#include <SCMinMinimizerMap.hh>

Inheritance diagram for core::pack::scmin::SCMinMinimizerMap:

[legend]

Public Member Functions
	SCMinMinimizerMap ()

	~SCMinMinimizerMap () override

virtual void	set_total_residue (Size total_residue)=0
	the SCMinMinimizerMap 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...

virtual void	clear_active_dofs ()=0
	Disable the minimization for all residues. Ammortized O(1). More...

virtual void	activate_residue_dofs (Size resindex)=0
	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=0
	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=0
	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...

virtual void	setup (AtomTreeCollectionOP trees)=0
	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...

virtual conformation::Residue const &	residue (Size seqpos) const =0
	Convenience lookup – turns over the request to the AtomTreeCollection. More...

virtual basic::datacache::BasicDataCache &	residue_data (Size seqpos) const =0

virtual Size	n_dof_nodes () const =0

virtual void	starting_dofs (optimization::Multivec &dofs) const =0
	Initialize a multivec with the dofs reflected in the current residue(s) More...

virtual void	assign_dofs_to_mobile_residues (optimization::Multivec const &dofs)=0
	Assign the chi values to the residue(s) More...

virtual optimization::DOF_Node &	dof_node (Size index)=0

virtual optimization::DOF_Node const &	dof_node_for_chi (Size resid, Size chiid) const =0

virtual id::TorsionID	tor_for_dof (id::DOF_ID const &dofid) const =0

virtual kinematics::tree::Atom const &	atom (AtomID const &atid) const =0

virtual void	zero_atom_derivative_vectors ()=0

virtual void	link_torsion_vectors ()=0
	propagate f1/f2's up from children to parents More...

virtual void	set_natoms_for_residue (Size resid, Size natoms)=0

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

void	set_nonideal (bool val_in)

virtual optimization::MultifuncOP	make_multifunc (pose::Pose &p, utility::vector1< conformation::ResidueCOP > const &bg_residues, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph)=0

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

	~MinimizerMapBase () override
	dstor More...

Protected Member Functions
virtual void	reset_dof_nodes ()=0

Protected Attributes
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_

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

◆ SCMinMinimizerMap()

core::pack::scmin::SCMinMinimizerMap::SCMinMinimizerMap ( )

inline

◆ ~SCMinMinimizerMap()

core::pack::scmin::SCMinMinimizerMap::~SCMinMinimizerMap ( )

inlineoverride

Member Function Documentation

◆ activate_residue_dofs()

virtual void core::pack::scmin::SCMinMinimizerMap::activate_residue_dofs ( Size resindex )

pure virtual

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

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

◆ active_residue()

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

inline

References active_residues_, and nactive_residues_.

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

◆ add_atom()

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

overridepure virtual

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::kinematics::MinimizerMapBase.

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

◆ add_torsion()

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

overridepure virtual

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::kinematics::MinimizerMapBase.

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

◆ assign_dofs_to_mobile_residues()

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

pure virtual

Assign the chi values to the residue(s)

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

◆ atom()

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

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

◆ atom_derivatives()

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

inline

References atom_derivatives_.

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

◆ clear_active_dofs()

virtual void core::pack::scmin::SCMinMinimizerMap::clear_active_dofs ( )

pure virtual

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

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

◆ dm()

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

inline

Inline accessor.

References domain_map_.

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

◆ dof_node()

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

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::scmin::SCMinMultifunc::dfunc(), and core::pack::scmin::SCMinMultifunc::scmin_numerical_derivative_check().

◆ dof_node_for_chi()

virtual optimization::DOF_Node const& core::pack::scmin::SCMinMinimizerMap::dof_node_for_chi	(	Size	resid,
		Size	chiid
	)		const

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

◆ domain_map()

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

inlineoverridevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

◆ link_torsion_vectors()

virtual void core::pack::scmin::SCMinMinimizerMap::link_torsion_vectors ( )

pure virtual

propagate f1/f2's up from children to parents

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

◆ make_multifunc()

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

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

◆ n_dof_nodes()

virtual Size core::pack::scmin::SCMinMinimizerMap::n_dof_nodes ( ) const

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::scmin::SCMinMultifunc::dfunc(), and core::pack::scmin::SCMinMultifunc::scmin_numerical_derivative_check().

◆ nactive_residues()

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

inline

Accessors.

References nactive_residues_.

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

◆ reset_dof_nodes()

virtual void core::pack::scmin::SCMinMinimizerMap::reset_dof_nodes ( )

protectedpure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

◆ residue()

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

pure virtual

Convenience lookup – turns over the request to the AtomTreeCollection.

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

◆ residue_data()

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

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

◆ set_natoms_for_residue()

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

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

◆ set_nonideal()

void core::pack::scmin::SCMinMinimizerMap::set_nonideal ( bool val_in )

inline

References nonideal_.

◆ set_total_residue()

virtual void core::pack::scmin::SCMinMinimizerMap::set_total_residue ( Size total_residue )

pure virtual

the SCMinMinimizerMap 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).

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

◆ setup()

virtual void core::pack::scmin::SCMinMinimizerMap::setup ( AtomTreeCollectionOP trees )

pure virtual

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

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

◆ starting_dofs()

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

pure virtual

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

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

◆ tor_for_dof()

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

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

◆ zero_atom_derivative_vectors()

virtual void core::pack::scmin::SCMinMinimizerMap::zero_atom_derivative_vectors ( )

pure virtual

Implemented in core::pack::scmin::CartSCMinMinimizerMap, and core::pack::scmin::AtomTreeSCMinMinimizerMap.

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

Member Data Documentation

◆ active_residue_index_for_res_

utility::vector1< Size > core::pack::scmin::SCMinMinimizerMap::active_residue_index_for_res_

protected

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::activate_residue_dofs(), core::pack::scmin::CartSCMinMinimizerMap::activate_residue_dofs(), core::pack::scmin::AtomTreeSCMinMinimizerMap::clear_active_dofs(), core::pack::scmin::CartSCMinMinimizerMap::clear_active_dofs(), core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node_for_chi(), core::pack::scmin::AtomTreeSCMinMinimizerMap::set_total_residue(), and core::pack::scmin::CartSCMinMinimizerMap::set_total_residue().

◆ active_residues_

utility::vector1< Size > core::pack::scmin::SCMinMinimizerMap::active_residues_

protected

◆ atom_derivatives_

utility::vector1< utility::vector1< scoring::DerivVectorPair > > core::pack::scmin::SCMinMinimizerMap::atom_derivatives_

protected

Referenced by atom_derivatives(), core::pack::scmin::AtomTreeSCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::CartSCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::AtomTreeSCMinMinimizerMap::set_total_residue(), core::pack::scmin::CartSCMinMinimizerMap::set_total_residue(), core::pack::scmin::AtomTreeSCMinMinimizerMap::zero_atom_derivative_vectors(), and core::pack::scmin::CartSCMinMinimizerMap::zero_atom_derivative_vectors().

◆ domain_map_

kinematics::DomainMap core::pack::scmin::SCMinMinimizerMap::domain_map_

protected

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::activate_residue_dofs(), core::pack::scmin::AtomTreeSCMinMinimizerMap::clear_active_dofs(), core::pack::scmin::AtomTreeSCMinMinimizerMap::dm(), dm(), core::pack::scmin::AtomTreeSCMinMinimizerMap::domain_map(), domain_map(), and core::pack::scmin::AtomTreeSCMinMinimizerMap::set_total_residue().

◆ focused_residue_

Size core::pack::scmin::SCMinMinimizerMap::focused_residue_

protected

each atom tree in the AtomTreeCollection will tell us that it represents residue 1. this variable tells us which residue is actually being represented.

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom(), core::pack::scmin::AtomTreeSCMinMinimizerMap::add_torsion(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), and core::pack::scmin::CartSCMinMinimizerMap::setup().

◆ nactive_residues_

Size core::pack::scmin::SCMinMinimizerMap::nactive_residues_

protected

◆ nonideal_

bool core::pack::scmin::SCMinMinimizerMap::nonideal_

protected

Referenced by set_nonideal(), and core::pack::scmin::AtomTreeSCMinMinimizerMap::setup().

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

src/core/pack/scmin/SCMinMinimizerMap.hh

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ SCMinMinimizerMap()

◆ ~SCMinMinimizerMap()

Member Function Documentation

◆ activate_residue_dofs()

◆ active_residue()

◆ add_atom()

◆ add_torsion()

◆ assign_dofs_to_mobile_residues()

◆ atom()

◆ atom_derivatives()

◆ clear_active_dofs()

◆ dm()

◆ dof_node()

◆ dof_node_for_chi()

◆ domain_map()

◆ link_torsion_vectors()

◆ make_multifunc()

◆ n_dof_nodes()

◆ nactive_residues()

◆ reset_dof_nodes()

◆ residue()

◆ residue_data()

◆ set_natoms_for_residue()

◆ set_nonideal()

◆ set_total_residue()

◆ setup()

◆ starting_dofs()

◆ tor_for_dof()

◆ zero_atom_derivative_vectors()

Member Data Documentation

◆ active_residue_index_for_res_

◆ active_residues_

◆ atom_derivatives_

◆ domain_map_

◆ focused_residue_

◆ nactive_residues_

◆ nonideal_