core::pack::scmin::SCMinMultifunc Class Reference

#include <SCMinMultifunc.hh>

Inheritance diagram for core::pack::scmin::SCMinMultifunc:

Public Types
typedef optimization::Multivec	Multivec
Public Types inherited from core::optimization::Multifunc
typedef utility::VirtualBase	parent

Public Member Functions
	SCMinMultifunc (pose::Pose &p, utility::vector1< conformation::ResidueCOP > const &bg_residues, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, SCMinMinimizerMap &scminmap)
	Constructor. The pose is only modified during setup-for-scoring calls. Its residue objects are untouched (though they are accessed). The SCMinMultifunc modifies the residues that are contained in the SCMinMinimizerMap's AtomTreeCollection. The minmap also describes which degrees of freedom are free. The minimization graph should have already been setup so that its edges connect all neighboring residues which will be involved in the minimization: any residue that's being minimized must have all of its neighbors represented by edges in the graph. Active edges and nodes must already have had "setup_for_minimizing_for_{residue/residue_pair}" invoked: basically, the SCMinMultifunc is absolved of all responsibility for setting up. More...
	~SCMinMultifunc () override
Real	operator() (Multivec const &chi) const override
void	dfunc (Multivec const &chi, Multivec &dE_dchi) const override
bool	abort_min (Multivec const &) const override
	Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN! More...
void	dump (Multivec const &, Multivec const &) const override
	Error state reached; dump out something corresponding to the var assignment. Default base class implementation: no_op();. More...
void	scmin_numerical_derivative_check (Multivec const &start_vars, Multivec &dE_dvars) const
Public Member Functions inherited from core::optimization::Multifunc
	~Multifunc () override=default
	Destructor. More...

Private Attributes
pose::Pose &	pose_
utility::vector1< conformation::ResidueCOP > const &	bg_residues_
scoring::ScoreFunction const &	sfxn_
scoring::MinimizationGraph &	g_
SCMinMinimizerMap &	scminmap_
scoring::ScoreTypes	scoretypes_

Additional Inherited Members
Protected Member Functions inherited from core::optimization::Multifunc
	Multifunc ()
	Default constructor. More...
	Multifunc (Multifunc const &)
	Copy constructor. More...
Multifunc &	operator= (Multifunc const &)
	Copy assignment. More...

Member Typedef Documentation

Multivec

typedef optimization::Multivec core::pack::scmin::SCMinMultifunc::Multivec

Constructor & Destructor Documentation

SCMinMultifunc()

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

Constructor. The pose is only modified during setup-for-scoring calls. Its residue objects are untouched (though they are accessed). The SCMinMultifunc modifies the residues that are contained in the SCMinMinimizerMap's AtomTreeCollection. The minmap also describes which degrees of freedom are free. The minimization graph should have already been setup so that its edges connect all neighboring residues which will be involved in the minimization: any residue that's being minimized must have all of its neighbors represented by edges in the graph. Active edges and nodes must already have had "setup_for_minimizing_for_{residue/residue_pair}" invoked: basically, the SCMinMultifunc is absolved of all responsibility for setting up.

~SCMinMultifunc()

core::pack::scmin::SCMinMultifunc::~SCMinMultifunc ( )

overridedefault

Member Function Documentation

abort_min()

bool core::pack::scmin::SCMinMultifunc::abort_min ( Multivec const &  ) const

overridevirtual

Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

Reimplemented from core::optimization::Multifunc.

dfunc()

void core::pack::scmin::SCMinMultifunc::dfunc ( Multivec const &  chi, Multivec &  dE_dchi  ) const

overridevirtual

Implements core::optimization::Multifunc.

References core::pack::scmin::SCMinMinimizerMap::active_residue(), core::pack::scmin::SCMinMinimizerMap::assign_dofs_to_mobile_residues(), core::pack::scmin::SCMinMinimizerMap::atom(), core::pack::scmin::SCMinMinimizerMap::atom_derivatives(), core::optimization::DOF_Node::atom_id(), core::optimization::DOF_Node::atoms(), bg_residues_, core::id::D, core::pack::scmin::SCMinMinimizerMap::dm(), core::optimization::DOF_Node::dof_id(), core::pack::scmin::SCMinMinimizerMap::dof_node(), core::scoring::eval_atom_derivatives_for_minedge(), core::scoring::eval_atom_derivatives_for_minnode(), core::scoring::eval_dof_deriv_for_minnode(), core::optimization::DOF_Node::F1(), core::optimization::DOF_Node::F2(), g_, core::scoring::MinimizationGraph::get_minimization_node(), core::pack::scmin::SCMinMinimizerMap::link_torsion_vectors(), core::pack::scmin::SCMinMinimizerMap::n_dof_nodes(), core::pack::scmin::SCMinMinimizerMap::nactive_residues(), core::id::PHI, pose_, core::scoring::MinimizationNode::res_min_data(), core::pack::scmin::SCMinMinimizerMap::residue(), core::pack::scmin::SCMinMinimizerMap::residue_data(), core::optimization::DOF_Node::rsd(), scminmap_, core::scoring::MinimizationNode::setup_for_derivatives(), core::scoring::MinimizationEdge::setup_for_derivatives(), sfxn_, core::id::THETA, core::pack::scmin::SCMinMinimizerMap::tor_for_dof(), core::optimization::torsional_derivative_from_cartesian_derivatives(), core::optimization::DOF_Node::type(), core::scoring::ScoreFunction::weights(), and core::pack::scmin::SCMinMinimizerMap::zero_atom_derivative_vectors().

dump()

void core::pack::scmin::SCMinMultifunc::dump ( Multivec const &  , Multivec const &    ) const

overridevirtual

Error state reached; dump out something corresponding to the var assignment. Default base class implementation: no_op();.

Reimplemented from core::optimization::Multifunc.

operator()()

Real core::pack::scmin::SCMinMultifunc::operator() ( Multivec const &  chi ) const

overridevirtual

Implements core::optimization::Multifunc.

References core::pack::scmin::SCMinMinimizerMap::active_residue(), core::pack::scmin::SCMinMinimizerMap::assign_dofs_to_mobile_residues(), bg_residues_, core::pack::scmin::SCMinMinimizerMap::dm(), core::scoring::EMapVector::dot(), core::scoring::eval_res_onebody_energies_for_minnode(), core::scoring::eval_res_pair_energy_for_minedge(), g_, core::scoring::MinimizationGraph::get_minimization_node(), core::pack::scmin::SCMinMinimizerMap::nactive_residues(), pose_, core::pack::scmin::SCMinMinimizerMap::residue(), core::pack::scmin::SCMinMinimizerMap::residue_data(), scminmap_, scoretypes_, core::scoring::MinimizationNode::setup_for_scoring(), core::scoring::MinimizationEdge::setup_for_scoring(), sfxn_, and core::scoring::ScoreFunction::weights().

scmin_numerical_derivative_check()

void core::pack::scmin::SCMinMultifunc::scmin_numerical_derivative_check	(	Multivec const &	start_vars,
		Multivec &	dE_dvars
	)		const

References protocols::comparative_modeling::features::A, core::pack::scmin::SCMinMinimizerMap::dof_node(), core::chemical::element::F, core::chemical::element::I, core::pack::scmin::SCMinMinimizerMap::n_dof_nodes(), scminmap_, core::pack::scmin::TR(), and core::optimization::DOF_Node::type().

Member Data Documentation

bg_residues_

utility::vector1< conformation::ResidueCOP > const& core::pack::scmin::SCMinMultifunc::bg_residues_

private

Referenced by dfunc(), and operator()().

g_

scoring::MinimizationGraph& core::pack::scmin::SCMinMultifunc::g_

private

Referenced by dfunc(), and operator()().

pose_

pose::Pose& core::pack::scmin::SCMinMultifunc::pose_

private

Referenced by dfunc(), and operator()().

scminmap_

SCMinMinimizerMap& core::pack::scmin::SCMinMultifunc::scminmap_

private

Referenced by dfunc(), operator()(), and scmin_numerical_derivative_check().

scoretypes_

scoring::ScoreTypes core::pack::scmin::SCMinMultifunc::scoretypes_

private

Referenced by operator()().

sfxn_

scoring::ScoreFunction const& core::pack::scmin::SCMinMultifunc::sfxn_

private

Referenced by dfunc(), and operator()().

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

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