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	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	DockingHighResFilter
	High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given (2) interface_score must be negative. More...
class	DockingHighResLegacy
	this mover does the high resolution refinement stage of the RosettaDock algorithm More...
class	DockingInitialPerturbation
	this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options More...
class	DockingInitialPerturbationCreator
class	DockingLowRes
class	DockingLowResEnsemble
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	DockingPrepackProtocol
class	DockingProtocol
	This is the standard RosettaDock protocol. More...
class	DockingProtocolCreator
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	DockMCMCycle
class	DockMCMProtocol
class	DockMinMover
class	DockSetupMover
	allows docking using simulated or parallel tempering More...
class	DockSetupMoverCreator
class	DockTaskFactory
class	EllipsoidalRandomizationMover
class	FaDockingSlideIntoContact
	Slides docking partners together by monitoring fa_rep. More...
class	InterfaceSidechainMinMover
class	RigidBodyInfo
class	SidechainMinMover
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 < 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 < RigidBodyInfo >	RigidBodyInfoOP
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

Functions
std::ostream &	operator<< (std::ostream &output, ConformerSwitchMover const &mover)
std::ostream &	operator<< (std::ostream &os, DockingSlideIntoContact const &mover)
std::ostream &	operator<< (std::ostream &os, FaDockingSlideIntoContact const &fadock)
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_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_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 5A 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)
std::ostream &	operator<< (std::ostream &out, const TemperedDocking &dp)
void	setup_foldtree (Pose &pose, string const &partner_chainID, DockJumps &movable_jumps)
	Setup foldtree for across an interface specified by a string for the partner chains (using pdb_chain identification). 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, std::string const &partner_chainID, DockJumps &movable_jumps, core::kinematics::FoldTree &ft)
void	setup_foldtree (Pose &pose, Size const interface_id, sessionOP db_session, DockJumps &movable_jumps)
void	setup_foldtree (core::pose::Pose const &pose, core::Size interface_id, utility::sql_database::sessionOP db_session, DockJumps &movable_jumps, core::kinematics::FoldTree &ft)
void	setup_foldtree (Pose &pose, map< Size, vector1< Size > > const &partner_to_chains, DockJumps &movable_jumps)
void	setup_foldtree (core::pose::Pose const &pose, std::map< core::Size, utility::vector1< core::Size > > const &partner_to_chains, DockJumps &movable_jumps, core::kinematics::FoldTree &ft)
void	setup_foldtree (Pose &pose, Size const cutpoint, DockJumps &movable_jumps)
void	setup_foldtree (core::pose::Pose const &pose, core::Size cutpoint, DockJumps &movable_jumps, core::kinematics::FoldTree &ft)
void	setup_foldtree (core::pose::Pose &pose, core::Size interface_id, utility::sql_database::sessionOP db_session, DockJumps &movable_jumps)
	Sets up a docking fold tree based on looking up the interface in a database. More...
void	setup_foldtree (core::pose::Pose &pose, std::map< core::Size, utility::vector1< core::Size > > const &partner_to_chains, DockJumps &movable_jumps)
	Sets up a docking fold tree based on a map of which chains are part of which partner. More...
void	setup_foldtree (core::pose::Pose &pose, core::Size cutpoint, DockJumps &movable_jumps)
	Sets up a docking fold tree based on user-specified chains for the first and second partner. More...

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Function Documentation

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(), is_protein_CA(), core::scoring::rmsd_with_super_subset(), and core::pose::Pose::total_residue().

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(), 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::total_residue(), and TR().

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

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(), getline(), utility::io::izstream::good(), core::pose::Pose::is_fullatom(), core::pose::Pose::residue(), and TR().

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(), 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::total_residue(), and TR().

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(), getline(), utility::io::izstream::good(), core::pose::Pose::is_fullatom(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and TR().

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::geometry::membrane_axis(), option, numeric::xyzVector< class >::to_string(), TR(), and user.

Referenced by protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::docking::DockingHighResFilter::apply(), and protocols::docking::DockingProtocol::apply().

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 5A of the interface at superposition along those same atoms.

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

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

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(), is_protein_backbone(), core::kinematics::FoldTree::partition_by_jump(), core::scoring::rmsd_no_super_subset(), and core::pose::Pose::total_residue().

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

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

References TR().

Referenced by calc_Fnat(), and calc_Fnonnat().

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

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

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

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

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

References I, and protocols::docking::TemperedDocking::movable_jumps_.

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

References protocols::docking::DockMCMProtocol::filter_, protocols::docking::DockMCMProtocol::movemap_, protocols::docking::DockMCMProtocol::scorefxn_docking(), and protocols::docking::DockMCMProtocol::scorefxn_packing().

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

References I, protocols::docking::DockMCMCycle::movable_jumps_, protocols::docking::DockMCMCycle::rot_magnitude_, protocols::docking::DockMCMCycle::scorefxn_, protocols::docking::DockMCMCycle::scorefxn_pack_, and protocols::docking::DockMCMCycle::trans_magnitude_.

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

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

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

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

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

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

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

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

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

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

void protocols::docking::setup_foldtree	(	core::pose::Pose &	pose,
		core::Size	interface_id,
		utility::sql_database::sessionOP	db_session,
		DockJumps &	movable_jumps
	)

Sets up a docking fold tree based on looking up the interface in a database.

void protocols::docking::setup_foldtree	(	core::pose::Pose &	pose,
		std::map< core::Size, utility::vector1< core::Size > > const &	partner_to_chains,
		DockJumps &	movable_jumps
	)

Sets up a docking fold tree based on a map of which chains are part of which partner.

void protocols::docking::setup_foldtree	(	core::pose::Pose &	pose,
		core::Size	cutpoint,
		DockJumps &	movable_jumps
	)

Sets up a docking fold tree based on user-specified chains for the first and second partner.

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

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

Sets up a docking fold tree based on user-specified chains for the first and second partner.

Detailed:

if partner_chainID == '_' -> use the first movable jump as the cutpoint if partner_chainID is of the form (pdb_chain_id)+_(pdb_chain_id)+ then use the jump between the last chain of the first partner and the first chain of the second partner as the cutpoint. For example 'ABC_DEF' has chains 'ABC' as the first partner and 'DEF' as the second partner.

With the current implementation, all of the chains of the first partner must be upstream of the chains of the second partner. If this behavior is too limiting, then the behavior can be extended.

Returns

The foldtree in the pose will have a jump from the center of mass of the first partner to the center of mass of the second partner and no other jumps between residues in different partners

the movable_jumps vector contains as it's only entry the number of the jump across the interface.

References core::pose::Pose::fold_tree().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::docking::DockSetupMover::apply(), protocols::antibody::design::AntibodyDesignModeler::apply_LH_A_foldtree(), protocols::antibody::design::AntibodyGraftDesignMover::apply_to_cdr(), protocols::antibody::design::AntibodyDesignModeler::dock_high_res(), protocols::antibody::design::AntibodyDesignModeler::dock_low_res(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingPrepackProtocol::finalize_setup(), protocols::docking::TemperedDocking::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs(), protocols::antibody::design::AntibodyDesignModeler::minimize_interface(), protocols::antibody::design::AntibodyDesignModeler::relax_cdrs(), protocols::antibody::design::AntibodyDesignModeler::relax_interface(), protocols::docking::EllipsoidalRandomizationMover::set_foldtree(), protocols::antibody::setup_A_LH_foldtree(), protocols::antibody::design::AntibodyDesignMoverGenerator::setup_dock_foldtree(), setup_foldtree(), protocols::antibody::design::AntibodyDesignMoverGenerator::setup_general_min_foldtree(), and protocols::antibody::setup_LH_A_foldtree().

void protocols::docking::setup_foldtree	(	core::pose::Pose const &	pose,
		std::string const &	partner_chainID,
		DockJumps &	movable_jumps,
		core::kinematics::FoldTree &	ft
	)

References core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), core::pose::Pose::pdb_info(), setup_foldtree(), utility::to_string(), and utility_exit_with_message.

void protocols::docking::setup_foldtree	(	Pose &	pose,
		Size const	interface_id,
		sessionOP	db_session,
		DockJumps &	movable_jumps
	)

Here is the protocol that the database should have:

CREATE TABLE IF NOT EXISTS interfaces ( struct_id BLOB, interface_id INTEGER, FOREIGN KEY (struct_id) REFERENCES structures (struct_id) DEFERRABLE INITIALLY DEFERRED, PRIMARY KEY(struct_id, interface_id));

CREATE TABLE IF NOT EXISTS interface_partners ( interface_id INTEGER, partner_id INTEGER, FOREIGN KEY (interface_id) REFERENCES interfaces (interface_id) DEFERRABLE INITIALLY DEFERRED, PRIMARY KEY(interface_id, partner_id));

CREATE TABLE IF NOT EXISTS interface_partner_chains ( partner_id INTEGER, chain_id INTEGER, FOREIGN KEY (interface_interface_id) REFERENCES interface_partners (interface_partner_id) DEFERRABLE INITIALLY DEFERRED, PRIMARY KEY(partner_id, chain_id));

References core::pose::Pose::fold_tree(), and setup_foldtree().

void protocols::docking::setup_foldtree	(	core::pose::Pose const &	pose,
		core::Size	interface_id,
		utility::sql_database::sessionOP	db_session,
		DockJumps &	movable_jumps,
		core::kinematics::FoldTree &	ft
	)

References safely_prepare_statement(), safely_read_from_database(), and setup_foldtree().

void protocols::docking::setup_foldtree	(	Pose &	pose,
		map< Size, vector1< Size > > const &	partner_to_chains,
		DockJumps &	movable_jumps
	)

References core::pose::Pose::fold_tree(), and setup_foldtree().

void protocols::docking::setup_foldtree	(	core::pose::Pose const &	pose,
		std::map< core::Size, utility::vector1< core::Size > > const &	partner_to_chains,
		DockJumps &	movable_jumps,
		core::kinematics::FoldTree &	ft
	)

References core::pose::Pose::chain(), core::pose::Pose::fold_tree(), setup_foldtree(), core::pose::Pose::total_residue(), and utility_exit_with_message.

void protocols::docking::setup_foldtree	(	Pose &	pose,
		Size const	cutpoint,
		DockJumps &	movable_jumps
	)

References core::pose::Pose::fold_tree(), and setup_foldtree().

void protocols::docking::setup_foldtree	(	core::pose::Pose const &	pose,
		core::Size	cutpoint,
		DockJumps &	movable_jumps,
		core::kinematics::FoldTree &	ft
	)

References core::pose::Pose::chain(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoint_by_jump(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::reorder(), core::pose::residue_center_of_mass(), runtime_assert, runtime_assert_string_msg, core::kinematics::FoldTree::simple_tree(), core::kinematics::FoldTree::slide_jump(), core::pose::Pose::total_residue(), and protocols::TR().