_atoms_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

get_atom_index()

Size core::pack::scmin::CartSCMinMinimizerMap::get_atom_index ( id::AtomID const &  atm )

inline

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

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

link_torsion_vectors()

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

overridevirtual

propagate f1/f2's up from children to parents

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

make_multifunc()

optimization::MultifuncOP core::pack::scmin::CartSCMinMinimizerMap::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.

n_dof_nodes()

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

inlineoverridevirtual

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

References nactive_moving_atoms_total_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

nactive_residues()

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

inline

Accessors.

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

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

reset_dof_nodes()

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

overrideprotectedvirtual

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

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

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

residue()

conformation::Residue const & core::pack::scmin::CartSCMinMinimizerMap::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 core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), and tor_for_dof().

residue_data()

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

overridevirtual

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

References atcs_for_residues_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::pack::scmin::CartSCMinMultifunc::operator()().

set_natoms_for_residue()

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

overridevirtual

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

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

set_total_residue()

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

overridevirtual

the CartSCMinMinimizerMap 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 core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_, core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, core::pack::scmin::SCMinMinimizerMap::atom_derivatives_, atoms_to_dofid_, dofid_to_atoms_, domain_map_, moving_atoms_, nactive_moving_atoms_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and reset_dof_nodes().

setup()

void core::pack::scmin::CartSCMinMinimizerMap::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(), core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, atom_tree_collection_, atoms_to_dofid_, dofid_to_atoms_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::first_sidechain_hydrogen(), core::pack::scmin::SCMinMinimizerMap::focused_residue_, protocols::mean_field::min(), moving_atoms_, nactive_moving_atoms_, nactive_moving_atoms_total_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), and reset_dof_nodes().

starting_dofs()

void core::pack::scmin::CartSCMinMinimizerMap::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 active_residue(), core::pack::scmin::SCMinMinimizerMap::active_residues_, atcs_for_residues_, moving_atoms_, nactive_moving_atoms_total_, core::pack::scmin::SCMinMinimizerMap::nactive_residues_, and core::conformation::Residue::xyz().

tor_for_dof()

id::TorsionID core::pack::scmin::CartSCMinMinimizerMap::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().

zero_atom_derivative_vectors()

void core::pack::scmin::CartSCMinMinimizerMap::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_.

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc().

Member Data Documentation

atcs_for_residues_

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

private

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

atom_tree_collection_

AtomTreeCollectionOP core::pack::scmin::CartSCMinMinimizerMap::atom_tree_collection_

private

Referenced by setup().

atoms_to_dofid_

utility::vector1< utility::vector1< Size > > core::pack::scmin::CartSCMinMinimizerMap::atoms_to_dofid_

private

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

dofid_to_atoms_

utility::vector1< id::AtomID > core::pack::scmin::CartSCMinMinimizerMap::dofid_to_atoms_

private

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

domain_map_

kinematics::DomainMap core::pack::scmin::CartSCMinMinimizerMap::domain_map_

private

Referenced by activate_residue_dofs(), clear_active_dofs(), dm(), domain_map(), and set_total_residue().

moving_atoms_

utility::vector1< utility::vector1< id::AtomID > > core::pack::scmin::CartSCMinMinimizerMap::moving_atoms_

private

Referenced by assign_dofs_to_mobile_residues(), set_total_residue(), setup(), and starting_dofs().

nactive_moving_atoms_

utility::vector1< core::Size > core::pack::scmin::CartSCMinMinimizerMap::nactive_moving_atoms_

private

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

nactive_moving_atoms_total_

core::Size core::pack::scmin::CartSCMinMinimizerMap::nactive_moving_atoms_total_

private

Referenced by assign_dofs_to_mobile_residues(), n_dof_nodes(), reset_dof_nodes(), setup(), and starting_dofs().

residue_coord_workspace_

utility::vector1< core::Vector > core::pack::scmin::CartSCMinMinimizerMap::residue_coord_workspace_

private

Referenced by assign_dofs_to_mobile_residues(), and CartSCMinMinimizerMap().

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

• src/core/pack/scmin/CartSCMinMinimizerMap.hh
• src/core/pack/scmin/CartSCMinMinimizerMap.cc