#include <SCMinMinimizerMap.hh>

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

Collaboration diagram for core::pack::scmin::SCMinMinimizerMap:

Public Member Functions
	SCMinMinimizerMap ()

virtual	~SCMinMinimizerMap ()

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...

virtual void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent)=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...

virtual void	add_atom (AtomID const &atom_id, DOF_ID const &dof_id)=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

virtual kinematics::DomainMap const &	domain_map () const
	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 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...

virtual	~MinimizerMapBase ()
	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

Detailed Description

Definition at line 60 of file SCMinMinimizerMap.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 63 of file SCMinMinimizerMap.hh.

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

inlinevirtual

Definition at line 70 of file SCMinMinimizerMap.hh.

Member Function Documentation

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

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

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

inline

Definition at line 119 of file SCMinMinimizerMap.hh.

References active_residues_, and nactive_residues_.

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

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

pure 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::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

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

pure 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::AtomTreeSCMinMinimizerMap, and core::pack::scmin::CartSCMinMinimizerMap.

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

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

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

pure virtual

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

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

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

inline

Definition at line 171 of file SCMinMinimizerMap.hh.

References atom_derivatives_.

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

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

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

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

inline

Inline accessor.

Definition at line 125 of file SCMinMinimizerMap.hh.

References domain_map_.

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

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

pure virtual

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

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

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

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

inlinevirtual

MinimizerMapBase class virtual accessor.

Implements core::kinematics::MinimizerMapBase.

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

Definition at line 122 of file SCMinMinimizerMap.hh.

References domain_map_.

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

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

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().

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

pure virtual

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

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

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

inline

Accessors.

Definition at line 118 of file SCMinMinimizerMap.hh.

References nactive_residues_.

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

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

protectedpure virtual

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

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

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

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

pure virtual

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

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

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

inline

Definition at line 176 of file SCMinMinimizerMap.hh.

References nonideal_.

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

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

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

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

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

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

pure virtual

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

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

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

pure virtual

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

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

Member Data Documentation

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

protected

Definition at line 201 of file SCMinMinimizerMap.hh.

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

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

protected

Definition at line 202 of file SCMinMinimizerMap.hh.

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

protected

Definition at line 199 of file SCMinMinimizerMap.hh.

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

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

protected

Definition at line 203 of file SCMinMinimizerMap.hh.

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().

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.

Definition at line 195 of file SCMinMinimizerMap.hh.

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