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Public Member Functions | Private Member Functions | Private Attributes | List of all members
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, core::Size repeats=5) 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< bool > model_cdrs_
 
utility::vector1< core::Size > overhangs_
 
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

◆ GeneralAntibodyModeler() [1/2]

protocols::antibody::design::GeneralAntibodyModeler::GeneralAntibodyModeler ( AntibodyInfoOP  ab_info)

References ab_dock_chains(), ab_info_, read_command_line_options(), set_defaults(), setup_scorefxns(), and setup_task_operations().

◆ ~GeneralAntibodyModeler()

protocols::antibody::design::GeneralAntibodyModeler::~GeneralAntibodyModeler ( )
overridedefault

◆ GeneralAntibodyModeler() [2/2]

protocols::antibody::design::GeneralAntibodyModeler::GeneralAntibodyModeler ( GeneralAntibodyModeler const &  src)

References ab_info_, cmd_line_operation_, docking_scorefxn_high_, docking_scorefxn_low_, interface_tf_, loops_operation_, min_scorefxn_, restrict_design_operation_, scorefxn_, and tf_.

Member Function Documentation

◆ ab_dock_chains()

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().

◆ apply_A_LH_foldtree()

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().

◆ backrub_cdrs()

void protocols::antibody::design::GeneralAntibodyModeler::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.

References protocols::antibody::design::add_loops_from_bool_vector(), protocols::antibody::design::backrub_protocol, cmd_line_operation_, core::scoring::dihedral_constraint, get_cdr_loops_with_overhang(), get_cdrs_movemap_with_overhang(), protocols::antibody::design::get_resnums_from_strings_with_ranges(), loops_operation_, min_scorefxn_, neighbor_dis_, restrict_design_operation_, core::pose::Pose::size(), tf_, tf_set_, and protocols::antibody::TR().

◆ cdr_overhang()

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().

◆ clone()

GeneralAntibodyModelerOP protocols::antibody::design::GeneralAntibodyModeler::clone ( ) const

◆ dock_high_res()

void protocols::antibody::design::GeneralAntibodyModeler::dock_high_res ( core::pose::Pose &  pose,
core::Size  first_cycle = 4,
core::Size  second_cycle = 45 
) const

References ab_dock_chains_, ab_info_, docking_scorefxn_high_, core::pose::Pose::fold_tree(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), scorefxn_, protocols::docking::setup_foldtree(), tf_, tf_set_, and protocols::antibody::TR().

◆ dock_low_res()

void protocols::antibody::design::GeneralAntibodyModeler::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.)

References ab_dock_chains_, ab_info_, protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), docking_scorefxn_low_, core::pose::Pose::fold_tree(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), repack_antigen_ab_interface(), protocols::docking::setup_foldtree(), and protocols::antibody::TR().

◆ extend_CDR()

void protocols::antibody::design::GeneralAntibodyModeler::extend_CDR ( core::pose::Pose &  pose,
CDRNameEnum  cdr 
) const

Randomizes the dihedrals of the CDR.

References ab_info_, protocols::loops::Loops::add_loop(), core::sequence::end, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), and protocols::loops::start.

◆ get_cdr_loop_with_overhang()

protocols::loops::Loop protocols::antibody::design::GeneralAntibodyModeler::get_cdr_loop_with_overhang ( core::pose::Pose const &  pose,
CDRNameEnum  cdr 
) const

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

Referenced by get_cdr_loops_with_overhang().

◆ get_cdr_loops()

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.

◆ get_cdr_loops_with_overhang()

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().

◆ get_cdrs_movemap_with_overhang()

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

References ab_info_, model_cdrs_, neighbor_dis_, overhangs_, protocols::loops::select_loop_residues(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::update_residue_neighbors().

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

◆ get_dock_chains()

std::string protocols::antibody::design::GeneralAntibodyModeler::get_dock_chains ( ) const

References ab_dock_chains_, ab_info_, and protocols::antibody::design::get_dock_chains_from_ab_dock_chains().

