Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Functions
protocols::docking Namespace Reference

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::vector1_int protocols::docking::DockJumps

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.

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.

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.

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

Referenced by calc_Fnat().

std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockSetupMover &  dp 
)
std::ostream & protocols::docking::operator<< ( std::ostream &  os,
ConformerSwitchMover const &  mover 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const TemperedDocking &  dp 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockMCMProtocol &  dmp 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockingLowRes &  dp 
)
std::ostream& protocols::docking::operator<< ( std::ostream &  out,
const DockMCMCycle &  dp 
)
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 
)
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(), 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));

References setup_foldtree().

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