core::scoring::methods Namespace Reference

Namespaces
	dfire

Classes
struct	ResidueAtomOverlaps
class	CartBondedParameters
class	BBIndepCartBondedParameters
class	BBDepCartBondedParameters
class	ContextDependentLRTwoBodyEnergy
class	ContextDependentOneBodyEnergy
class	ContextDependentTwoBodyEnergy
class	ContextIndependentLRTwoBodyEnergy
class	ContextIndependentOneBodyEnergy
class	ContextIndependentTwoBodyEnergy
class	EnergyMethod
	base class for the energy method hierarchy More...
class	EnergyMethodCreator
	The EnergyMethodCreator class's responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one. More...
class	EnergyMethodOptions
class	EnergyMethodRegistrator
	This templated class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	FreeDOF_Options
class	LongRangeTwoBodyEnergy
class	MMBondAngleEnergy
class	MMBondAngleEnergyCreator
class	MMBondLengthEnergy
class	MMBondLengthEnergyCreator
class	MMLJEnergyInter
class	MMLJEnergyInterCreator
class	NeighborListData
class	MMLJEnergyIntra
class	MMLJEnergyIntraCreator
class	MMTorsionEnergy
class	MMTorsionEnergyCreator
class	OneBodyEnergy
class	PyEnergyMethodRegistrator
	This class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	ShortRangeTwoBodyEnergy
class	TwoBodyEnergy
class	WholeStructureEnergy
	Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...
class	NMerPSSMEnergy
class	NMerPSSMEnergyCreator
class	NMerRefEnergy
class	NMerRefEnergyCreator
class	NMerSVMEnergy
class	NMerSVMEnergyCreator

Typedefs
typedef utility::pointer::weak_ptr< CartBondedParameters >	CartBondedParametersAP
typedef utility::pointer::weak_ptr< CartBondedParameters const >	CartBondedParametersCAP
typedef utility::pointer::shared_ptr< CartBondedParameters >	CartBondedParametersOP
typedef utility::pointer::shared_ptr< CartBondedParameters const >	CartBondedParametersCOP
typedef utility::pointer::shared_ptr< ContextDependentLRTwoBodyEnergy >	ContextDependentLRTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< ContextDependentLRTwoBodyEnergy const >	ContextDependentLRTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< ContextDependentOneBodyEnergy >	ContextDependentOneBodyEnergyOP
typedef utility::pointer::shared_ptr< ContextDependentTwoBodyEnergy >	ContextDependentTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< ContextDependentTwoBodyEnergy const >	ContextDependentTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< ContextIndependentLRTwoBodyEnergy >	ContextIndependentLRTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< ContextIndependentLRTwoBodyEnergy const >	ContextIndependentLRTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< ContextIndependentOneBodyEnergy >	ContextIndependentOneBodyEnergyOP
typedef utility::pointer::shared_ptr< ContextIndependentOneBodyEnergy const >	ContextIndependentOneBodyEnergyCOP
typedef utility::pointer::shared_ptr< ContextIndependentTwoBodyEnergy >	ContextIndependentTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< ContextIndependentTwoBodyEnergy const >	ContextIndependentTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< EnergyMethod >	EnergyMethodOP
typedef utility::pointer::shared_ptr< EnergyMethod const >	EnergyMethodCOP
typedef utility::pointer::shared_ptr< EnergyMethodCreator >	EnergyMethodCreatorOP
typedef utility::pointer::shared_ptr< EnergyMethodCreator const >	EnergyMethodCreatorCOP
typedef utility::pointer::shared_ptr< EnergyMethodOptions >	EnergyMethodOptionsOP
typedef utility::pointer::shared_ptr< EnergyMethodOptions const >	EnergyMethodOptionsCOP
typedef utility::pointer::shared_ptr< FreeDOF_Options >	FreeDOF_OptionsOP
typedef utility::pointer::shared_ptr< FreeDOF_Options const >	FreeDOF_OptionsCOP
typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy >	LongRangeTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy const >	LongRangeTwoBodyEnergyCOP
typedef utility::pointer::weak_ptr< MMBondAngleEnergy >	MMBondAngleEnergyAP
typedef utility::pointer::weak_ptr< MMBondAngleEnergy const >	MMBondAngleEnergyCAP
typedef utility::pointer::shared_ptr< MMBondAngleEnergy >	MMBondAngleEnergyOP
typedef utility::pointer::shared_ptr< MMBondAngleEnergy const >	MMBondAngleEnergyCOP
typedef utility::pointer::weak_ptr< MMBondLengthEnergy >	MMBondLengthEnergyAP
typedef utility::pointer::weak_ptr< MMBondLengthEnergy const >	MMBondLengthEnergyCAP
typedef utility::pointer::shared_ptr< MMBondLengthEnergy >	MMBondLengthEnergyOP
typedef utility::pointer::shared_ptr< MMBondLengthEnergy const >	MMBondLengthEnergyCOP
typedef utility::pointer::weak_ptr< MMLJEnergyInter >	MMLJEnergyInterAP
typedef utility::pointer::weak_ptr< MMLJEnergyInter const >	MMLJEnergyInterCAP
typedef utility::pointer::shared_ptr< MMLJEnergyInter >	MMLJEnergyInterOP
typedef utility::pointer::shared_ptr< MMLJEnergyInter const >	MMLJEnergyInterCOP
typedef utility::pointer::weak_ptr< MMLJEnergyIntra >	MMLJEnergyIntraAP
typedef utility::pointer::weak_ptr< MMLJEnergyIntra const >	MMLJEnergyIntraCAP
typedef utility::pointer::shared_ptr< MMLJEnergyIntra >	MMLJEnergyIntraOP
typedef utility::pointer::shared_ptr< MMLJEnergyIntra const >	MMLJEnergyIntraCOP
typedef utility::pointer::shared_ptr< NeighborListData >	NeighborListDataOP
typedef utility::pointer::shared_ptr< NeighborListData const >	NeighborListDataCOP
typedef std::pair< mm::mm_torsion_atom_quad, core::Real >	mm_torsion_atom_quad_angle_pair
using	mmtaqap_iter = utility::vector1< mm_torsion_atom_quad_angle_pair >::const_iterator
typedef utility::pointer::weak_ptr< MMTorsionEnergy >	MMTorsionEnergyAP
typedef utility::pointer::weak_ptr< MMTorsionEnergy const >	MMTorsionEnergyCAP
typedef utility::pointer::shared_ptr< MMTorsionEnergy >	MMTorsionEnergyOP
typedef utility::pointer::shared_ptr< MMTorsionEnergy const >	MMTorsionEnergyCOP
typedef utility::pointer::shared_ptr< OneBodyEnergy >	OneBodyEnergyOP
typedef utility::pointer::shared_ptr< OneBodyEnergy const >	OneBodyEnergyCOP
typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy >	ShortRangeTwoBodyEnergyOP
typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy const >	ShortRangeTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< TwoBodyEnergy >	TwoBodyEnergyOP
typedef utility::pointer::shared_ptr< TwoBodyEnergy const >	TwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< WholeStructureEnergy >	WholeStructureEnergyOP
typedef utility::pointer::shared_ptr< NMerPSSMEnergy >	NMerPSSMEnergyOP
typedef utility::pointer::shared_ptr< NMerPSSMEnergy const >	NMerPSSMEnergyCOP
typedef utility::pointer::shared_ptr< NMerRefEnergy >	NMerRefEnergyOP
typedef utility::pointer::shared_ptr< NMerRefEnergy const >	NMerRefEnergyCOP
typedef utility::pointer::shared_ptr< NMerSVMEnergy >	NMerSVMEnergyOP
typedef utility::pointer::shared_ptr< NMerSVMEnergy const >	NMerSVMEnergyCOP

Enumerations
enum	EnergyMethodType {   ci_2b = 1 , cd_2b , ci_lr_2b , cd_lr_2b ,   ci_1b , cd_1b , ws , n_energy_method_types = ws }
enum	EnergyMethods {   etable_method = 1 , dunbrack_method , hbond_method , elec_method ,   lkball_method , mm_lj_energy_inter_method , pair_e_method , reference_e_method ,   vdw_method , ramachandran_method , n_energy_methods = ramachandran_method }
enum	LongRangeEnergyType {   constraints_lr = 1 , gen_born_lr , multipole_elec_lr , vdw_tinker_lr ,   sasa_lr , epr_deer_lr , PB_elec_lr , cart_bonded_lr ,   dna_dihedral_lr , gen_bonded_lr , rama2b_lr , ramaprepro_lr ,   aspartimide_penalty_lr , rna_suite_lr , tna_suite_lr , rna_stub_coord_lr ,   DFIRE , sym_bonus_lr , elec_dens_energy , elec_dens_fast_energy ,   elec_dens_cen_energy , elec_dens_allatom_cen_energy , elec_dens_atomwise_energy , patterson_corr_energy ,   fa_disulfide_energy , disulfide_matching_energy , centroid_disulfide_energy , n_long_range_types = centroid_disulfide_energy }

Functions
void	find_relevant_connections_onersd (pose::Pose const &pose, Size const seqpos, ResidueAtomOverlaps &branch_connection)
void	find_relevant_connections (pose::Pose const &pose, utility::vector1< ResidueAtomOverlaps > &branch_connections)
bool	is_lower_cutpoint (core::Size residue, core::pose::Pose const &pose)
bool	is_upper_cutpoint (core::Size residue, core::pose::Pose const &pose)
void	find_cutpoint_variants (core::pose::Pose const &pose, core::kinematics::FoldTree const &, utility::vector1< int > &cutpoints)
bool	lower_upper_connected_across_cutpoint (core::conformation::Residue const &lower_rsd, core::conformation::Residue const &upper_rsd)
	Helper function for looking at residue connections to get lower/upper partners. More...
Size	get_upper_cutpoint_partner_for_lower (core::pose::Pose const &pose, core::Size const lower_res)
	Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper. More...
Size	get_lower_cutpoint_partner_for_upper (core::pose::Pose const &pose, core::Size const upper_res)
	Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper. More...
bool	operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator== More...
bool	operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator== More...
std::ostream &	operator<< (std::ostream &out, EnergyMethodOptions const &options)
bool	operator== (FreeDOF_Options const &a, FreeDOF_Options const &b)
std::ostream &	operator<< (std::ostream &out, const FreeDOF_Options &options)
static basic::Tracer	TR ("core.mm.MMBondAngleEnergy")
static basic::Tracer	TR ("core.mm.MMBondLengthEnergy")
static basic::Tracer	TR ("core.scoring.methods.MMTorsionEnergy")
static basic::Tracer	TR ("core.scoring.methods.OneBodyEnergy")
static basic::Tracer	TR ("core.scoring.methods.TwoBodyEnergy")
static basic::Tracer	tr ("core.scoring.methods")
core::Real	get_residue_weight_by_ss (const char ss)
bool	residues_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::Real const interaction_cutoff)
bool	atoms_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::id::AtomID const &id1, core::id::AtomID const &id2, core::Real const interaction_cutoff)
void	determine_lo_and_hi_residues (core::pose::Pose const &pose, core::Size const rsd1, core::Size const rsd2, bool &res1_is_lo, bool &res2_is_lo)
	Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper. More...
void	create_long_range_energy_container (core::pose::Pose &pose, core::scoring::ScoreType const scoretype, core::scoring::methods::LongRangeEnergyType const lr_type)
	Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary. More...

Typedef Documentation

CartBondedParametersAP

typedef utility::pointer::weak_ptr< CartBondedParameters > core::scoring::methods::CartBondedParametersAP

CartBondedParametersCAP

typedef utility::pointer::weak_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCAP

CartBondedParametersCOP

typedef utility::pointer::shared_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCOP

CartBondedParametersOP

typedef utility::pointer::shared_ptr< CartBondedParameters > core::scoring::methods::CartBondedParametersOP

ContextDependentLRTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextDependentLRTwoBodyEnergy const > core::scoring::methods::ContextDependentLRTwoBodyEnergyCOP

ContextDependentLRTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextDependentLRTwoBodyEnergy > core::scoring::methods::ContextDependentLRTwoBodyEnergyOP

ContextDependentOneBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextDependentOneBodyEnergy > core::scoring::methods::ContextDependentOneBodyEnergyOP

ContextDependentTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextDependentTwoBodyEnergy const > core::scoring::methods::ContextDependentTwoBodyEnergyCOP

ContextDependentTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextDependentTwoBodyEnergy > core::scoring::methods::ContextDependentTwoBodyEnergyOP

ContextIndependentLRTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextIndependentLRTwoBodyEnergy const > core::scoring::methods::ContextIndependentLRTwoBodyEnergyCOP

ContextIndependentLRTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextIndependentLRTwoBodyEnergy > core::scoring::methods::ContextIndependentLRTwoBodyEnergyOP

ContextIndependentOneBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextIndependentOneBodyEnergy const > core::scoring::methods::ContextIndependentOneBodyEnergyCOP

ContextIndependentOneBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextIndependentOneBodyEnergy > core::scoring::methods::ContextIndependentOneBodyEnergyOP

ContextIndependentTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ContextIndependentTwoBodyEnergy const > core::scoring::methods::ContextIndependentTwoBodyEnergyCOP

ContextIndependentTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ContextIndependentTwoBodyEnergy > core::scoring::methods::ContextIndependentTwoBodyEnergyOP

EnergyMethodCOP

typedef utility::pointer::shared_ptr< EnergyMethod const > core::scoring::methods::EnergyMethodCOP

EnergyMethodCreatorCOP

typedef utility::pointer::shared_ptr< EnergyMethodCreator const > core::scoring::methods::EnergyMethodCreatorCOP

EnergyMethodCreatorOP

typedef utility::pointer::shared_ptr< EnergyMethodCreator > core::scoring::methods::EnergyMethodCreatorOP

EnergyMethodOP

typedef utility::pointer::shared_ptr< EnergyMethod > core::scoring::methods::EnergyMethodOP

EnergyMethodOptionsCOP

typedef utility::pointer::shared_ptr< EnergyMethodOptions const > core::scoring::methods::EnergyMethodOptionsCOP

EnergyMethodOptionsOP

typedef utility::pointer::shared_ptr< EnergyMethodOptions > core::scoring::methods::EnergyMethodOptionsOP

FreeDOF_OptionsCOP

typedef utility::pointer::shared_ptr< FreeDOF_Options const > core::scoring::methods::FreeDOF_OptionsCOP

FreeDOF_OptionsOP

typedef utility::pointer::shared_ptr< FreeDOF_Options > core::scoring::methods::FreeDOF_OptionsOP

LongRangeTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy const > core::scoring::methods::LongRangeTwoBodyEnergyCOP

LongRangeTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy > core::scoring::methods::LongRangeTwoBodyEnergyOP

mm_torsion_atom_quad_angle_pair

typedef std::pair< mm::mm_torsion_atom_quad, core::Real > core::scoring::methods::mm_torsion_atom_quad_angle_pair

MMBondAngleEnergyAP

typedef utility::pointer::weak_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyAP

MMBondAngleEnergyCAP

typedef utility::pointer::weak_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCAP

MMBondAngleEnergyCOP

typedef utility::pointer::shared_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCOP

MMBondAngleEnergyOP

typedef utility::pointer::shared_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyOP

MMBondLengthEnergyAP

typedef utility::pointer::weak_ptr< MMBondLengthEnergy > core::scoring::methods::MMBondLengthEnergyAP

MMBondLengthEnergyCAP

typedef utility::pointer::weak_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCAP

MMBondLengthEnergyCOP

typedef utility::pointer::shared_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCOP

MMBondLengthEnergyOP

typedef utility::pointer::shared_ptr< MMBondLengthEnergy > core::scoring::methods::MMBondLengthEnergyOP

MMLJEnergyInterAP

typedef utility::pointer::weak_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterAP

MMLJEnergyInterCAP

typedef utility::pointer::weak_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCAP

MMLJEnergyInterCOP

typedef utility::pointer::shared_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCOP

MMLJEnergyInterOP

typedef utility::pointer::shared_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterOP

MMLJEnergyIntraAP

typedef utility::pointer::weak_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraAP

MMLJEnergyIntraCAP

typedef utility::pointer::weak_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCAP

MMLJEnergyIntraCOP

typedef utility::pointer::shared_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCOP

MMLJEnergyIntraOP

typedef utility::pointer::shared_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraOP

mmtaqap_iter

using core::scoring::methods::mmtaqap_iter = typedef utility::vector1<mm_torsion_atom_quad_angle_pair>::const_iterator

MMTorsionEnergyAP

typedef utility::pointer::weak_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyAP

MMTorsionEnergyCAP

typedef utility::pointer::weak_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCAP

MMTorsionEnergyCOP

typedef utility::pointer::shared_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCOP

MMTorsionEnergyOP

typedef utility::pointer::shared_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyOP

NeighborListDataCOP

typedef utility::pointer::shared_ptr< NeighborListData const > core::scoring::methods::NeighborListDataCOP

NeighborListDataOP

typedef utility::pointer::shared_ptr< NeighborListData > core::scoring::methods::NeighborListDataOP

NMerPSSMEnergyCOP

typedef utility::pointer::shared_ptr< NMerPSSMEnergy const > core::scoring::methods::NMerPSSMEnergyCOP

NMerPSSMEnergyOP

typedef utility::pointer::shared_ptr< NMerPSSMEnergy > core::scoring::methods::NMerPSSMEnergyOP

NMerRefEnergyCOP

typedef utility::pointer::shared_ptr< NMerRefEnergy const > core::scoring::methods::NMerRefEnergyCOP

NMerRefEnergyOP

typedef utility::pointer::shared_ptr< NMerRefEnergy > core::scoring::methods::NMerRefEnergyOP

NMerSVMEnergyCOP

typedef utility::pointer::shared_ptr< NMerSVMEnergy const > core::scoring::methods::NMerSVMEnergyCOP

NMerSVMEnergyOP

typedef utility::pointer::shared_ptr< NMerSVMEnergy > core::scoring::methods::NMerSVMEnergyOP

OneBodyEnergyCOP

typedef utility::pointer::shared_ptr< OneBodyEnergy const > core::scoring::methods::OneBodyEnergyCOP

OneBodyEnergyOP

typedef utility::pointer::shared_ptr< OneBodyEnergy > core::scoring::methods::OneBodyEnergyOP

ShortRangeTwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy const > core::scoring::methods::ShortRangeTwoBodyEnergyCOP

ShortRangeTwoBodyEnergyOP

typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy > core::scoring::methods::ShortRangeTwoBodyEnergyOP

TwoBodyEnergyCOP

typedef utility::pointer::shared_ptr< TwoBodyEnergy const > core::scoring::methods::TwoBodyEnergyCOP

TwoBodyEnergyOP

typedef utility::pointer::shared_ptr< TwoBodyEnergy > core::scoring::methods::TwoBodyEnergyOP

WholeStructureEnergyOP

typedef utility::pointer::shared_ptr< WholeStructureEnergy > core::scoring::methods::WholeStructureEnergyOP

Enumeration Type Documentation

EnergyMethods

enum core::scoring::methods::EnergyMethods

Enumerator
etable_method
dunbrack_method
hbond_method
elec_method
lkball_method
mm_lj_energy_inter_method
pair_e_method
reference_e_method
vdw_method
ramachandran_method
n_energy_methods

EnergyMethodType

enum core::scoring::methods::EnergyMethodType

Enumerator
ci_2b
cd_2b
ci_lr_2b
cd_lr_2b
ci_1b
cd_1b
ws
n_energy_method_types

LongRangeEnergyType

enum core::scoring::methods::LongRangeEnergyType

Enumerator
constraints_lr
gen_born_lr
multipole_elec_lr
vdw_tinker_lr
sasa_lr
epr_deer_lr
PB_elec_lr
cart_bonded_lr
dna_dihedral_lr
gen_bonded_lr
rama2b_lr
ramaprepro_lr
aspartimide_penalty_lr
rna_suite_lr
tna_suite_lr
rna_stub_coord_lr
DFIRE
sym_bonus_lr
elec_dens_energy
elec_dens_fast_energy
elec_dens_cen_energy
elec_dens_allatom_cen_energy
elec_dens_atomwise_energy
patterson_corr_energy
fa_disulfide_energy
disulfide_matching_energy
centroid_disulfide_energy
n_long_range_types

Function Documentation

atoms_interact()

bool core::scoring::methods::atoms_interact	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		core::id::AtomID const &	id1,
		core::id::AtomID const &	id2,
		core::Real const	interaction_cutoff
	)

References core::id::AtomID::atomno(), core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().

create_long_range_energy_container()

void core::scoring::methods::create_long_range_energy_container	(	core::pose::Pose &	pose,
		core::scoring::ScoreType const	scoretype,
		core::scoring::methods::LongRangeEnergyType const	lr_type
	)

Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), core::scoring::Energies::nonconst_long_range_container(), and core::scoring::Energies::set_long_range_container().

