Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
protocols::antibody::design::AntibodyDesignModeler Class Reference

Class that runs the modeling for AntibodyDesign protocols. Could be moved to antibody. More...

#include <AntibodyDesignModeler.hh>

Public Member Functions

 AntibodyDesignModeler (AntibodyInfoOP ab_info)
 
virtual ~AntibodyDesignModeler ()
 
void set_cdr (CDRNameEnum const cdr, bool setting)
 Set to model CDRs. Default is all of them false. More...
 
void set_cdr_only (CDRNameEnum const cdr, bool setting)
 Set to model only one cdr, or all others but one. More...
 
void set_cdr_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool setting)
 Set a range of CDRs. More...
 
void set_scorefunction (ScoreFunctionCOP scorefxn)
 
void set_interface_detection_dis (core::Real interface_distance)
 Set a value for interface detection across the class. More...
 
void set_neighbor_detection_dis (core::Real neighbor_distance)
 
core::Real get_interface_detection_dis ()
 
core::Real get_neighbor_detection_dis ()
 
void set_ab_dock_chains (std::string ab_dock_chains)
 Override the command line default of LH to L or H or something strange. Used primarily for bivalent antibody design, or if you are designing an antibody to primarily bind light or heavy chain. This is only used by docking and rigid-body jump minimization functions. More...
 
std::string get_ab_dock_chains ()
 Get the ab_dock_chains string, set via command line. More...
 
void relax_cdrs (Pose &pose, bool centroid_mode, bool starting_coordinate_constraints=false, bool min_interface=false, std::string dock_chains="L_H") const
 Relax CDRs only either using FastRelax or CentroidRelax. More...
 
void relax_cdrs_and_neighbor_sc (Pose &pose, bool starting_coordinate_constraints=false, bool min_interface=false, std::string dock_chains="L_H") const
 
void relax_interface (Pose &pose, std::string dock_chains, bool min_interface_sc=true) const
 
void minimize_cdrs (Pose &pose, bool min_interface=false, std::string dock_chains="L_H") const
 Vanilla minimizer using dfpmin_armijo_nonmonotone at .01 tolerance. More...
 
void minimize_cdrs_and_neighbor_sc (Pose &pose, bool min_interface=false, std::string dock_chains="L_H") const
 
void minimize_interface (Pose &pose, std::string dock_chains, bool min_interface_sc=true) const
 
void repack_antigen_ab_interface (Pose &pose) const
 Repack the interface between Antibody and Antigen. Foldtree for docking (LH_A/etc.) must be set. More...
 
void repack_antigen_interface (Pose &pose) const
 Repack the interface between antibody and antigen, but only pack antigen. More...
 
void repack_antibody_interface (Pose &pose) const
 Repack the interface between antibody and antigen, but only pack antibody. More...
 
void repack_CDRs (Pose &pose)
 Repack the CDRs given. Nothing special. More...
 
void repack_CDRs_and_neighbors (Pose &pose)
 Repack CDRs and their neighbors within distance. More...
 
void dock_LH_A_low_res (Pose &pose, bool pack_interface=false) const
 
void dock_LH_A_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const
 
void dock_A_LH_low_res (Pose &pose, bool pack_interface=false) const
 
void dock_A_LH_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const
 
void dock_L_H_low_res (Pose &pose, bool pack_interface=false) const
 
void dock_L_H_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const
 
void dock_H_L_low_res (Pose &pose, bool pack_interface=false) const
 
void dock_H_L_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const
 
void extend_CDR (Pose &pose, CDRNameEnum cdr) const
 Randomizes the dihedrals of the CDR. More...
 

Protected Member Functions

void read_command_line_options ()
 
void apply_LH_A_foldtree (core::pose::Pose &pose) const
 Applies an LH-A Foldtree. Forked from AbInfo - Its version uses hardcoded order of the PDB. Need to refactor that using this. Need to find out if they are exactly the same first. More...
 
void dock_high_res (core::pose::Pose &pose, std::string dock_chains, int first_cycle=4, int second_cycle=45) const
 Main High-res docker. More...
 
void dock_low_res (core::pose::Pose &pose, std::string dock_chains, bool pack_interface=false) const
 Main Low-res docker. More...
 
protocols::loops::LoopsOP get_cdr_loops (Pose &pose) const
 AntibodyInfo has this function. Need to refactor more to get single loop on the fly. More...
 

Protected Attributes

AntibodyInfoOP ab_info_
 
ScoreFunctionOP scorefxn_
 
ScoreFunctionOP docking_scorefxn_high_
 
TaskFactoryOP antigen_interface_tf_
 
TaskFactoryOP tf_
 
protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsOP loops_operation_
 
operation::InitializeFromCommandlineOP cmd_line_operation_
 
operation::RestrictToRepackingOP restrict_design_operation_
 
core::Real interface_dis_
 
core::Real neighbor_dis_
 
std::string ab_dock_chains_
 
vector1< boolcdrs_
 

Detailed Description

Class that runs the modeling for AntibodyDesign protocols. Could be moved to antibody.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodyDesignModeler::AntibodyDesignModeler ( AntibodyInfoOP  ab_info)
protocols::antibody::design::AntibodyDesignModeler::~AntibodyDesignModeler ( )
virtual

Member Function Documentation

void protocols::antibody::design::AntibodyDesignModeler::apply_LH_A_foldtree ( core::pose::Pose pose) const
protected

Applies an LH-A Foldtree. Forked from AbInfo - Its version uses hardcoded order of the PDB. Need to refactor that using this. Need to find out if they are exactly the same first.

References protocols::docking::setup_foldtree().

void protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_high_res ( Pose pose,
int  first_cycle = 4,
int  second_cycle = 45 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_low_res ( Pose pose,
bool  pack_interface = false 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_H_L_high_res ( Pose pose,
int  first_cycle = 4,
int  second_cycle = 45 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_H_L_low_res ( Pose pose,
bool  pack_interface = false 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_high_res ( core::pose::Pose pose,
std::string  dock_chains,
int  first_cycle = 4,
int  second_cycle = 45 
) const
protected
void protocols::antibody::design::AntibodyDesignModeler::dock_L_H_high_res ( Pose pose,
int  first_cycle = 4,
int  second_cycle = 45 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_L_H_low_res ( Pose pose,
bool  pack_interface = false 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_high_res ( Pose pose,
int  first_cycle = 4,
int  second_cycle = 45 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_low_res ( Pose pose,
bool  pack_interface = false 
) const
void protocols::antibody::design::AntibodyDesignModeler::dock_low_res ( core::pose::Pose pose,
std::string  dock_chains,
bool  pack_interface = false 
) const
protected
void protocols::antibody::design::AntibodyDesignModeler::extend_CDR ( Pose pose,
CDRNameEnum  cdr 
) const
std::string protocols::antibody::design::AntibodyDesignModeler::get_ab_dock_chains ( )

Get the ab_dock_chains string, set via command line.

protocols::loops::LoopsOP protocols::antibody::design::AntibodyDesignModeler::get_cdr_loops ( Pose pose) const
protected

AntibodyInfo has this function. Need to refactor more to get single loop on the fly.

References protocols::antibody::CDRNameEnum_total, protocols::loops::start, and protocols::loops::stop.

core::Real protocols::antibody::design::AntibodyDesignModeler::get_interface_detection_dis ( )
inline
core::Real protocols::antibody::design::AntibodyDesignModeler::get_neighbor_detection_dis ( )
inline
void protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs ( Pose pose,
bool  min_interface = false,
std::string  dock_chains = "L_H" 
) const
void protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs_and_neighbor_sc ( Pose pose,
bool  min_interface = false,
std::string  dock_chains = "L_H" 
) const
void protocols::antibody::design::AntibodyDesignModeler::minimize_interface ( Pose pose,
std::string  dock_chains,
bool  min_interface_sc = true 
) const
void protocols::antibody::design::AntibodyDesignModeler::read_command_line_options ( )
protected
void protocols::antibody::design::AntibodyDesignModeler::relax_cdrs ( Pose pose,
bool  centroid_mode,
bool  starting_coordinate_constraints = false,
bool  min_interface = false,
std::string  dock_chains = "L_H" 
) const

Relax CDRs only either using FastRelax or CentroidRelax.

Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed.

References protocols::antibody::CDRNameEnum_total, chainbreak, core::scoring::ScoreFunction::clone(), core::pose::Pose::fold_tree(), core::scoring::constraints::remove_constraints_of_type(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::relax_cdrs_and_neighbor_sc ( Pose pose,
bool  starting_coordinate_constraints = false,
bool  min_interface = false,
std::string  dock_chains = "L_H" 
) const
void protocols::antibody::design::AntibodyDesignModeler::relax_interface ( Pose pose,
std::string  dock_chains,
bool  min_interface_sc = true 
) const
void protocols::antibody::design::AntibodyDesignModeler::repack_antibody_interface ( Pose pose) const
void protocols::antibody::design::AntibodyDesignModeler::repack_antigen_ab_interface ( Pose pose) const

Repack the interface between Antibody and Antigen. Foldtree for docking (LH_A/etc.) must be set.

References protocols::simple_moves::PackRotamersMover::apply(), core::pose::Pose::fold_tree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_antigen_interface ( Pose pose) const
void protocols::antibody::design::AntibodyDesignModeler::repack_CDRs ( Pose pose)

Repack the CDRs given. Nothing special.

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_CDRs_and_neighbors ( Pose pose)

Repack CDRs and their neighbors within distance.

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::set_ab_dock_chains ( std::string  ab_dock_chains)

Override the command line default of LH to L or H or something strange. Used primarily for bivalent antibody design, or if you are designing an antibody to primarily bind light or heavy chain. This is only used by docking and rigid-body jump minimization functions.

void protocols::antibody::design::AntibodyDesignModeler::set_cdr ( CDRNameEnum const  cdr,
bool  setting 
)

Set to model CDRs. Default is all of them false.

void protocols::antibody::design::AntibodyDesignModeler::set_cdr_only ( CDRNameEnum const  cdr,
bool  setting 
)

Set to model only one cdr, or all others but one.

References protocols::antibody::CDRNameEnum_start, and protocols::antibody::CDRNameEnum_total.

void protocols::antibody::design::AntibodyDesignModeler::set_cdr_range ( CDRNameEnum const  cdr_start,
CDRNameEnum const  cdr_end,
bool  setting 
)

Set a range of CDRs.

References protocols::antibody::cdr_end.

void protocols::antibody::design::AntibodyDesignModeler::set_interface_detection_dis ( core::Real  interface_distance)

Set a value for interface detection across the class.

void protocols::antibody::design::AntibodyDesignModeler::set_neighbor_detection_dis ( core::Real  neighbor_distance)
void protocols::antibody::design::AntibodyDesignModeler::set_scorefunction ( ScoreFunctionCOP  scorefxn)

Member Data Documentation

std::string protocols::antibody::design::AntibodyDesignModeler::ab_dock_chains_
protected
AntibodyInfoOP protocols::antibody::design::AntibodyDesignModeler::ab_info_
protected
TaskFactoryOP protocols::antibody::design::AntibodyDesignModeler::antigen_interface_tf_
protected
vector1<bool> protocols::antibody::design::AntibodyDesignModeler::cdrs_
protected
operation::InitializeFromCommandlineOP protocols::antibody::design::AntibodyDesignModeler::cmd_line_operation_
protected
ScoreFunctionOP protocols::antibody::design::AntibodyDesignModeler::docking_scorefxn_high_
protected
core::Real protocols::antibody::design::AntibodyDesignModeler::interface_dis_
protected
protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodyDesignModeler::loops_operation_
protected
core::Real protocols::antibody::design::AntibodyDesignModeler::neighbor_dis_
protected
operation::RestrictToRepackingOP protocols::antibody::design::AntibodyDesignModeler::restrict_design_operation_
protected
ScoreFunctionOP protocols::antibody::design::AntibodyDesignModeler::scorefxn_
protected
TaskFactoryOP protocols::antibody::design::AntibodyDesignModeler::tf_
protected

The documentation for this class was generated from the following files: