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protocols::antibody::design::GeneralAntibodyModeler Class Reference

Basic Class that can run modeling for various protocols. Does not do any design. Setup design TF via AntibodySeqDesignTFCreator. More...

#include <GeneralAntibodyModeler.hh>

Inheritance diagram for protocols::antibody::design::GeneralAntibodyModeler:
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Public Member Functions

 GeneralAntibodyModeler (AntibodyInfoOP ab_info)
 
 ~GeneralAntibodyModeler () override
 
 GeneralAntibodyModeler (GeneralAntibodyModeler const &src)
 
GeneralAntibodyModelerOP clone () const
 
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_cdrs (utility::vector1< bool > cdrs)
 
void set_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_scorefunction_min (core::scoring::ScoreFunctionCOP scorefxn)
 Set scorefunction used for bb minimization. More...
 
void set_overhang (core::Size const overhang)
 Set the overhang for all cdrs. (Default is 0) More...
 
void cdr_overhang (CDRNameEnum const cdr, core::Size const overhang)
 How many residues on either side of the CDR to include in CDR - modeling? (Default is 0) More...
 
void ab_dock_chains (std::string ab_dock_chains)
 Set the ab_dock chains, which will be used for any docking or minimization on the jump. (LH_A, L_H, etc. - A for antigen) More...
 
void interface_detection_dis (core::Real interface_distance)
 Set a value for interface detection across the class. More...
 
core::Real interface_detection_dis () const
 
void neighbor_detection_dis (core::Real neighbor_distance)
 
core::Real neighbor_detection_dis () const
 
void repack_cdrs (core::pose::Pose &pose, bool include_neighbor_sc=true)
 Repack the CDRs given. Nothing special. More...
 
void minimize_cdrs (core::pose::Pose &pose, bool min_sc=true, bool include_neighbor_sc=true, bool min_interface=false, bool cartmin=false, bool use_talaris_cartmin=false) const
 Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). More...
 
void relax_cdrs (core::pose::Pose &pose, bool include_neighbor_sc=true, bool starting_coordinate_constraints=false, bool min_interface=false, bool dualspace=false) const
 Relax CDRs using FastRelax. CentroidRelax unfortunately does not work well. Perhaps with centroid rotamers.. More...
 
void minimize_interface (core::pose::Pose &pose, bool min_interface_sc=true) const
 
void relax_interface (core::pose::Pose &pose, bool min_interface_sc=true) const
 
void repack_antigen_ab_interface (core::pose::Pose &pose) const
 Repack the interface between Antibody and Antigen. More...
 
void repack_antigen_interface (core::pose::Pose &pose) const
 Repack the interface between antibody and antigen, but only pack antigen. More...
 
void repack_antibody_interface (core::pose::Pose &pose) const
 Repack the interface between antibody and antigen, but only pack antibody. More...
 
void backrub_cdrs (core::pose::Pose &pose, bool min_sc=true, bool include_neighbor_sc=true) const
 Run the BackrubProtocol on the CDRs. Control backrub through cmd-line. More...
 
void dock_low_res (core::pose::Pose &pose, bool pack_interface=false) const
 Dock the antibody. Using A for designation of Antigen chains. Not full antigen chains. (L_A, LH_A, L_H, etc.) More...
 
void dock_high_res (core::pose::Pose &pose, core::Size first_cycle=4, core::Size second_cycle=45) const
 
void set_dock_low_res_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_dock_high_res_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_task_factory (core::pack::task::TaskFactoryOP tf)
 
void reset_task_factory ()
 
void extend_CDR (core::pose::Pose &pose, CDRNameEnum cdr) const
 Randomizes the dihedrals of the CDR. More...
 
void apply_A_LH_foldtree (core::pose::Pose &pose) const
 Applies a docking foldtree.. Forked from AbInfo - Its version uses hardcoded order of the PDB. However, this calls docking FT, which is hard coded as well for now. Fix Me. More...
 
protocols::loops::LoopsOP get_cdr_loops (core::pose::Pose const &pose) const
 Get CDR loops with cutpoint in the middle. More...
 
protocols::loops::LoopsOP get_cdr_loops_with_overhang (core::pose::Pose const &pose) const
 Get CDR loops with set overhang with cutpoint at the stop position +1. More...
 
protocols::loops::Loop get_cdr_loop_with_overhang (core::pose::Pose const &pose, CDRNameEnum cdr) const
 
core::kinematics::MoveMapOP get_cdrs_movemap_with_overhang (core::pose::Pose &pose, bool min_bb=true, bool min_sc=true, bool include_neighbor_sc=true, bool include_neighbor_bb=false) const
 
core::kinematics::MoveMapOP get_movemap_from_task (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task) const
 
std::string get_dock_chains () const
 

Private Member Functions

void set_defaults ()
 
void read_command_line_options ()
 
void setup_scorefxns ()
 
void setup_task_operations ()
 

Private Attributes

AntibodyInfoOP ab_info_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP min_scorefxn_
 
core::scoring::ScoreFunctionOP docking_scorefxn_low_
 
core::scoring::ScoreFunctionOP docking_scorefxn_high_
 
core::pack::task::TaskFactoryOP interface_tf_
 
core::pack::task::TaskFactoryOP tf_
 
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP loops_operation_
 
core::pack::task::operation::InitializeFromCommandlineOP cmd_line_operation_
 
core::pack::task::operation::RestrictToRepackingOP restrict_design_operation_
 
core::Real interface_dis_
 
core::Real neighbor_dis_
 
std::string ab_dock_chains_
 
utility::vector1< boolmodel_cdrs_
 
utility::vector1< core::Sizeoverhangs_
 
bool tf_set_
 
core::Real atom_pair_weight_
 

Detailed Description

Basic Class that can run modeling for various protocols. Does not do any design. Setup design TF via AntibodySeqDesignTFCreator.

Constructor & Destructor Documentation

protocols::antibody::design::GeneralAntibodyModeler::GeneralAntibodyModeler ( AntibodyInfoOP  ab_info)
protocols::antibody::design::GeneralAntibodyModeler::~GeneralAntibodyModeler ( )
overridedefault
protocols::antibody::design::GeneralAntibodyModeler::GeneralAntibodyModeler ( GeneralAntibodyModeler const &  src)

Member Function Documentation

void protocols::antibody::design::GeneralAntibodyModeler::ab_dock_chains ( std::string  ab_dock_chains)

Set the ab_dock chains, which will be used for any docking or minimization on the jump. (LH_A, L_H, etc. - A for antigen)

References ab_dock_chains_.

Referenced by GeneralAntibodyModeler().

void protocols::antibody::design::GeneralAntibodyModeler::apply_A_LH_foldtree ( core::pose::Pose pose) const

Applies a docking foldtree.. Forked from AbInfo - Its version uses hardcoded order of the PDB. However, this calls docking FT, which is hard coded as well for now. Fix Me.

References ab_info_, and protocols::docking::setup_foldtree().

Referenced by repack_antibody_interface(), repack_antigen_ab_interface(), and repack_antigen_interface().

void protocols::antibody::design::GeneralAntibodyModeler::backrub_cdrs ( core::pose::Pose pose,
bool  min_sc = true,
bool  include_neighbor_sc = true 
) const
void protocols::antibody::design::GeneralAntibodyModeler::cdr_overhang ( CDRNameEnum const  cdr,
core::Size const  overhang 
)

How many residues on either side of the CDR to include in CDR - modeling? (Default is 0)

References overhangs_.

Referenced by protocols::antibody::AntibodyCDRGrafter::apply().

GeneralAntibodyModelerOP protocols::antibody::design::GeneralAntibodyModeler::clone ( ) const
void protocols::antibody::design::GeneralAntibodyModeler::dock_high_res ( core::pose::Pose pose,
core::Size  first_cycle = 4,
core::Size  second_cycle = 45 
) const
void protocols::antibody::design::GeneralAntibodyModeler::dock_low_res ( core::pose::Pose pose,
bool  pack_interface = false 
) const
void protocols::antibody::design::GeneralAntibodyModeler::extend_CDR ( core::pose::Pose pose,
CDRNameEnum  cdr 
) const
protocols::loops::Loop protocols::antibody::design::GeneralAntibodyModeler::get_cdr_loop_with_overhang ( core::pose::Pose const &  pose,
CDRNameEnum  cdr 
) const
protocols::loops::LoopsOP protocols::antibody::design::GeneralAntibodyModeler::get_cdr_loops ( core::pose::Pose const &  pose) const

Get CDR loops with cutpoint in the middle.

References ab_info_, model_cdrs_, protocols::loops::start, and protocols::loops::stop.

protocols::loops::LoopsOP protocols::antibody::design::GeneralAntibodyModeler::get_cdr_loops_with_overhang ( core::pose::Pose const &  pose) const

Get CDR loops with set overhang with cutpoint at the stop position +1.

References ab_info_, get_cdr_loop_with_overhang(), and model_cdrs_.

Referenced by backrub_cdrs(), minimize_cdrs(), relax_cdrs(), and repack_cdrs().

MoveMapOP protocols::antibody::design::GeneralAntibodyModeler::get_cdrs_movemap_with_overhang ( core::pose::Pose pose,
bool  min_bb = true,
bool  min_sc = true,
bool  include_neighbor_sc = true,
bool  include_neighbor_bb = false 
) const
std::string protocols::antibody::design::GeneralAntibodyModeler::get_dock_chains ( ) const
MoveMapOP protocols::antibody::design::GeneralAntibodyModeler::get_movemap_from_task ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP  task 
) const
void protocols::antibody::design::GeneralAntibodyModeler::interface_detection_dis ( core::Real  interface_distance)

Set a value for interface detection across the class.

References interface_dis_.

core::Real protocols::antibody::design::GeneralAntibodyModeler::interface_detection_dis ( ) const
inline

References interface_dis_.

Referenced by read_command_line_options().

void protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs ( core::pose::Pose pose,
bool  min_sc = true,
bool  include_neighbor_sc = true,
bool  min_interface = false,
bool  cartmin = false,
bool  use_talaris_cartmin = false 
) const
void protocols::antibody::design::GeneralAntibodyModeler::minimize_interface ( core::pose::Pose pose,
bool  min_interface_sc = true 
) const
void protocols::antibody::design::GeneralAntibodyModeler::neighbor_detection_dis ( core::Real  neighbor_distance)

References neighbor_dis_.

core::Real protocols::antibody::design::GeneralAntibodyModeler::neighbor_detection_dis ( ) const
inline

References neighbor_dis_.

Referenced by read_command_line_options().

void protocols::antibody::design::GeneralAntibodyModeler::read_command_line_options ( )
private
void protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs ( core::pose::Pose pose,
bool  include_neighbor_sc = true,
bool  starting_coordinate_constraints = false,
bool  min_interface = false,
bool  dualspace = false 
) const
void protocols::antibody::design::GeneralAntibodyModeler::relax_interface ( core::pose::Pose pose,
bool  min_interface_sc = true 
) const
void protocols::antibody::design::GeneralAntibodyModeler::repack_antibody_interface ( core::pose::Pose pose) const
void protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_ab_interface ( core::pose::Pose pose) const
void protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_interface ( core::pose::Pose pose) const
void protocols::antibody::design::GeneralAntibodyModeler::repack_cdrs ( core::pose::Pose pose,
bool  include_neighbor_sc = true 
)
void protocols::antibody::design::GeneralAntibodyModeler::reset_task_factory ( )
void protocols::antibody::design::GeneralAntibodyModeler::set_cdr ( CDRNameEnum const  cdr,
bool  setting 
)

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

References model_cdrs_.

Referenced by set_cdr_only(), and set_cdr_range().

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

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

References protocols::antibody::CDRNameEnum_proto_total, protocols::antibody::CDRNameEnum_start, set_cdr(), and set_cdr_range().

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

Set a range of CDRs.

References protocols::antibody::cdr_end, and set_cdr().

Referenced by set_cdr_only().

void protocols::antibody::design::GeneralAntibodyModeler::set_cdrs ( utility::vector1< bool cdrs)
void protocols::antibody::design::GeneralAntibodyModeler::set_defaults ( )
private
void protocols::antibody::design::GeneralAntibodyModeler::set_dock_high_res_scorefunction ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::antibody::design::GeneralAntibodyModeler::set_dock_low_res_scorefunction ( core::scoring::ScoreFunctionCOP  scorefxn)

References docking_scorefxn_low_.

void protocols::antibody::design::GeneralAntibodyModeler::set_overhang ( core::Size const  overhang)

Set the overhang for all cdrs. (Default is 0)

References protocols::antibody::CDRNameEnum_proto_total, and overhangs_.

void protocols::antibody::design::GeneralAntibodyModeler::set_scorefunction ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::antibody::design::GeneralAntibodyModeler::set_scorefunction_min ( core::scoring::ScoreFunctionCOP  scorefxn)

Set scorefunction used for bb minimization.

References min_scorefxn_.

Referenced by protocols::antibody::AntibodyCDRGrafter::apply().

void protocols::antibody::design::GeneralAntibodyModeler::set_task_factory ( core::pack::task::TaskFactoryOP  tf)

References tf_, and tf_set_.

void protocols::antibody::design::GeneralAntibodyModeler::setup_scorefxns ( )
private
void protocols::antibody::design::GeneralAntibodyModeler::setup_task_operations ( )
private

Member Data Documentation

std::string protocols::antibody::design::GeneralAntibodyModeler::ab_dock_chains_
private
AntibodyInfoOP protocols::antibody::design::GeneralAntibodyModeler::ab_info_
private
core::Real protocols::antibody::design::GeneralAntibodyModeler::atom_pair_weight_
private
core::pack::task::operation::InitializeFromCommandlineOP protocols::antibody::design::GeneralAntibodyModeler::cmd_line_operation_
private
core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::docking_scorefxn_high_
private
core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::docking_scorefxn_low_
private
core::Real protocols::antibody::design::GeneralAntibodyModeler::interface_dis_
private
core::pack::task::TaskFactoryOP protocols::antibody::design::GeneralAntibodyModeler::interface_tf_
private
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::GeneralAntibodyModeler::loops_operation_
private
core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::min_scorefxn_
private
utility::vector1<bool> protocols::antibody::design::GeneralAntibodyModeler::model_cdrs_
private
core::Real protocols::antibody::design::GeneralAntibodyModeler::neighbor_dis_
private
utility::vector1<core::Size> protocols::antibody::design::GeneralAntibodyModeler::overhangs_
private
core::pack::task::operation::RestrictToRepackingOP protocols::antibody::design::GeneralAntibodyModeler::restrict_design_operation_
private
core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::scorefxn_
private
core::pack::task::TaskFactoryOP protocols::antibody::design::GeneralAntibodyModeler::tf_
private
bool protocols::antibody::design::GeneralAntibodyModeler::tf_set_
private

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