◆ get_movemap_from_task()

MoveMapOP protocols::antibody::design::GeneralAntibodyModeler::get_movemap_from_task ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP  task 
) const

References core::pose::Pose::size().

Referenced by minimize_interface(), and relax_interface().

◆ interface_detection_dis() [1/2]

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

References interface_dis_.

Referenced by read_command_line_options().

◆ interface_detection_dis() [2/2]

void protocols::antibody::design::GeneralAntibodyModeler::interface_detection_dis ( core::Real  interface_distance)

Set a value for interface detection across the class.

References interface_dis_.

◆ minimize_cdrs()

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

Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin).

References ab_dock_chains_, ab_info_, protocols::loops::add_cutpoint_variants(), protocols::minimization_packing::MinMover::apply(), core::scoring::cart_bonded, protocols::minimization_packing::MinMover::cartesian(), core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), get_cdr_loops_with_overhang(), get_cdrs_movemap_with_overhang(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), protocols::minimization_packing::MinMover::min_options(), min_scorefxn_, protocols::minimization_packing::MinMover::min_type(), core::scoring::pro_close, protocols::loops::remove_cutpoint_variants(), protocols::docking::setup_foldtree(), and protocols::antibody::TR().

◆ minimize_interface()

void protocols::antibody::design::GeneralAntibodyModeler::minimize_interface ( core::pose::Pose &  pose,
bool  min_interface_sc = true 
) const

References ab_dock_chains_, ab_info_, protocols::minimization_packing::MinMover::apply(), core::scoring::atom_pair_constraint, atom_pair_weight_, core::pose::Pose::fold_tree(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), get_movemap_from_task(), interface_tf_, scorefxn_, protocols::docking::setup_foldtree(), and protocols::antibody::TR().

◆ neighbor_detection_dis() [1/2]

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

References neighbor_dis_.

Referenced by read_command_line_options().

◆ neighbor_detection_dis() [2/2]

void protocols::antibody::design::GeneralAntibodyModeler::neighbor_detection_dis ( core::Real  neighbor_distance)

References neighbor_dis_.

◆ read_command_line_options()

void protocols::antibody::design::GeneralAntibodyModeler::read_command_line_options ( )
private

References atom_pair_weight_, interface_detection_dis(), and neighbor_detection_dis().

Referenced by GeneralAntibodyModeler().

◆ relax_cdrs()

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,
core::Size  repeats = 5 
) const

Relax CDRs using FastRelax. CentroidRelax unfortunately does not work well. Perhaps with centroid rotamers..

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

References ab_dock_chains_, ab_info_, protocols::loops::add_cutpoint_variants(), core::scoring::cart_bonded, core::scoring::chainbreak, cmd_line_operation_, protocols::antibody::design::dualspace, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), get_cdr_loops_with_overhang(), get_cdrs_movemap_with_overhang(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), loops_operation_, min_scorefxn_, neighbor_dis_, core::scoring::pro_close, core::scoring::constraints::remove_constraints_of_type(), protocols::loops::remove_cutpoint_variants(), restrict_design_operation_, protocols::docking::setup_foldtree(), tf_, tf_set_, and protocols::antibody::TR().

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

◆ relax_interface()

void protocols::antibody::design::GeneralAntibodyModeler::relax_interface ( core::pose::Pose &  pose,
bool  min_interface_sc = true 
) const

References ab_dock_chains_, ab_info_, core::pose::Pose::fold_tree(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), get_movemap_from_task(), interface_tf_, scorefxn_, protocols::docking::setup_foldtree(), tf_, and tf_set_.

◆ repack_antibody_interface()

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

Repack the interface between antibody and antigen, but only pack antibody.

References ab_info_, protocols::minimization_packing::PackRotamersMover::apply(), apply_A_LH_foldtree(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), interface_tf_, scorefxn_, and protocols::antibody::TR().

◆ repack_antigen_ab_interface()

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

Repack the interface between Antibody and Antigen.

