protocols::docking Namespace Reference

Namespaces
	membrane
	stateless

Classes
class	ConformerSwitchMover
	this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction. More...
class	ConformerSwitchMoverCreator
class	DockingLowResFilter
	Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners, (2) clashes are limited so partners are not overlapping and (3) constraints, if present, are met. More...
class	DockingHighResFilter
	High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given (2) interface_score must be negative. More...
class	DockingEnsemble
	this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction. More...
class	DockingEnsemblePrepackProtocol
class	DockingHighRes
class	DockingHighResFactory
	DockingHighResFactory uses the MoverFactory to create instances of DockingHighRes. More...
class	DockingHighResLegacy
	this mover does the high resolution refinement stage of the RosettaDock algorithm More...
class	DockingHighResLegacyCreator
class	DockingInitialPerturbation
	this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options More...
class	DockingSlideIntoContact
	Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently). More...
class	FaDockingSlideIntoContact
	Slides docking partners together by monitoring fa_rep. More...
class	SlideIntoContact
	More general function for low-res or highres DockingSlideIntoContact. More...
class	DockingInitialPerturbationCreator
class	DockingLowRes
class	DockingLowResEnsemble
class	DockingPrepackProtocol
class	DockingPrepackProtocolCreator
class	DockingProtocol
	This is the standard RosettaDock protocol. More...
class	DockingProtocolCreator
class	DockingSlideIntoContactCreator
class	DockMCMCycle
class	DockMCMProtocol
class	DockMCMProtocolCreator
class	DockMinMover
class	DockMinMoverCreator
class	DockSetupMover
	allows docking using simulated or parallel tempering More...
class	DockSetupMoverCreator
class	DockTaskFactory
class	EllipsoidalRandomizationMover
class	EnsureExclusivelySharedJumpMover
class	EnsureExclusivelySharedJumpMoverCreator
class	RigidBodyInfo
class	SidechainMinMover
class	InterfaceSidechainMinMover
class	TemperedDocking
	allows docking using simulated or parallel tempering More...
class	TemperedDockingCreator

Typedefs
typedef utility::pointer::shared_ptr< ConformerSwitchMover >	ConformerSwitchMoverOP
typedef utility::pointer::shared_ptr< ConformerSwitchMover const >	ConformerSwitchMoverCOP
typedef utility::pointer::shared_ptr< DockingLowResFilter >	DockingLowResFilterOP
typedef utility::pointer::shared_ptr< DockingLowResFilter const >	DockingLowResFilterCOP
typedef utility::pointer::shared_ptr< DockingHighResFilter >	DockingHighResFilterOP
typedef utility::pointer::shared_ptr< DockingHighResFilter const >	DockingHighResFilterCOP
typedef utility::pointer::shared_ptr< DockingEnsemble >	DockingEnsembleOP
typedef utility::pointer::shared_ptr< DockingEnsemble const >	DockingEnsembleCOP
typedef utility::pointer::shared_ptr< DockingEnsemblePrepackProtocol >	DockingEnsemblePrepackProtocolOP
typedef utility::pointer::shared_ptr< DockingEnsemblePrepackProtocol const >	DockingEnsemblePrepackProtocolCOP
typedef utility::pointer::shared_ptr< DockingHighRes >	DockingHighResOP
typedef utility::pointer::shared_ptr< DockingHighRes const >	DockingHighResCOP
typedef utility::pointer::shared_ptr< DockingHighResLegacy >	DockingHighResLegacyOP
typedef utility::pointer::shared_ptr< DockingHighResLegacy const >	DockingHighResLegacyCOP
typedef utility::pointer::shared_ptr< DockingInitialPerturbation >	DockingInitialPerturbationOP
typedef utility::pointer::shared_ptr< DockingInitialPerturbation const >	DockingInitialPerturbationCOP
typedef utility::pointer::shared_ptr< DockingSlideIntoContact >	DockingSlideIntoContactOP
typedef utility::pointer::shared_ptr< DockingSlideIntoContact const >	DockingSlideIntoContactCOP
typedef utility::pointer::shared_ptr< FaDockingSlideIntoContact >	FaDockingSlideIntoContactOP
typedef utility::pointer::shared_ptr< FaDockingSlideIntoContact const >	FaDockingSlideIntoContactCOP
typedef utility::pointer::shared_ptr< SlideIntoContact >	SlideIntoContactOP
typedef utility::pointer::shared_ptr< SlideIntoContact const >	SlideIntoContactCOP
typedef utility::pointer::shared_ptr< DockingLowRes >	DockingLowResOP
typedef utility::pointer::shared_ptr< DockingLowRes const >	DockingLowResCOP
typedef utility::pointer::shared_ptr< DockingLowResEnsemble >	DockingLowResEnsembleOP
typedef utility::pointer::shared_ptr< DockingLowResEnsemble const >	DockingLowResEnsembleCOP
typedef utility::pointer::shared_ptr< DockingPrepackProtocol >	DockingPrepackProtocolOP
typedef utility::pointer::shared_ptr< DockingPrepackProtocol const >	DockingPrepackProtocolCOP
typedef utility::pointer::shared_ptr< DockingProtocol >	DockingProtocolOP
typedef utility::pointer::shared_ptr< DockMCMCycle >	DockMCMCycleOP
typedef utility::pointer::shared_ptr< DockMCMCycle const >	DockMCMCycleCOP
typedef utility::pointer::shared_ptr< DockMCMProtocol >	DockMCMProtocolOP
typedef utility::pointer::shared_ptr< DockMCMProtocol const >	DockMCMProtocolCOP
typedef utility::pointer::shared_ptr< DockMinMover >	DockMinMoverOP
typedef utility::pointer::shared_ptr< DockMinMover const >	DockMinMoverCOP
typedef utility::pointer::shared_ptr< DockingSetupMover >	DockingSetupMoverOP
typedef utility::pointer::shared_ptr< DockTaskFactory >	DockTaskFactoryOP
typedef utility::pointer::shared_ptr< DockTaskFactory const >	DockTaskFactoryCOP
typedef utility::pointer::shared_ptr< EllipsoidalRandomizationMover >	EllipsoidalRandomizationMoverOP
typedef utility::pointer::shared_ptr< EllipsoidalRandomizationMover const >	EllipsoidalRandomizationMoverCOP
typedef utility::pointer::shared_ptr< EnsureExclusivelySharedJumpMover >	EnsureExclusivelySharedJumpMoverOP
typedef utility::pointer::shared_ptr< EnsureExclusivelySharedJumpMover const >	EnsureExclusivelySharedJumpMoverCOP
typedef utility::pointer::shared_ptr< RigidBodyInfo >	RigidBodyInfoOP
typedef utility::pointer::shared_ptr< RigidBodyInfo const >	RigidBodyInfoCOP
typedef utility::pointer::shared_ptr< SidechainMinMover >	SidechainMinMoverOP
typedef utility::pointer::shared_ptr< SidechainMinMover >	SidechainMinMoverCOP
typedef utility::pointer::shared_ptr< InterfaceSidechainMinMover >	InterfaceSidechainMinMoverOP
typedef utility::pointer::shared_ptr< InterfaceSidechainMinMover >	InterfaceSidechainMinMoverCOP
typedef utility::pointer::shared_ptr< TemperedDocking >	TemperedDockingOP
typedef utility::vector1_int	DockJumps

Enumerations
enum class	DHR_Type {   DockingHighResLegacy , DockingPrepackProtocol , DockMCMProtocol , DockMinMover ,   SnugDock }
	These are the valid names of classes that can be instantiated by DockingHighResFactory. More...

Functions
std::ostream &	operator<< (std::ostream &output, ConformerSwitchMover const &mover)
static basic::Tracer	TR ("protocols.docking.DockingHighResFactory")
std::ostream &	operator<< (std::ostream &os, DockingSlideIntoContact const &mover)
std::ostream &	operator<< (std::ostream &os, FaDockingSlideIntoContact const &fadock)
void	move_apart (core::pose::Pose &pose, int jump, core::Vector const &axis)
void	move_together (core::pose::Pose &pose, int jump, core::scoring::ScoreFunctionOP sfxn)
std::ostream &	operator<< (std::ostream &out, const DockingLowRes &dp)
std::ostream &	operator<< (std::ostream &out, const DockingProtocol &dp)
std::ostream &	operator<< (std::ostream &out, const DockMCMCycle &dp)
std::ostream &	operator<< (std::ostream &out, const DockMCMProtocol &dmp)
std::ostream &	operator<< (std::ostream &out, const DockSetupMover &dp)
std::ostream &	operator<< (std::ostream &output, EllipsoidalRandomizationMover const &object_to_output)
core::Real	calc_intf_score (const core::pose::Pose &pose, const core::scoring::ScoreFunctionOP scorefxn, int const jump)
	Compute interface score between the input complex and complex with the two partners at 500A from each other. More...
core::Real	calc_interaction_energy (const core::pose::Pose &pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other. More...
core::Real	calc_Lrmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, DockJumps const movable_jumps)
	Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner. More...
core::Real	calc_P1rmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, DockJumps const movable_jumps)
	Calculates C-alpha RMSD of the superimposed larger partner. More...
core::Real	calc_P2rmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, DockJumps const movable_jumps)
	Calculates C-alpha RMSD of the superimposed smaller partner. More...
core::Real	calc_Irmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the all-atom RMSD of all residues within 10A of the interface at superposition along those same atoms. More...
core::Real	calc_Irmsd_legacy (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the backbone RMSD of all residues within 8A of the interface at superposition along those same atoms. More...
core::Real	calc_CA_Irmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms More...
core::Real	calc_Fnat (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the fraction of native contacts recovered between the input and native pose. A native-contact is defined as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. More...
core::Real	calc_Fnat (const core::pose::Pose &pose, std::string const &list_file, DockJumps const movable_jumps)
	Calculates the fraction of native contacts from the given native contacts pair list. More...
core::Real	calc_Fnonnat (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the fraction of non-native contacts recovered between the input and native pose. A native-contact is defined as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact. More...
core::Real	calc_Fnonnat (const core::pose::Pose &pose, std::string const &list_file, DockJumps const movable_jumps)
	Calculates the fraction of non-native contacts from the given native contacts pari list. More...
bool	calc_res_contact (conformation::ResidueOP rsd1, conformation::ResidueOP rsd2, Real dist_cutoff)
core::Size	calc_CAPRI_rank (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
std::ostream &	operator<< (std::ostream &out, const TemperedDocking &dp)
std::string	comma_separated_partner_chains (std::string const &chains)
void	setup_edges_for_partner (core::pose::Pose const &pose, utility::vector1< bool > const &partner, core::Size const center_of_mass_residue, core::kinematics::FoldTree &ft)
core::Size	setup_dock_jump (core::Size const partner1_CoM, core::Size const partner2_CoM, core::kinematics::FoldTree &ft, bool const make_dock_jump_label_1=false)
void	setup_foldtree (core::pose::Pose &pose, std::string const &partner_chainID, DockJumps &movable_jumps, bool rand_jump_res_partner2=false)
	Setup FoldTree for docking across an interface. The partners are described by a string for the partner chains (using pdb_chain identification) separated by "_". The foldtree is set up such that the jump points are at the center of masses of the two partners. More...
void	setup_foldtree (core::pose::Pose const &pose, utility::vector1< bool > const &partner1, DockJumps &movable_jumps, core::kinematics::FoldTree &ft, bool rand_jump_res_partner2=false)
	Setup foldtree for docking across an interface. The partners are described by a vector of booleans of the same length as the number of residues in the pose. The FoldTree is set up such that the jump points are at the center of masses of the two partners. More...

Typedef Documentation

ConformerSwitchMoverCOP

typedef utility::pointer::shared_ptr< ConformerSwitchMover const > protocols::docking::ConformerSwitchMoverCOP

ConformerSwitchMoverOP

typedef utility::pointer::shared_ptr< ConformerSwitchMover > protocols::docking::ConformerSwitchMoverOP

DockingEnsembleCOP

typedef utility::pointer::shared_ptr< DockingEnsemble const > protocols::docking::DockingEnsembleCOP

DockingEnsembleOP

typedef utility::pointer::shared_ptr< DockingEnsemble > protocols::docking::DockingEnsembleOP

DockingEnsemblePrepackProtocolCOP

typedef utility::pointer::shared_ptr< DockingEnsemblePrepackProtocol const > protocols::docking::DockingEnsemblePrepackProtocolCOP

DockingEnsemblePrepackProtocolOP

typedef utility::pointer::shared_ptr< DockingEnsemblePrepackProtocol > protocols::docking::DockingEnsemblePrepackProtocolOP

DockingHighResCOP

typedef utility::pointer::shared_ptr< DockingHighRes const > protocols::docking::DockingHighResCOP

DockingHighResFilterCOP

typedef utility::pointer::shared_ptr< DockingHighResFilter const > protocols::docking::DockingHighResFilterCOP

DockingHighResFilterOP

typedef utility::pointer::shared_ptr< DockingHighResFilter > protocols::docking::DockingHighResFilterOP

DockingHighResLegacyCOP

typedef utility::pointer::shared_ptr< DockingHighResLegacy const > protocols::docking::DockingHighResLegacyCOP

DockingHighResLegacyOP

typedef utility::pointer::shared_ptr< DockingHighResLegacy > protocols::docking::DockingHighResLegacyOP

DockingHighResOP

typedef utility::pointer::shared_ptr< DockingHighRes > protocols::docking::DockingHighResOP

DockingInitialPerturbationCOP

typedef utility::pointer::shared_ptr< DockingInitialPerturbation const > protocols::docking::DockingInitialPerturbationCOP

DockingInitialPerturbationOP

typedef utility::pointer::shared_ptr< DockingInitialPerturbation > protocols::docking::DockingInitialPerturbationOP

DockingLowResCOP

typedef utility::pointer::shared_ptr< DockingLowRes const > protocols::docking::DockingLowResCOP

DockingLowResEnsembleCOP

typedef utility::pointer::shared_ptr< DockingLowResEnsemble const > protocols::docking::DockingLowResEnsembleCOP

DockingLowResEnsembleOP

typedef utility::pointer::shared_ptr< DockingLowResEnsemble > protocols::docking::DockingLowResEnsembleOP

DockingLowResFilterCOP

typedef utility::pointer::shared_ptr< DockingLowResFilter const > protocols::docking::DockingLowResFilterCOP

DockingLowResFilterOP

typedef utility::pointer::shared_ptr< DockingLowResFilter > protocols::docking::DockingLowResFilterOP

DockingLowResOP

typedef utility::pointer::shared_ptr< DockingLowRes > protocols::docking::DockingLowResOP

DockingPrepackProtocolCOP

typedef utility::pointer::shared_ptr< DockingPrepackProtocol const > protocols::docking::DockingPrepackProtocolCOP

DockingPrepackProtocolOP

typedef utility::pointer::shared_ptr< DockingPrepackProtocol > protocols::docking::DockingPrepackProtocolOP

DockingProtocolOP

typedef utility::pointer::shared_ptr< DockingProtocol > protocols::docking::DockingProtocolOP

DockingSetupMoverOP

typedef utility::pointer::shared_ptr< DockingSetupMover > protocols::docking::DockingSetupMoverOP

DockingSlideIntoContactCOP

typedef utility::pointer::shared_ptr< DockingSlideIntoContact const > protocols::docking::DockingSlideIntoContactCOP

DockingSlideIntoContactOP

typedef utility::pointer::shared_ptr< DockingSlideIntoContact > protocols::docking::DockingSlideIntoContactOP

DockJumps

typedef utility::vector1_int protocols::docking::DockJumps

DockMCMCycleCOP

typedef utility::pointer::shared_ptr< DockMCMCycle const > protocols::docking::DockMCMCycleCOP

DockMCMCycleOP

typedef utility::pointer::shared_ptr< DockMCMCycle > protocols::docking::DockMCMCycleOP

DockMCMProtocolCOP

typedef utility::pointer::shared_ptr< DockMCMProtocol const > protocols::docking::DockMCMProtocolCOP

DockMCMProtocolOP

typedef utility::pointer::shared_ptr< DockMCMProtocol > protocols::docking::DockMCMProtocolOP

DockMinMoverCOP

typedef utility::pointer::shared_ptr< DockMinMover const > protocols::docking::DockMinMoverCOP

DockMinMoverOP

typedef utility::pointer::shared_ptr< DockMinMover > protocols::docking::DockMinMoverOP

DockTaskFactoryCOP

typedef utility::pointer::shared_ptr< DockTaskFactory const > protocols::docking::DockTaskFactoryCOP

DockTaskFactoryOP

typedef utility::pointer::shared_ptr< DockTaskFactory > protocols::docking::DockTaskFactoryOP

EllipsoidalRandomizationMoverCOP

typedef utility::pointer::shared_ptr< EllipsoidalRandomizationMover const > protocols::docking::EllipsoidalRandomizationMoverCOP

EllipsoidalRandomizationMoverOP

typedef utility::pointer::shared_ptr< EllipsoidalRandomizationMover > protocols::docking::EllipsoidalRandomizationMoverOP

EnsureExclusivelySharedJumpMoverCOP

typedef utility::pointer::shared_ptr< EnsureExclusivelySharedJumpMover const > protocols::docking::EnsureExclusivelySharedJumpMoverCOP

EnsureExclusivelySharedJumpMoverOP

typedef utility::pointer::shared_ptr< EnsureExclusivelySharedJumpMover > protocols::docking::EnsureExclusivelySharedJumpMoverOP

FaDockingSlideIntoContactCOP

typedef utility::pointer::shared_ptr< FaDockingSlideIntoContact const > protocols::docking::FaDockingSlideIntoContactCOP

FaDockingSlideIntoContactOP

typedef utility::pointer::shared_ptr< FaDockingSlideIntoContact > protocols::docking::FaDockingSlideIntoContactOP

InterfaceSidechainMinMoverCOP

typedef utility::pointer::shared_ptr< InterfaceSidechainMinMover > protocols::docking::InterfaceSidechainMinMoverCOP

InterfaceSidechainMinMoverOP

typedef utility::pointer::shared_ptr< InterfaceSidechainMinMover > protocols::docking::InterfaceSidechainMinMoverOP

RigidBodyInfoCOP

typedef utility::pointer::shared_ptr< RigidBodyInfo const > protocols::docking::RigidBodyInfoCOP

RigidBodyInfoOP

typedef utility::pointer::shared_ptr< RigidBodyInfo > protocols::docking::RigidBodyInfoOP

SidechainMinMoverCOP

typedef utility::pointer::shared_ptr< SidechainMinMover > protocols::docking::SidechainMinMoverCOP

SidechainMinMoverOP

typedef utility::pointer::shared_ptr< SidechainMinMover > protocols::docking::SidechainMinMoverOP

SlideIntoContactCOP

typedef utility::pointer::shared_ptr< SlideIntoContact const > protocols::docking::SlideIntoContactCOP

SlideIntoContactOP

typedef utility::pointer::shared_ptr< SlideIntoContact > protocols::docking::SlideIntoContactOP

TemperedDockingOP

typedef utility::pointer::shared_ptr< TemperedDocking > protocols::docking::TemperedDockingOP

Enumeration Type Documentation

DHR_Type

enum protocols::docking::DHR_Type

strong

These are the valid names of classes that can be instantiated by DockingHighResFactory.

Enumerator
DockingHighResLegacy
DockingPrepackProtocol
DockMCMProtocol
DockMinMover
SnugDock

Function Documentation

calc_CA_Irmsd()

core::Real protocols::docking::calc_CA_Irmsd	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms

References core::kinematics::FoldTree::clone(), core::pose::Pose::fold_tree(), core::scoring::is_protein_CA(), core::scoring::rmsd_with_super_subset(), and core::pose::Pose::size().

calc_CAPRI_rank()

core::Size protocols::docking::calc_CAPRI_rank	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

References calc_Fnat(), calc_Irmsd_legacy(), and calc_Lrmsd().

Referenced by protocols::docking::DockingProtocol::apply().

calc_Fnat() [1/2]

core::Real protocols::docking::calc_Fnat	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

Calculates the fraction of native contacts recovered between the input and native pose. A native-contact is defined as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure.

References calc_res_contact(), protocols::scoring::Interface::calculate(), core::kinematics::FoldTree::clone(), protocols::scoring::Interface::distance(), core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), protocols::scoring::Interface::is_interface(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by protocols::docking::DockingProtocol::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::protein_interface_design::filters::FNatFilter::compute(), and protocols::glycopeptide_docking::record_pose_metrics().

calc_Fnat() [2/2]

core::Real protocols::docking::calc_Fnat	(	const core::pose::Pose &	pose,
		std::string const &	list_file,
		DockJumps const	movable_jumps
	)

Calculates the fraction of native contacts from the given native contacts pair list.

References calc_res_contact(), core::conformation::membrane::in, core::pose::Pose::is_fullatom(), core::pose::Pose::residue(), and TR().

Referenced by calc_CAPRI_rank().

calc_Fnonnat() [1/2]

core::Real protocols::docking::calc_Fnonnat	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

Calculates the fraction of non-native contacts recovered between the input and native pose. A native-contact is defined as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact.

References calc_res_contact(), protocols::scoring::Interface::calculate(), core::kinematics::FoldTree::clone(), protocols::scoring::Interface::distance(), core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), protocols::scoring::Interface::is_interface(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply().

calc_Fnonnat() [2/2]

core::Real protocols::docking::calc_Fnonnat	(	const core::pose::Pose &	pose,
		std::string const &	list_file,
		DockJumps const	movable_jumps
	)

Calculates the fraction of non-native contacts from the given native contacts pari list.

References calc_res_contact(), core::pose::Pose::fold_tree(), core::conformation::membrane::in, core::pose::Pose::is_fullatom(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

calc_interaction_energy()

core::Real protocols::docking::calc_interaction_energy	(	const core::pose::Pose &	pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other.

References core::scoring::atom_pair_constraint, core::pose::Pose::clone(), protocols::membrane::membrane_axis(), and TR().

Referenced by protocols::docking::DockingProtocol::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::docking::DockingHighResFilter::apply(), protocols::glycan_docking::GlycanDockProtocol::docking_filter(), protocols::glycopeptide_docking::record_pose_metrics(), and protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics().

calc_intf_score()

core::Real protocols::docking::calc_intf_score	(	const core::pose::Pose &	pose,
		const core::scoring::ScoreFunctionOP	scorefxn,
		int const	jump
	)

Compute interface score between the input complex and complex with the two partners at 500A from each other.

References protocols::membrane::membrane_axis().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply().

calc_Irmsd()

core::Real protocols::docking::calc_Irmsd	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

Calculates the all-atom RMSD of all residues within 10A of the interface at superposition along those same atoms.

References core::kinematics::FoldTree::clone(), core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::scoring::is_heavyatom(), core::scoring::rmsd_with_super_subset(), core::pose::Pose::size(), and TR().

Referenced by protocols::docking::DockingProtocol::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), and protocols::protein_interface_design::filters::IRmsdFilter::compute().

calc_Irmsd_legacy()

core::Real protocols::docking::calc_Irmsd_legacy	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		const core::scoring::ScoreFunctionCOP	dock_scorefxn,
		DockJumps const	movable_jumps
	)

Calculates the backbone RMSD of all residues within 8A of the interface at superposition along those same atoms.

References core::kinematics::FoldTree::clone(), core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::scoring::is_protein_backbone(), core::scoring::rmsd_with_super_subset(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::docking::DockingProtocol::apply(), and calc_CAPRI_rank().

calc_Lrmsd()

core::Real protocols::docking::calc_Lrmsd	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		DockJumps const	movable_jumps
	)

Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner.

References core::pose::Pose::fold_tree(), core::scoring::is_protein_backbone(), core::kinematics::FoldTree::partition_by_jump(), core::scoring::rmsd_no_super_subset(), and core::pose::Pose::size().

Referenced by protocols::docking::DockingProtocol::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), calc_CAPRI_rank(), and protocols::protein_interface_design::filters::LRmsdFilter::compute().

calc_P1rmsd()

core::Real protocols::docking::calc_P1rmsd	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		DockJumps const	movable_jumps
	)

Calculates C-alpha RMSD of the superimposed larger partner.

The larger partner is the fixed partner; this is mostly for membrane proteins, where we move the partners apart, then do relax on both partners

References core::pose::Pose::fold_tree(), core::scoring::is_protein_backbone(), core::kinematics::FoldTree::partition_by_jump(), core::scoring::rmsd_with_super_subset(), and core::pose::Pose::size().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply(), and protocols::docking::membrane::QuickRelaxPartnersSeparately::apply().

calc_P2rmsd()

core::Real protocols::docking::calc_P2rmsd	(	const core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose,
		DockJumps const	movable_jumps
	)

Calculates C-alpha RMSD of the superimposed smaller partner.

This calculates the RMSD of the smaller partner after superimposing it The computed RMSD is not from the docking, but from the flexible backbone relax

References core::pose::Pose::fold_tree(), core::scoring::is_protein_backbone(), core::kinematics::FoldTree::partition_by_jump(), core::scoring::rmsd_with_super_subset(), and core::pose::Pose::size().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply().

calc_res_contact()

bool protocols::docking::calc_res_contact	(	conformation::ResidueOP	rsd1,
		conformation::ResidueOP	rsd2,
		Real	dist_cutoff
	)

References TR().

Referenced by calc_Fnat(), and calc_Fnonnat().

comma_separated_partner_chains()

std::string protocols::docking::comma_separated_partner_chains

(

std::string const &

chains

)

Converts a string representation of the partner from the dock_partners flag to a comma-separated list of chains that can be passed into a ChainSeletor. For example, the dock_partners flags "ABC_D" will split into two partners: "ABC" and "D". This function will convert "ABC" to "A,B,C".

Returns

A comma-separated list of chains (e.g. "A,B,C")

References TR().

Referenced by setup_foldtree(), and protocols::glycan_docking::setup_glycoligand_selector().

move_apart()

void protocols::docking::move_apart	(	core::pose::Pose &	pose,
		int	jump,
		core::Vector const &	axis
	)

References protocols::membrane::geometry::EmbeddingDef::center(), TR(), and protocols::membrane::update_partner_embeddings().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply().

move_together()

void protocols::docking::move_together	(	core::pose::Pose &	pose,
		int	jump,
		core::scoring::ScoreFunctionOP	sfxn
	)

References protocols::scoring::Interface::calculate(), protocols::membrane::geometry::EmbeddingDef::center(), core::pose::partition_pose_by_jump(), core::scoring::rg, TR(), and protocols::membrane::update_partner_embeddings().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply().

operator<<() [1/10]

std::ostream & protocols::docking::operator<<	(	std::ostream &	os,
		DockingSlideIntoContact const &	mover
	)

References protocols::docking::DockingSlideIntoContact::show().

operator<<() [2/10]

std::ostream & protocols::docking::operator<<	(	std::ostream &	os,
		FaDockingSlideIntoContact const &	fadock
	)

References protocols::docking::FaDockingSlideIntoContact::show().

operator<<() [3/10]

std::ostream& protocols::docking::operator<<	(	std::ostream &	out,
		const DockingLowRes &	dp
	)

operator<<() [4/10]

std::ostream & protocols::docking::operator<<	(	std::ostream &	out,
		const DockingProtocol &	dp
	)

References core::conformation::membrane::out, and protocols::docking::DockingProtocol::show().

operator<<() [5/10]

std::ostream& protocols::docking::operator<<	(	std::ostream &	out,
		const DockMCMCycle &	dp
	)

operator<<() [6/10]

std::ostream& protocols::docking::operator<<	(	std::ostream &	out,
		const DockMCMProtocol &	dmp
	)

operator<<() [7/10]

std::ostream& protocols::docking::operator<<	(	std::ostream &	out,
		const DockSetupMover &	dp
	)

operator<<() [8/10]

std::ostream& protocols::docking::operator<<	(	std::ostream &	out,
		const TemperedDocking &	dp
	)

operator<<() [9/10]

std::ostream & protocols::docking::operator<<	(	std::ostream &	output,
		ConformerSwitchMover const &	mover
	)

References protocols::docking::ConformerSwitchMover::show().

operator<<() [10/10]

std::ostream & protocols::docking::operator<<	(	std::ostream &	output,
		EllipsoidalRandomizationMover const &	object_to_output
	)

References protocols::docking::EllipsoidalRandomizationMover::show().

setup_dock_jump()

core::Size protocols::docking::setup_dock_jump	(	core::Size const	partner1_CoM,
		core::Size const	partner2_CoM,
		core::kinematics::FoldTree &	ft,
		bool const	make_dock_jump_label_1 = false
	)

Creates a Jump connecting the center of mass residues in the FoldTree that is passed through. By default, the dock Jump will be ft.num_jump() + 1. This function can optionally ensure that the dock jump has the label "1".

Returns

The label of the dock Jump as a core::Size.

The appropriate FoldTree is configured and accessible by the caller of this function.

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::jump_edge(), core::kinematics::Edge::label(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and core::kinematics::FoldTree::update_edge_label().

Referenced by setup_foldtree().

setup_edges_for_partner()

void protocols::docking::setup_edges_for_partner	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	partner,
		core::Size const	center_of_mass_residue,
		core::kinematics::FoldTree &	ft
	)

Creates Edges for each of the continuous stretches of residues belonging to a particular partner. If one partner spans multiple chains, the chains will be connected by a Jump. No Edge will span the center_of_mass_residue of the partner. Instead, two Edges will be created: the first will span the beginning of the chain and end at the CoM residue, and the second will begin at the CoM residue and stop at the end of the chain.

Returns

The appropriate FoldTree is configured and accessible by the caller of this function.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::chain(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::split_existing_edge_at_residue(), protocols::loops::start, and protocols::loops::stop.

Referenced by setup_foldtree().

setup_foldtree() [1/2]

void protocols::docking::setup_foldtree	(	core::pose::Pose &	pose,
		std::string const &	partner_chainID,
		DockJumps &	movable_jumps,
		bool	rand_jump_res_partner2
	)

Setup FoldTree for docking across an interface. The partners are described by a string for the partner chains (using pdb_chain identification) separated by "_". The foldtree is set up such that the jump points are at the center of masses of the two partners.

If partner_chainID is "_", the first chain will be docked to the rest of the complex. If partner_chainID is of the form (pdb_chain_id)+_(pdb_chain_id)+, a jump will be created between the residue nearest to the center of mass of the first partner and the residue nearest to the center of mass of the second partner. For example, "ABC_DEF" has chains "ABC" as the first partner and "DEF" as the second partner. Chains can be listed in any order.

Returns

The constructed FoldTree is set to the pose.

The movable_jumps vector contains the number of the jump across the interface.

References core::pose::Pose::chain(), core::conformation::Conformation::chain_end(), comma_separated_partner_chains(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), and core::pose::Pose::size().

Referenced by protocols::docking::DockSetupMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::antibody::design::GeneralAntibodyModeler::apply_A_LH_foldtree(), protocols::antibody::design::GeneralAntibodyModeler::dock_high_res(), protocols::antibody::design::GeneralAntibodyModeler::dock_low_res(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingPrepackProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::docking::TemperedDocking::finalize_setup(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_interface(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::relax_interface(), protocols::docking::EllipsoidalRandomizationMover::set_foldtree(), protocols::antibody::setup_A_LH_foldtree(), protocols::glycan_docking::GlycanDockProtocol::setup_docking_foldtree(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), and protocols::antibody::setup_LH_A_foldtree().

setup_foldtree() [2/2]

void protocols::docking::setup_foldtree	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	partner1,
		DockJumps &	movable_jumps,
		core::kinematics::FoldTree &	ft,
		bool	rand_jump_res_partner2
	)

Setup foldtree for docking across an interface. The partners are described by a vector of booleans of the same length as the number of residues in the pose. The FoldTree is set up such that the jump points are at the center of masses of the two partners.

This function only supports two-body docking. The vector of boolean values is used to differentiate residues that belong to one partner (a true value) or the other (a false value). Edges are constructed for continuous stretches of residues belonging to a particular partner. If one partner spans multiple chains, the chains will be connected by a Jump. The docking Jump is always set to be Jump number 1. WARNING: This function clears the incoming FoldTree. CHEMICAL Edges are then restored.

Returns

The appropriate FoldTree is configured and accessible by the caller of this function.

The movable_jumps vector contains the number of the jump across the interface.

References core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::delete_self_edges(), core::kinematics::FoldTree::edge_label(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_chemical_edges(), core::kinematics::FoldTree::get_jump_edges(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::replace_edge(), core::pose::residue_center_of_mass(), core::scoring::rg, setup_dock_jump(), setup_edges_for_partner(), core::pose::Pose::size(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), TR(), and core::kinematics::FoldTree::update_edge_label().

TR()

static basic::Tracer protocols::docking::TR ( "protocols.docking.DockingHighResFactory"  )

static

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::docking::EnsureExclusivelySharedJumpMover::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::docking::DockingHighResLegacy::apply(), protocols::docking::DockingInitialPerturbation::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::docking::SlideIntoContact::apply(), protocols::docking::DockingLowRes::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::DockMCMCycle::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::docking::membrane::MPDockingMover::apply(), protocols::docking::membrane::MPDockingSetupMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), protocols::docking::EllipsoidalRandomizationMover::calculate_geometry(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::docking::DockingEnsemble::calculate_lowres_ref_energy(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility(), comma_separated_partner_chains(), protocols::docking::DockingHighResFactory::create_docking_high_res_mover(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::docking::DockingEnsemble::DockingEnsemble(), protocols::docking::DockingLowResFilter::DockingLowResFilter(), protocols::docking::DockingLowResEnsemble::ensemble1_trial(), protocols::docking::DockingLowResEnsemble::ensemble2_trial(), protocols::docking::membrane::MPDockingMover::finalize_setup(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::docking::membrane::MPFindInterfaceMover::finalize_setup(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::docking::membrane::MPFindInterfaceMover::fractions_small_residues(), protocols::docking::DockingLowRes::get_current_conformer_ensemble1(), protocols::docking::DockingLowRes::get_current_conformer_ensemble2(), protocols::docking::membrane::MPDockingMover::init_from_cmd(), protocols::docking::membrane::MPFindInterfaceMover::init_from_cmd(), protocols::docking::DockingInitialPerturbation::init_from_options(), protocols::docking::DockMCMCycle::init_mc(), protocols::docking::DockingEnsemble::load_ensemble(), protocols::docking::DockingLowRes::lowres_inner_cycle(), move_apart(), protocols::docking::DockingEnsemblePrepackProtocol::move_away(), protocols::docking::DockingEnsemblePrepackProtocol::move_back(), move_together(), protocols::docking::DockingInitialPerturbation::parse_my_tag(), protocols::docking::DockingEnsemble::recover_and_pack_conformer_sidechains(), protocols::docking::DockingLowRes::rigid_body_trial(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_min_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), protocols::docking::membrane::MPDockingMover::set_docking_protocol(), protocols::docking::DockingProtocol::setup_constraints(), setup_foldtree(), protocols::docking::DockingHighResLegacy::setup_packing(), protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner(), protocols::docking::membrane::MPDockingSetupMover::transform_pose_into_membrane(), and protocols::docking::DockingEnsemble::update_pdblist_file().