Referenced by core::energy_methods::RamaPreProEnergy::setup_for_scoring(), and core::energy_methods::AspartimidePenaltyEnergy::setup_for_scoring().

determine_lo_and_hi_residues()

void core::scoring::methods::determine_lo_and_hi_residues	(	core::pose::Pose const &	pose,
		core::Size const	rsd1,
		core::Size const	rsd2,
		bool &	res1_is_lo,
		bool &	res2_is_lo
	)

Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper.

Inputs are rsd1 and rsd2; outputs are rsd1_is_lo and rsd2_is_lo. Both will be false if the residues aren't connected (s.t. the C of one connected to some connection of the other).

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::conformation::Residue::has_upper_connect(), core::chemical::ResidueConnection::index(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::upper_connect().

Referenced by core::energy_methods::AspartimidePenaltyEnergy::defines_residue_pair_energy(), core::energy_methods::RamaPreProEnergy::defines_residue_pair_energy(), core::energy_methods::AspartimidePenaltyEnergy::residue_pair_energy(), and core::energy_methods::RamaPreProEnergy::residue_pair_energy().

find_cutpoint_variants()

void core::scoring::methods::find_cutpoint_variants	(	core::pose::Pose const &	pose,
		core::kinematics::FoldTree const &	,
		utility::vector1< int > &	cutpoints
	)

References is_lower_cutpoint(), and core::pose::Pose::size().

Referenced by core::energy_methods::ChainbreakEnergy::finalize_total_energy(), and core::energy_methods::LinearChainbreakEnergy::finalize_total_energy().

find_relevant_connections()

void core::scoring::methods::find_relevant_connections	(	pose::Pose const &	pose,
		utility::vector1< ResidueAtomOverlaps > &	branch_connections
	)

References core::chemical::C2_BRANCH_POINT, core::chemical::FIVEPRIME_CAP, core::chemical::ResidueTypeBase::has_variant_type(), core::scoring::methods::ResidueAtomOverlaps::res1, core::scoring::methods::ResidueAtomOverlaps::res1_ovl1_overlaps, core::scoring::methods::ResidueAtomOverlaps::res1_ovl2_overlaps, core::scoring::methods::ResidueAtomOverlaps::res2, core::scoring::methods::ResidueAtomOverlaps::res2_ovu1_overlaps, core::pose::Pose::residue(), core::conformation::Residue::residue_connection_conn_id(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by core::energy_methods::BranchEnergy::finalize_total_energy(), and core::energy_methods::LinearBranchEnergy::finalize_total_energy().

find_relevant_connections_onersd()

void core::scoring::methods::find_relevant_connections_onersd	(	pose::Pose const &	pose,
		Size const	seqpos,
		ResidueAtomOverlaps &	branch_connection
	)

References core::chemical::C2_BRANCH_POINT, core::chemical::FIVEPRIME_CAP, core::chemical::ResidueTypeBase::has_variant_type(), core::scoring::methods::ResidueAtomOverlaps::res1, core::scoring::methods::ResidueAtomOverlaps::res1_ovl1_overlaps, core::scoring::methods::ResidueAtomOverlaps::res1_ovl2_overlaps, core::scoring::methods::ResidueAtomOverlaps::res2, core::scoring::methods::ResidueAtomOverlaps::res2_ovu1_overlaps, core::pose::Pose::residue(), core::conformation::Residue::residue_connection_conn_id(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by core::energy_methods::BranchEnergy::eval_atom_derivative(), and core::energy_methods::LinearBranchEnergy::eval_atom_derivative().

get_lower_cutpoint_partner_for_upper()

core::Size core::scoring::methods::get_lower_cutpoint_partner_for_upper	(	pose::Pose const &	pose,
		Size const	upper_res
	)

Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper.

References core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_resconn(), lower_upper_connected_across_cutpoint(), and core::pose::Pose::residue().

Referenced by core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::pose::rna::is_cutpoint_closed_torsion(), and core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes().

get_residue_weight_by_ss()

core::Real core::scoring::methods::get_residue_weight_by_ss

(

const char

ss

)

References tr().

Referenced by core::energy_methods::EnvEnergy::residue_energy(), and core::energy_methods::CenPairEnergy::residue_pair_energy().

get_upper_cutpoint_partner_for_lower()

core::Size core::scoring::methods::get_upper_cutpoint_partner_for_lower	(	pose::Pose const &	pose,
		Size const	lower_res
	)

Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper.

Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper. Important in handling cyclized nucleotides.

References core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_resconn(), lower_upper_connected_across_cutpoint(), and core::pose::Pose::residue().

Referenced by protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), protocols::stepwise::modeler::figure_out_moving_chain_break_res(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::rna::movers::RNA_LoopCloser::get_chainbreak_xyz(), protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed(), protocols::stepwise::modeler::is_cutpoint_closed(), core::pose::rna::is_cutpoint_closed_torsion(), protocols::rna::movers::RNA_LoopCloser::passes_fast_scan(), core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes(), and protocols::rna::movers::RNA_LoopCloser::rna_ccd_close().

is_lower_cutpoint()

bool core::scoring::methods::is_lower_cutpoint	(	core::Size	residue,
		core::pose::Pose const &	pose
	)

References core::chemical::CUTPOINT_LOWER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::residue().

Referenced by core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), and find_cutpoint_variants().

is_upper_cutpoint()

bool core::scoring::methods::is_upper_cutpoint	(	core::Size	residue,
		core::pose::Pose const &	pose
	)

References core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::residue().

Referenced by core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative().

lower_upper_connected_across_cutpoint()

bool core::scoring::methods::lower_upper_connected_across_cutpoint	(	core::conformation::Residue const &	lower_rsd,
		core::conformation::Residue const &	upper_rsd
	)

Helper function for looking at residue connections to get lower/upper partners.

helper function for looking at residue connections to get lower/upper partners

References core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::seqpos(), and core::conformation::Residue::upper_connect_atom().

Referenced by get_lower_cutpoint_partner_for_upper(), and get_upper_cutpoint_partner_for_lower().

operator!=()

bool core::scoring::methods::operator!=	(	EnergyMethodOptions const &	a,
		EnergyMethodOptions const &	b
	)

used inside ScoreFunctionInfo::operator==

operator<<() [1/2]

std::ostream& core::scoring::methods::operator<<	(	std::ostream &	out,
		const FreeDOF_Options &	options
	)

operator<<() [2/2]

std::ostream & core::scoring::methods::operator<<	(	std::ostream &	out,
		EnergyMethodOptions const &	options
	)

References core::conformation::membrane::out, and core::scoring::methods::EnergyMethodOptions::show().

operator==() [1/2]

bool core::scoring::methods::operator==	(	EnergyMethodOptions const &	a,
		EnergyMethodOptions const &	b
	)

used inside ScoreFunctionInfo::operator==

operator==() [2/2]

bool core::scoring::methods::operator==	(	FreeDOF_Options const &	a,
		FreeDOF_Options const &	b
	)

residues_interact()

bool core::scoring::methods::residues_interact	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		core::Real const	interaction_cutoff
	)

References core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), and core::conformation::Residue::xyz().

TR() [1/5]

static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondAngleEnergy"  )

static

Referenced by core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::TwoBodyEnergy::eval_intrares_energy_ext(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssms_from_options(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svms_from_options(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), core::scoring::methods::NMerRefEnergy::read_nmer_table_list(), core::scoring::methods::NMerRefEnergy::read_nmer_tables_from_options(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::TwoBodyEnergy::residue_pair_energy_ext(), core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(), core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue(), and core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair().

TR() [2/5]

static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondLengthEnergy"  )

static

tr()

static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods"  )

static

Referenced by get_residue_weight_by_ss().

TR() [3/5]

static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.MMTorsionEnergy"  )

static

TR() [4/5]

static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.OneBodyEnergy"  )

static

TR() [5/5]

static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.TwoBodyEnergy"  )

static