References ab_info_, protocols::minimization_packing::PackRotamersMover::apply(), apply_A_LH_foldtree(), core::pose::Pose::fold_tree(), interface_tf_, scorefxn_, tf_, tf_set_, and protocols::antibody::TR().

Referenced by dock_low_res().

◆ repack_antigen_interface()

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

Repack the interface between antibody and antigen, but only pack antigen.

References ab_info_, protocols::minimization_packing::PackRotamersMover::apply(), apply_A_LH_foldtree(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), interface_tf_, scorefxn_, and protocols::antibody::TR().

◆ repack_cdrs()

void protocols::antibody::design::GeneralAntibodyModeler::repack_cdrs ( core::pose::Pose &  pose,
bool  include_neighbor_sc = true 
)

Repack the CDRs given. Nothing special.

References protocols::minimization_packing::PackRotamersMover::apply(), cmd_line_operation_, get_cdr_loops_with_overhang(), loops_operation_, neighbor_dis_, restrict_design_operation_, scorefxn_, tf_, tf_set_, and protocols::antibody::TR().

◆ reset_task_factory()

void protocols::antibody::design::GeneralAntibodyModeler::reset_task_factory ( )

References setup_task_operations().

◆ set_cdr()

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().

◆ set_cdr_only()

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().

◆ 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, protocols::antibody::cdr_start, and set_cdr().

Referenced by set_cdr_only().

◆ set_cdrs()

void protocols::antibody::design::GeneralAntibodyModeler::set_cdrs ( utility::vector1< bool >  cdrs)

References model_cdrs_.

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

◆ set_defaults()

void protocols::antibody::design::GeneralAntibodyModeler::set_defaults ( )
private

References protocols::antibody::CDRNameEnum_proto_total, protocols::antibody::h4, protocols::antibody::l4, model_cdrs_, and overhangs_.

Referenced by GeneralAntibodyModeler().

◆ set_dock_high_res_scorefunction()

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

References docking_scorefxn_high_.

◆ set_dock_low_res_scorefunction()

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

References docking_scorefxn_low_.

◆ set_overhang()

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_.

◆ set_scorefunction()

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

References scorefxn_.

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

◆ set_scorefunction_min()

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().

◆ set_task_factory()

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

References tf_, and tf_set_.

◆ setup_scorefxns()

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

References docking_scorefxn_high_, docking_scorefxn_low_, protocols::antibody::design::get_ab_design_dock_high_scorefxn(), protocols::antibody::design::get_ab_design_dock_low_scorefxn(), protocols::antibody::design::get_ab_design_global_scorefxn(), protocols::antibody::design::get_ab_design_min_scorefxn(), min_scorefxn_, and scorefxn_.

Referenced by GeneralAntibodyModeler().

◆ setup_task_operations()

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

References cmd_line_operation_, interface_dis_, interface_tf_, loops_operation_, restrict_design_operation_, tf_, and tf_set_.

Referenced by GeneralAntibodyModeler(), and reset_task_factory().

Member Data Documentation

◆ ab_dock_chains_

std::string protocols::antibody::design::GeneralAntibodyModeler::ab_dock_chains_
private

Referenced by ab_dock_chains(), dock_high_res(), dock_low_res(), get_dock_chains(), minimize_cdrs(), minimize_interface(), relax_cdrs(), and relax_interface().

◆ ab_info_

AntibodyInfoOP protocols::antibody::design::GeneralAntibodyModeler::ab_info_
private

Referenced by apply_A_LH_foldtree(), dock_high_res(), dock_low_res(), extend_CDR(), GeneralAntibodyModeler(), get_cdr_loop_with_overhang(), get_cdr_loops(), get_cdr_loops_with_overhang(), get_cdrs_movemap_with_overhang(), get_dock_chains(), minimize_cdrs(), minimize_interface(), relax_cdrs(), relax_interface(), repack_antibody_interface(), repack_antigen_ab_interface(), and repack_antigen_interface().

◆ atom_pair_weight_

core::Real protocols::antibody::design::GeneralAntibodyModeler::atom_pair_weight_
private

Referenced by minimize_interface(), and read_command_line_options().

◆ cmd_line_operation_

core::pack::task::operation::InitializeFromCommandlineOP protocols::antibody::design::GeneralAntibodyModeler::cmd_line_operation_
private

Referenced by backrub_cdrs(), GeneralAntibodyModeler(), relax_cdrs(), repack_cdrs(), and setup_task_operations().

◆ docking_scorefxn_high_

core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::docking_scorefxn_high_
private

Referenced by dock_high_res(), GeneralAntibodyModeler(), set_dock_high_res_scorefunction(), and setup_scorefxns().

◆ docking_scorefxn_low_

core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::docking_scorefxn_low_
private

Referenced by dock_low_res(), GeneralAntibodyModeler(), set_dock_low_res_scorefunction(), and setup_scorefxns().

◆ interface_dis_

core::Real protocols::antibody::design::GeneralAntibodyModeler::interface_dis_
private

Referenced by interface_detection_dis(), and setup_task_operations().

◆ interface_tf_

core::pack::task::TaskFactoryOP protocols::antibody::design::GeneralAntibodyModeler::interface_tf_
private

Referenced by GeneralAntibodyModeler(), minimize_interface(), relax_interface(), repack_antibody_interface(), repack_antigen_ab_interface(), repack_antigen_interface(), and setup_task_operations().

◆ loops_operation_

protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::GeneralAntibodyModeler::loops_operation_
private

Referenced by backrub_cdrs(), GeneralAntibodyModeler(), relax_cdrs(), repack_cdrs(), and setup_task_operations().

◆ min_scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::min_scorefxn_
private

Referenced by backrub_cdrs(), GeneralAntibodyModeler(), minimize_cdrs(), relax_cdrs(), set_scorefunction_min(), and setup_scorefxns().

◆ model_cdrs_

utility::vector1<bool> protocols::antibody::design::GeneralAntibodyModeler::model_cdrs_
private

Referenced by get_cdr_loops(), get_cdr_loops_with_overhang(), get_cdrs_movemap_with_overhang(), set_cdr(), set_cdrs(), and set_defaults().

◆ neighbor_dis_

core::Real protocols::antibody::design::GeneralAntibodyModeler::neighbor_dis_
private

Referenced by backrub_cdrs(), get_cdrs_movemap_with_overhang(), neighbor_detection_dis(), relax_cdrs(), and repack_cdrs().

◆ overhangs_

utility::vector1<core::Size> protocols::antibody::design::GeneralAntibodyModeler::overhangs_
private

Referenced by cdr_overhang(), get_cdr_loop_with_overhang(), get_cdrs_movemap_with_overhang(), set_defaults(), and set_overhang().

◆ restrict_design_operation_

core::pack::task::operation::RestrictToRepackingOP protocols::antibody::design::GeneralAntibodyModeler::restrict_design_operation_
private

Referenced by backrub_cdrs(), GeneralAntibodyModeler(), relax_cdrs(), repack_cdrs(), and setup_task_operations().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::design::GeneralAntibodyModeler::scorefxn_
private

Referenced by dock_high_res(), GeneralAntibodyModeler(), minimize_interface(), relax_interface(), repack_antibody_interface(), repack_antigen_ab_interface(), repack_antigen_interface(), repack_cdrs(), set_scorefunction(), and setup_scorefxns().

◆ tf_

core::pack::task::TaskFactoryOP protocols::antibody::design::GeneralAntibodyModeler::tf_
private

Referenced by backrub_cdrs(), dock_high_res(), GeneralAntibodyModeler(), relax_cdrs(), relax_interface(), repack_antigen_ab_interface(), repack_cdrs(), set_task_factory(), and setup_task_operations().

◆ tf_set_

bool protocols::antibody::design::GeneralAntibodyModeler::tf_set_
private

Referenced by backrub_cdrs(), dock_high_res(), relax_cdrs(), relax_interface(), repack_antigen_ab_interface(), repack_cdrs(), set_task_factory(), and setup_task_operations().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 08:14:18 for Rosetta by doxygen 1.9.1