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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  DockingHighResFactory
 DockingHighResFactory uses the MoverFactory to create instances of DockingHighRes. 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  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  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  DockingPrepackProtocolCreator
 
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  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  FaDockingSlideIntoContact
 Slides docking partners together by monitoring fa_rep. More...
 
class  InterfaceSidechainMinMover
 
class  RigidBodyInfo
 
class  SidechainMinMover
 
class  SlideIntoContact
 More general function for low-res or highres DockingSlideIntoContact. More...
 
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
< 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  DHR_Type {
  DHR_Type::DockingHighResLegacy, DHR_Type::DockingPrepackProtocol, DHR_Type::DockMCMProtocol, DHR_Type::DockMinMover,
  DHR_Type::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)
 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)
 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

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< 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< 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< 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::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< FaDockingSlideIntoContact const > protocols::docking::FaDockingSlideIntoContactCOP
typedef utility::pointer::shared_ptr< RigidBodyInfo const > protocols::docking::RigidBodyInfoCOP
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< SlideIntoContact const > protocols::docking::SlideIntoContactCOP
typedef utility::pointer::shared_ptr< SlideIntoContact > protocols::docking::SlideIntoContactOP
typedef utility::pointer::shared_ptr< TemperedDocking > protocols::docking::TemperedDockingOP

Enumeration Type Documentation

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

Enumerator
DockingHighResLegacy 
DockingPrepackProtocol 
DockMCMProtocol 
DockMinMover 
SnugDock 

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

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 
)
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 
)
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().

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().

core::Real protocols::docking::calc_Fnonnat ( const core::pose::Pose pose,
std::string const &  list_file,
DockJumps const  movable_jumps 
)
core::Real protocols::docking::calc_interaction_energy ( const core::pose::Pose pose,
const core::scoring::ScoreFunctionCOP  dock_scorefxn,
DockJumps const  movable_jumps 
)
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().

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 
)
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 
)
core::Real protocols::docking::calc_Lrmsd ( const core::pose::Pose pose,
const core::pose::Pose native_pose,
DockJumps const  movable_jumps 
)
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::QuickRelaxPartnersSeparately::apply(), and protocols::docking::membrane::MPFindInterfaceMover::apply().

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().

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::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().

void protocols::docking::move_apart ( core::pose::Pose pose,
int  jump,
core::Vector const &  axis 
)
void protocols::docking::move_together ( core::pose::Pose pose,
int  jump,
core::scoring::ScoreFunctionOP  sfxn 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockSetupMover &  dp 
)
std::ostream & protocols::docking::operator<< ( std::ostream &  output,
ConformerSwitchMover const &  mover 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockMCMProtocol &  dmp 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const TemperedDocking &  dp 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockMCMCycle &  dp 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockingLowRes &  dp 
)
std::ostream & protocols::docking::operator<< ( std::ostream &  output,
EllipsoidalRandomizationMover const &  object_to_output 
)
std::ostream & protocols::docking::operator<< ( std::ostream &  os,
DockingSlideIntoContact const &  mover 
)
std::ostream & protocols::docking::operator<< ( std::ostream &  os,
FaDockingSlideIntoContact const &  fadock 
)
std::ostream & protocols::docking::operator<< ( std::ostream &  out,
const DockingProtocol &  dp 
)
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::FoldTree::num_jump(), and core::kinematics::FoldTree::update_edge_label().

Referenced by setup_foldtree().

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(), protocols::make_rot_lib::PEPTIDE, core::kinematics::FoldTree::split_existing_edge_at_residue(), protocols::loops::start, and protocols::loops::stop.

Referenced by setup_foldtree().

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

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::protein_interface_design::movers::SetAtomTree::apply(), protocols::docking::DockSetupMover::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::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::docking::TemperedDocking::finalize_setup(), protocols::docking::DockingProtocol::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(), and protocols::antibody::setup_LH_A_foldtree().

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

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(), setup_dock_jump(), setup_edges_for_partner(), core::pose::Pose::size(), TR(), and core::kinematics::FoldTree::update_edge_label().

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

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::docking::DockingInitialPerturbation::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::docking::DockMCMCycle::apply(), protocols::docking::DockingLowRes::apply(), protocols::docking::DockingHighResLegacy::apply(), protocols::docking::membrane::MPDockingSetupMover::apply(), protocols::docking::membrane::MPDockingMover::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::docking::SlideIntoContact::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::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::docking::membrane::MPFindInterfaceMover::finalize_setup(), protocols::docking::membrane::MPDockingMover::finalize_setup(), protocols::docking::DockingProtocol::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::MPFindInterfaceMover::init_from_cmd(), protocols::docking::membrane::MPDockingMover::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(), 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::DockingProtocol::setup_constraints(), setup_foldtree(), protocols::docking::DockingHighResLegacy::setup_packing(), protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner(), and protocols::docking::membrane::MPDockingSetupMover::transform_pose_into_membrane().