Fullatom Membrane Environment Energy. More...

#include <FaMPEnvEnergy.hh>

Inheritance diagram for core::energy_methods::FaMPEnvEnergy:

Public Types
typedef core::scoring::methods::ContextDependentOneBodyEnergy	parent

Public Types inherited from core::scoring::methods::ContextDependentOneBodyEnergy
typedef OneBodyEnergy	parent

Public Types inherited from core::scoring::methods::OneBodyEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::VirtualBase	parent

Public Member Functions
	FaMPEnvEnergy (core::scoring::etable::MembEtableCAP memb_etable_in)
	Construct Energy Method from Etable. More...

core::scoring::methods::EnergyMethodOP	clone () const override
	Clone Energy Method. More...

void	residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, core::scoring::EnergyMap &emap) const override
	Compute Per-Residue Energies. More...

void	finalize_total_energy (pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &emap) const override
	Fianlzie Total Per-Residue Energies. More...

void	setup_for_derivatives (pose::Pose &pose, core::scoring::ScoreFunction const &scfxn) const override
	Setup for Computing Derivatives. More...

void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap const &emap, Vector &F1, Vector &F2) const override
	Evaluate Per-Atom Derivatives. More...

void	indicate_required_context_graphs (utility::vector1< bool > &) const override
	Fa_MbenvEnergy is context independent. More...

void	setup_for_scoring (pose::Pose &pose, core::scoring::ScoreFunction const &) const override
	Setup Method for initial scoring. More...

Public Member Functions inherited from core::scoring::methods::ContextDependentOneBodyEnergy
	ContextDependentOneBodyEnergy (EnergyMethodCreatorOP)
	Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More...

EnergyMethodType	method_type () const override
	Returns the cd_1b element of the EnergyMethodType enumeration; this method should NOT be overridden by derived classes. More...

Public Member Functions inherited from core::scoring::methods::OneBodyEnergy
	OneBodyEnergy (EnergyMethodCreatorOP)
	Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More...

	~OneBodyEnergy () override

virtual bool	defines_score_for_residue (conformation::Residue const &) const
	During minimization, energy methods are allowed to decide that they say nothing about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return "true" for all residues. More...

virtual bool	use_extended_residue_energy_interface () const
	Rely on the extended version of the residue_energy function during score-function evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return 'true' for the extended version. The default method implemented in this class returns 'false'. More...

virtual void	residue_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const
	Evaluate the one-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

virtual void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, basic::datacache::BasicDataCache &, ResSingleMinimizationData &) const
	Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
	Do any setup work should the coordinates of this residue, who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...

virtual bool	requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...

virtual void	setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const
	Do any setup work necessary before evaluating the derivatives for this residue. More...

virtual void	eval_residue_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
	Evaluate the derivative for an atom in a residue in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. DEPRECATED – too slow. More...

virtual bool	defines_dof_derivatives (pose::Pose const &p) const
	Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...

virtual utility::vector1 < id::PartialAtomID >	atoms_with_dof_derivatives (conformation::Residue const &res, pose::Pose const &pose) const
	For a particular residue, list which atoms go into defining the DOF derivatives, including any atoms on adjacent residues. The Pose is provided for context, but there is no requirement that res be a member of that Pose. More...

virtual Real	eval_residue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
	Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
	if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
	if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
	If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More...

virtual void	setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
	Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...

virtual void	finalize_after_minimizing (pose::Pose &pose) const
	Called after minimization, allowing a derived class to do some teardown steps. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

virtual void	show_additional_info (std::ostream &, pose::Pose &, bool) const
	show additional information of the energy method More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
Real	eval_fa_mbenv (conformation::Atom const &atom1, Real const &f1) const
	Evaluate Per-Atom Env term. More...

core::Size	version () const override
	Versioning. More...

void	init (pose::Pose &pose) const
	Initialize Energy Method data for derivatives. More...

core::Real	compute_fa_proj (core::Real z_position, core::Real thickness, core::Real steepness) const
	Helper Method - Compute Fa Proj. More...

core::Real	compute_fa_deriv (core::Real z_position, core::Real thickness, core::Real steepness) const
	Helper Method - Compute Fa Derivatives. More...

core::Vector	compute_fa_proj_coord (core::Real z_position, core::Vector xyz, core::Vector center, core::Vector normal) const
	Helper Method - Compute Fa Proj coordinate. More...

void	setup_for_fullatom (pose::Pose &pose) const
	Allocate memory for derivatives. More...

Private Attributes
core::scoring::etable::MembEtableCAP	memb_etable_

ObjexxFCL::FArray1< Real > const &	lk_dgrefce_

ObjexxFCL::FArray1< Real > const &	memb_lk_dgrefce_

Real	fa_mbenv_weight_

utility::vector1 < utility::vector1< Real > >	fa_proj_

utility::vector1 < utility::vector1< Real > >	fa_z_position_

utility::vector1 < utility::vector1< Vector > >	fa_proj_coord_

utility::vector1 < utility::vector1< Real > >	fa_proj_deriv_

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...

Detailed Description

Fullatom Membrane Environment Energy.

Member Typedef Documentation

typedef core::scoring::methods::ContextDependentOneBodyEnergy core::energy_methods::FaMPEnvEnergy::parent

Constructor & Destructor Documentation

core::energy_methods::FaMPEnvEnergy::FaMPEnvEnergy ( core::scoring::etable::MembEtableCAP memb_etable_in )

Construct Energy Method from Etable.

Member Function Documentation

core::scoring::methods::EnergyMethodOP core::energy_methods::FaMPEnvEnergy::clone ( ) const

overridevirtual

Clone Energy Method.

Implements core::scoring::methods::EnergyMethod.

core::Real core::energy_methods::FaMPEnvEnergy::compute_fa_deriv	(	core::Real	z_position,
		core::Real	thickness,
		core::Real	steepness
	)		const

private

Helper Method - Compute Fa Derivatives.

References core::conformation::membrane::thickness.

Referenced by init().

core::Real core::energy_methods::FaMPEnvEnergy::compute_fa_proj	(	core::Real	z_position,
		core::Real	thickness,
		core::Real	steepness
	)		const

private

Helper Method - Compute Fa Proj.

References core::conformation::membrane::thickness.

Referenced by init().

core::Vector core::energy_methods::FaMPEnvEnergy::compute_fa_proj_coord	(	core::Real	z_position,
		core::Vector	xyz,
		core::Vector	center,
		core::Vector	normal
	)		const

private

Helper Method - Compute Fa Proj coordinate.

References core::conformation::membrane::normal, and protocols::kinmatch::xyz().

Referenced by init().

void core::energy_methods::FaMPEnvEnergy::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	domain_map,
		core::scoring::ScoreFunction const &	sfxn,
		core::scoring::EnergyMap const &	emap,
		Vector &	F1,
		Vector &	F2
	)		const

overridevirtual

Evaluate Per-Atom Derivatives.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::id::AtomID::atomno(), fa_mbenv_weight_, fa_proj_coord_, fa_proj_deriv_, lk_dgrefce_, memb_lk_dgrefce_, core::pose::Pose::residue(), and core::id::AtomID::rsd().

Real core::energy_methods::FaMPEnvEnergy::eval_fa_mbenv	(	conformation::Atom const &	atom1,
		Real const &	f1
	)		const

private

Evaluate Per-Atom Env term.

References lk_dgrefce_, memb_lk_dgrefce_, protocols::hybridization::score, and core::conformation::Atom::type().

Referenced by residue_energy().

void core::energy_methods::FaMPEnvEnergy::finalize_total_energy	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	,
		core::scoring::EnergyMap &	emap
	)		const

overridevirtual

Fianlzie Total Per-Residue Energies.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::FaMPEnv.

void core::energy_methods::FaMPEnvEnergy::indicate_required_context_graphs ( utility::vector1< bool > & ) const

overridevirtual

Fa_MbenvEnergy is context independent.

Implements core::scoring::methods::EnergyMethod.

void core::energy_methods::FaMPEnvEnergy::init ( pose::Pose & pose ) const

private

Initialize Energy Method data for derivatives.

References core::conformation::membrane::center, compute_fa_deriv(), compute_fa_proj(), compute_fa_proj_coord(), core::pose::Pose::conformation(), fa_proj_, fa_proj_coord_, fa_proj_deriv_, fa_z_position_, core::conformation::Residue::nheavyatoms(), core::conformation::membrane::normal, core::pose::Pose::residue(), setup_for_fullatom(), core::pose::Pose::size(), core::conformation::membrane::thickness, protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by setup_for_derivatives(), and setup_for_scoring().

void core::energy_methods::FaMPEnvEnergy::residue_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		core::scoring::EnergyMap &	emap
	)		const

overridevirtual

Compute Per-Residue Energies.

Implements core::scoring::methods::ContextDependentOneBodyEnergy.

References core::conformation::Residue::atom(), eval_fa_mbenv(), fa_proj_, core::scoring::FaMPEnv, core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::seqpos().

void core::energy_methods::FaMPEnvEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scfxn
	)		const

overridevirtual

Setup for Computing Derivatives.

Reimplemented from core::scoring::methods::EnergyMethod.

References fa_mbenv_weight_, core::scoring::FaMPEnv, init(), and core::scoring::ScoreFunction::weights().

void core::energy_methods::FaMPEnvEnergy::setup_for_fullatom ( pose::Pose & pose ) const

private

Allocate memory for derivatives.

Setup Data Members for Fullatom Info.

References fa_proj_, fa_proj_coord_, fa_proj_deriv_, fa_z_position_, protocols::mean_field::max(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by init().

void core::energy_methods::FaMPEnvEnergy::setup_for_scoring	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &
	)		const

overridevirtual

Setup Method for initial scoring.

Reimplemented from core::scoring::methods::EnergyMethod.

References init().

core::Size core::energy_methods::FaMPEnvEnergy::version ( ) const

overrideprivatevirtual

Versioning.

Implements core::scoring::methods::EnergyMethod.

Member Data Documentation

Real core::energy_methods::FaMPEnvEnergy::fa_mbenv_weight_

mutableprivate

Referenced by eval_atom_derivative(), and setup_for_derivatives().

utility::vector1< utility::vector1 < Real > > core::energy_methods::FaMPEnvEnergy::fa_proj_

mutableprivate

Referenced by init(), residue_energy(), and setup_for_fullatom().

utility::vector1< utility::vector1 < Vector > > core::energy_methods::FaMPEnvEnergy::fa_proj_coord_

mutableprivate

Referenced by eval_atom_derivative(), init(), and setup_for_fullatom().

utility::vector1< utility::vector1 < Real > > core::energy_methods::FaMPEnvEnergy::fa_proj_deriv_

mutableprivate

Referenced by eval_atom_derivative(), init(), and setup_for_fullatom().

utility::vector1< utility::vector1 < Real > > core::energy_methods::FaMPEnvEnergy::fa_z_position_

mutableprivate

Referenced by init(), and setup_for_fullatom().

ObjexxFCL::FArray1< Real > const& core::energy_methods::FaMPEnvEnergy::lk_dgrefce_

private

Referenced by eval_atom_derivative(), and eval_fa_mbenv().

core::scoring::etable::MembEtableCAP core::energy_methods::FaMPEnvEnergy::memb_etable_

private

ObjexxFCL::FArray1< Real > const& core::energy_methods::FaMPEnvEnergy::memb_lk_dgrefce_

private

Referenced by eval_atom_derivative(), and eval_fa_mbenv().

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

src/core/energy_methods/FaMPEnvEnergy.hh
src/core/energy_methods/FaMPEnvEnergy.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation