Namespaces
	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	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	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	DockingInitialPerturbationCreator

class	DockingLowRes

class	DockingLowResEnsemble

class	DockingPrepackProtocol

class	DockingProtocol
	This is the standard RosettaDock protocol. More...

class	DockingProtocolCreator

class	DockMCMCycle

class	DockMCMProtocol

class	DockMinMover

class	DockSetupMover
	allows docking using simulated or parallel tempering More...

class	DockSetupMoverCreator

class	DockTaskFactory

class	RigidBodyInfo

class	SidechainMinMover

class	InterfaceSidechainMinMover

class	TemperedDocking
	allows docking using simulated or parallel tempering More...

class	TemperedDockingCreator

Typedefs
typedef utility::pointer::owning_ptr < ConformerSwitchMover >	ConformerSwitchMoverOP

typedef utility::pointer::owning_ptr < ConformerSwitchMover const >	ConformerSwitchMoverCOP

typedef utility::pointer::owning_ptr < DockingLowResFilter >	DockingLowResFilterOP

typedef utility::pointer::owning_ptr < DockingLowResFilter const >	DockingLowResFilterCOP

typedef utility::pointer::owning_ptr < DockingHighResFilter >	DockingHighResFilterOP

typedef utility::pointer::owning_ptr < DockingHighResFilter const >	DockingHighResFilterCOP

typedef utility::pointer::owning_ptr < DockingEnsemble >	DockingEnsembleOP

typedef utility::pointer::owning_ptr < DockingEnsemble const >	DockingEnsembleCOP

typedef utility::pointer::owning_ptr < DockingEnsemblePrepackProtocol >	DockingEnsemblePrepackProtocolOP

typedef utility::pointer::owning_ptr < DockingEnsemblePrepackProtocol const >	DockingEnsemblePrepackProtocolCOP

typedef utility::pointer::owning_ptr < DockingHighRes >	DockingHighResOP

typedef utility::pointer::owning_ptr < DockingHighRes const >	DockingHighResCOP

typedef utility::pointer::owning_ptr < DockingHighResLegacy >	DockingHighResLegacyOP

typedef utility::pointer::owning_ptr < DockingHighResLegacy const >	DockingHighResLegacyCOP

typedef utility::pointer::owning_ptr < DockingInitialPerturbation >	DockingInitialPerturbationOP

typedef utility::pointer::owning_ptr < DockingInitialPerturbation const >	DockingInitialPerturbationCOP

typedef utility::pointer::owning_ptr < DockingSlideIntoContact >	DockingSlideIntoContactOP

typedef utility::pointer::owning_ptr < DockingSlideIntoContact const >	DockingSlideIntoContactCOP

typedef utility::pointer::owning_ptr < FaDockingSlideIntoContact >	FaDockingSlideIntoContactOP

typedef utility::pointer::owning_ptr < FaDockingSlideIntoContact const >	FaDockingSlideIntoContactCOP

typedef utility::pointer::owning_ptr < DockingLowRes >	DockingLowResOP

typedef utility::pointer::owning_ptr < DockingLowRes const >	DockingLowResCOP

typedef utility::pointer::owning_ptr < DockingLowResEnsemble >	DockingLowResEnsembleOP

typedef utility::pointer::owning_ptr < DockingLowResEnsemble const >	DockingLowResEnsembleCOP

typedef utility::pointer::owning_ptr < DockingPrepackProtocol >	DockingPrepackProtocolOP

typedef utility::pointer::owning_ptr < DockingPrepackProtocol const >	DockingPrepackProtocolCOP

typedef utility::pointer::owning_ptr < DockingProtocol >	DockingProtocolOP

typedef utility::pointer::owning_ptr < DockMCMCycle >	DockMCMCycleOP

typedef utility::pointer::owning_ptr < DockMCMCycle const >	DockMCMCycleCOP

typedef utility::pointer::owning_ptr < DockMCMProtocol >	DockMCMProtocolOP

typedef utility::pointer::owning_ptr < DockMCMProtocol const >	DockMCMProtocolCOP

typedef utility::pointer::owning_ptr < DockMinMover >	DockMinMoverOP

typedef utility::pointer::owning_ptr < DockMinMover const >	DockMinMoverCOP

typedef utility::pointer::owning_ptr < DockingSetupMover >	DockingSetupMoverOP

typedef utility::pointer::owning_ptr < DockTaskFactory >	DockTaskFactoryOP

typedef utility::pointer::owning_ptr < DockTaskFactory const >	DockTaskFactoryCOP

typedef utility::pointer::owning_ptr < RigidBodyInfo >	RigidBodyInfoOP

typedef utility::pointer::owning_ptr < SidechainMinMover >	SidechainMinMoverOP

typedef utility::pointer::owning_ptr < SidechainMinMover >	SidechainMinMoverCOP

typedef utility::pointer::owning_ptr < InterfaceSidechainMinMover >	InterfaceSidechainMinMoverOP

typedef utility::pointer::owning_ptr < InterfaceSidechainMinMover >	InterfaceSidechainMinMoverCOP

typedef utility::pointer::owning_ptr < TemperedDocking >	TemperedDockingOP

typedef utility::vector1_int	DockJumps

Functions
std::ostream &	operator<< (std::ostream &os, 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)

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_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...

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 (Pose &pose, Size const interface_id, sessionOP db_session, DockJumps &movable_jumps)

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

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

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::owning_ptr< ConformerSwitchMover const > protocols::docking::ConformerSwitchMoverCOP

Definition at line 28 of file ConformerSwitchMover.fwd.hh.

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

Definition at line 26 of file ConformerSwitchMover.fwd.hh.

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

Definition at line 26 of file DockingEnsemble.fwd.hh.

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

Definition at line 24 of file DockingEnsemble.fwd.hh.

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

Definition at line 28 of file DockingEnsemblePrepackProtocol.fwd.hh.

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

Definition at line 26 of file DockingEnsemblePrepackProtocol.fwd.hh.

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

Definition at line 26 of file DockingHighRes.fwd.hh.

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

Definition at line 29 of file DockFilters.fwd.hh.

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

Definition at line 27 of file DockFilters.fwd.hh.

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

Definition at line 25 of file DockingHighResLegacy.fwd.hh.

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

Definition at line 23 of file DockingHighResLegacy.fwd.hh.

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

Definition at line 24 of file DockingHighRes.fwd.hh.

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

Definition at line 25 of file DockingInitialPerturbation.fwd.hh.

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

Definition at line 23 of file DockingInitialPerturbation.fwd.hh.

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

Definition at line 26 of file DockingLowRes.fwd.hh.

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

Definition at line 26 of file DockingLowResEnsemble.fwd.hh.

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

Definition at line 24 of file DockingLowResEnsemble.fwd.hh.

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

Definition at line 25 of file DockFilters.fwd.hh.

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

Definition at line 23 of file DockFilters.fwd.hh.

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

Definition at line 24 of file DockingLowRes.fwd.hh.

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

Definition at line 28 of file DockingPrepackProtocol.fwd.hh.

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

Definition at line 26 of file DockingPrepackProtocol.fwd.hh.

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

Definition at line 22 of file DockingProtocol.fwd.hh.

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

Definition at line 22 of file DockSetupMover.fwd.hh.

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

Definition at line 29 of file DockingInitialPerturbation.fwd.hh.

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

Definition at line 27 of file DockingInitialPerturbation.fwd.hh.

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

Definition at line 24 of file types.hh.

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

Definition at line 25 of file DockMCMCycle.fwd.hh.

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

Definition at line 23 of file DockMCMCycle.fwd.hh.

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

Definition at line 25 of file DockMCMProtocol.fwd.hh.

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

Definition at line 23 of file DockMCMProtocol.fwd.hh.

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

Definition at line 25 of file DockMinMover.fwd.hh.

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

Definition at line 23 of file DockMinMover.fwd.hh.

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

Definition at line 25 of file DockTaskFactory.fwd.hh.

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

Definition at line 23 of file DockTaskFactory.fwd.hh.

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

Definition at line 33 of file DockingInitialPerturbation.fwd.hh.

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

Definition at line 31 of file DockingInitialPerturbation.fwd.hh.

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

Definition at line 28 of file SidechainMinMover.fwd.hh.

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

Definition at line 26 of file SidechainMinMover.fwd.hh.

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

Definition at line 19 of file RigidBodyInfo.fwd.hh.

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

Definition at line 24 of file SidechainMinMover.fwd.hh.

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

Definition at line 22 of file SidechainMinMover.fwd.hh.

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

Definition at line 22 of file TemperedDocking.fwd.hh.

Function Documentation

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.

Definition at line 164 of file metrics.cc.

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 core::TR().

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

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.

Definition at line 54 of file metrics.cc.

References core::scoring::atom_pair_constraint.

Referenced by 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.

Definition at line 127 of file metrics.cc.

References 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 core::TR().

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

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.

Definition at line 101 of file metrics.cc.

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::total_residue().

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

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

Definition at line 238 of file metrics.cc.

Referenced by calc_Fnat().

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

Definition at line 136 of file DockSetupMover.cc.

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

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

Definition at line 228 of file ConformerSwitchMover.cc.

References protocols::docking::ConformerSwitchMover::get_temperature(), protocols::moves::operator<<(), and protocols::docking::ConformerSwitchMover::use_random_conformer().

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

Definition at line 292 of file TemperedDocking.cc.

References protocols::comparative_modeling::features::A, and protocols::docking::TemperedDocking::movable_jumps_.

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

Definition at line 296 of file DockMCMProtocol.cc.

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 DockingLowRes &	dp
	)

Definition at line 322 of file DockingLowRes.cc.

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

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

Definition at line 335 of file DockMCMCycle.cc.

References 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 &	os,
		DockingSlideIntoContact const &	mover
	)

Definition at line 442 of file DockingInitialPerturbation.cc.

References protocols::docking::DockingSlideIntoContact::get_jump_num(), and protocols::moves::operator<<().

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

Definition at line 562 of file DockingInitialPerturbation.cc.

References protocols::docking::FaDockingSlideIntoContact::get_jump_num(), protocols::docking::FaDockingSlideIntoContact::get_tolerance(), and protocols::moves::operator<<().

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

Definition at line 1096 of file DockingProtocol.cc.

References protocols::comparative_modeling::features::A, protocols::docking::DockingProtocol::docking_highres_mover_, protocols::docking::DockingProtocol::docking_lowres_mover_, protocols::docking::DockingProtocol::highres_filter_, protocols::docking::DockingProtocol::lowres_filter_, and protocols::docking::DockingProtocol::movable_jumps_.

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.

Definition at line 96 of file util.cc.

References core::pose::Pose::fold_tree(), core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::docking::DockSetupMover::apply(), protocols::docking::DockingPrepackProtocol::finalize_setup(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::TemperedDocking::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), and setup_foldtree().

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));

Definition at line 176 of file util.cc.

References setup_foldtree().

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

Definition at line 209 of file util.cc.

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

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

Definition at line 281 of file util.cc.

References core::pose::Pose::chain(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::pose::Pose::fold_tree(), core::pose::datacache::CacheableDataType::INTERFACE_INFO, protocols::geometry::residue_center_of_mass(), core::pose::Pose::total_residue(), and protocols::TR().

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation