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protocols::antibody::design::AntibodySeqDesignTFCreator Class Reference

Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design. More...

#include <AntibodySeqDesignTFCreator.hh>

Inheritance diagram for protocols::antibody::design::AntibodySeqDesignTFCreator:
Inheritance graph
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Public Member Functions

 AntibodySeqDesignTFCreator (AntibodyInfoCOP ab_info, bool force_north_paper_db=false)
 Constructor with default set of options. You probably do not want this! More...
 
 AntibodySeqDesignTFCreator (AntibodyInfoCOP ab_info, utility::vector1< CDRSeqDesignOptionsOP > const design_options, bool force_north_paper_db=false, core::Size stem_size=2)
 Constructor with a CDRSeqDesignOptionsOP for each CDR. More...
 
AntibodySeqDesignTFCreatorOP clone () const
 
void set_cdr_design_options (CDRNameEnum cdr, CDRSeqDesignOptionsCOP design_options)
 Set design options for single CDR. More...
 
void set_cdr_design_options (utility::vector1< CDRSeqDesignOptionsOP > const design_options)
 Set design options for All CDRs. More...
 
utility::vector1
< CDRSeqDesignOptionsOP
get_cdr_design_options ()
 Get modifiable options. More...
 
CDRSeqDesignOptionsOP get_cdr_design_options (CDRNameEnum cdr)
 Get modifiable options. More...
 
void design_antigen (bool antigen_design)
 Normally, we do not want to design the antigen residues - but perhaps someday we will. If False, turn design off for the antigen for any TF creation. More...
 
void design_framework (bool framework_design)
 Design any framework residues included in the task. Default True. If False, turn design off for the framework for any TF creation. More...
 
core::pack::task::TaskFactoryOP generate_tf_seq_design (core::pose::Pose const &pose, bool disable_non_designing_cdrs=false)
 Create the FULL TaskFactory for antibody sequence design. There are no limits to repacking or design - AKA NO RestrictToLoops. Optionally disable framework residues for design Optionally disable antigen residues for design. Optionally disable framework conservative residues -> Combine with other Tasks for general design requirements. More...
 
core::pack::task::TaskFactoryOP generate_tf_seq_design_graft_design (core::pose::Pose const &pose, CDRNameEnum cdr, utility::vector1< bool >const &neighbor_cdr_min)
 Create the TaskFactory used for sequence design during the GraftDesign stage. This limits design to the passed CDR, optionally designing neighbor CDRs specified in options and included in min. More...
 
task_operations::AddCDRProfilesOperationOP generate_task_op_cdr_profiles (core::pose::Pose const &pose)
 Explicitly Generate a TF for framework-optimization only based design. This will only design neighboring framework residues of the grafted CDR. It will ignore the CDRs set to design in the SeqDesign options. More...
 
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP generate_task_op_cdr_design (core::pose::Pose const &pose, bool design_neighbors=true) const
 Create a TaskOp to limit Packing and Design to only CDR loops with design on. Use neighbor distance. More...
 
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP generate_task_op_cdr_design (core::pose::Pose const &pose, utility::vector1< bool > cdrs, bool design_neighbors=true) const
 Create a TaskOp for only CDR loops set to True in the boolean vector. More...
 
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP generate_task_op_all_cdr_design (core::pose::Pose const &pose, bool design_neighbors=true) const
 Create a TaskOp to limit Packing and Design to CDR loops and neighbors. More...
 
void disable_design_for_non_designing_cdrs (core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose)
 Some helper functions. More...
 
void disable_proline_design (core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) const
 
void disable_disallowed_aa (core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) const
 
void neighbor_detection_dis (core::Real const neighbor_distance)
 Create a TaskOp for profile-based design of CDRs according to SeqDesign options. More...
 
void design_proline (bool const setting)
 Keep proline fixed for design. If using profile design, this should not really come into play. More...
 
void set_design_framework_conservative (bool design_framework_conservative)
 Use the Conservative Design TaskOP if designing Framework residues. Default true. Recommended. More...
 
void set_design_framework_conserved_res (bool design_framework_conserved_res)
 Enable design of 100% conserved framework positions during TF generation. Default false. Will be expanded. More...
 
void set_zero_prob_weight_at (core::Real const weight)
 Use these weights during probabilistic design for data that is normally zero. More...
 
void set_probability_data_cutoff (core::Size const cutoff)
 Use conservative mutations (or alternative method) instead of using cluster sequence probabilities for design if the number of sequences in the particular CDR's cluster probability data is lower than this cutoff. Default is 10. This is why we try and stay in type 1 lengths during graft. More...
 
void set_design_H3_stem (bool design_H3_stem)
 Enable design of the first 2 and last 3 residues of the H3 loop. These are off by default as to help hinder the transition from extended to kinked and vice versa during sequence design. More...
 
void set_no_probability (bool no_probability)
 Set to sample all available AAs per position instead of sampling based on weights. More...
 

Private Member Functions

void setup_default_options ()
 
void read_command_line_options ()
 
protocols::loops::LoopsOP get_design_cdr_loops (core::pose::Pose const &pose, core::Size stem_size=0) const
 Get a LoopsOP for CDRs set to design. More...
 
protocols::loops::LoopsOP get_design_cdr_loops_with_stem (core::pose::Pose const &pose) const
 Explicitly get design cdr loops with stem. More...
 
protocols::task_operations::ConservativeDesignOperationOP get_framework_conservative_op (core::pose::Pose const &pose)
 
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP get_general_loop_task_op (protocols::loops::LoopsOP loops, bool design_neighbors=true) const
 
void add_extra_restrict_operations (core::pack::task::TaskFactoryOP tf, const core::pose::Pose &pose) const
 Add restrictions for non-CDR positions and residue types according to options. More...
 

Private Attributes

utility::pointer::DeepCopyOP
< AntibodyInfo const > 
ab_info_
 
utility::vector1
< utility::pointer::DeepCopyOP
< CDRSeqDesignOptions > > 
cdr_design_options_
 
core::Real zero_prob_weight_
 
core::Real neighbor_dis_
 
core::Size prob_cutoff_
 
core::Size profile_picking_rounds_
 
core::Size stem_size_
 
bool design_proline_
 
bool design_antigen_
 
bool design_framework_
 
bool design_framework_conservative_
 
bool design_framework_conserved_res_
 
bool design_h3_stem_
 
bool force_north_paper_db_
 
utility::vector1< boolno_data_cdrs_
 
bool use_outliers_
 
bool no_probability_ = false
 

Detailed Description

Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodySeqDesignTFCreator::AntibodySeqDesignTFCreator ( AntibodyInfoCOP  ab_info,
bool  force_north_paper_db = false 
)

Constructor with default set of options. You probably do not want this!

References read_command_line_options(), setup_default_options(), and stem_size_.

protocols::antibody::design::AntibodySeqDesignTFCreator::AntibodySeqDesignTFCreator ( AntibodyInfoCOP  ab_info,
utility::vector1< CDRSeqDesignOptionsOP > const  design_options,
bool  force_north_paper_db = false,
core::Size  stem_size = 2 
)

Constructor with a CDRSeqDesignOptionsOP for each CDR.

References cdr_design_options_, read_command_line_options(), and setup_default_options().

Member Function Documentation

void protocols::antibody::design::AntibodySeqDesignTFCreator::add_extra_restrict_operations ( core::pack::task::TaskFactoryOP  tf,
const core::pose::Pose pose 
) const
private
AntibodySeqDesignTFCreatorOP protocols::antibody::design::AntibodySeqDesignTFCreator::clone ( ) const
void protocols::antibody::design::AntibodySeqDesignTFCreator::design_antigen ( bool  antigen_design)

Normally, we do not want to design the antigen residues - but perhaps someday we will. If False, turn design off for the antigen for any TF creation.

References design_antigen_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework ( bool  framework_design)

Design any framework residues included in the task. Default True. If False, turn design off for the framework for any TF creation.

References design_framework_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::design_proline ( bool const  setting)

Keep proline fixed for design. If using profile design, this should not really come into play.

References design_proline_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::disable_design_for_non_designing_cdrs ( core::pack::task::TaskFactoryOP  tf,
const core::pose::Pose pose 
)

Some helper functions.

Turns off CDRs for design that are set to off.

References ab_info_, cdr_design_options_, and protocols::antibody::design::disable_design_cdr().

Referenced by generate_tf_seq_design().

void protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa ( core::pack::task::TaskFactoryOP  tf,
const core::pose::Pose pose 
) const
void protocols::antibody::design::AntibodySeqDesignTFCreator::disable_proline_design ( core::pack::task::TaskFactoryOP  tf,
const core::pose::Pose pose 
) const
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodySeqDesignTFCreator::generate_task_op_all_cdr_design ( core::pose::Pose const &  pose,
bool  design_neighbors = true 
) const

Create a TaskOp to limit Packing and Design to CDR loops and neighbors.

References ab_info_, get_general_loop_task_op(), and stem_size_.

protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodySeqDesignTFCreator::generate_task_op_cdr_design ( core::pose::Pose const &  pose,
bool  design_neighbors = true 
) const

Create a TaskOp to limit Packing and Design to only CDR loops with design on. Use neighbor distance.

References get_design_cdr_loops(), and get_general_loop_task_op().

Referenced by generate_tf_seq_design_graft_design().

protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodySeqDesignTFCreator::generate_task_op_cdr_design ( core::pose::Pose const &  pose,
utility::vector1< bool cdrs,
bool  design_neighbors = true 
) const

Create a TaskOp for only CDR loops set to True in the boolean vector.

References ab_info_, get_general_loop_task_op(), and stem_size_.

AddCDRProfilesOperationOP protocols::antibody::design::AntibodySeqDesignTFCreator::generate_task_op_cdr_profiles ( core::pose::Pose const &  pose)

Explicitly Generate a TF for framework-optimization only based design. This will only design neighboring framework residues of the grafted CDR. It will ignore the CDRs set to design in the SeqDesign options.

Setup the CDRProfilesOperation and conservative/basic design according to primary and fallback strategies and which CDRs are set to design. Pre-load the data

References ab_info_, cdr_design_options_, force_north_paper_db_, no_probability_, prob_cutoff_, profile_picking_rounds_, use_outliers_, and zero_prob_weight_.

Referenced by generate_tf_seq_design(), and generate_tf_seq_design_graft_design().

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodySeqDesignTFCreator::generate_tf_seq_design ( core::pose::Pose const &  pose,
bool  disable_non_designing_cdrs = false 
)

Create the FULL TaskFactory for antibody sequence design. There are no limits to repacking or design - AKA NO RestrictToLoops. Optionally disable framework residues for design Optionally disable antigen residues for design. Optionally disable framework conservative residues -> Combine with other Tasks for general design requirements.

References add_extra_restrict_operations(), design_framework_conservative_, disable_design_for_non_designing_cdrs(), generate_task_op_cdr_profiles(), and get_framework_conservative_op().

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodySeqDesignTFCreator::generate_tf_seq_design_graft_design ( core::pose::Pose const &  pose,
CDRNameEnum  cdr,
utility::vector1< bool >const &  neighbor_cdr_min 
)

Create the TaskFactory used for sequence design during the GraftDesign stage. This limits design to the passed CDR, optionally designing neighbor CDRs specified in options and included in min.

Basically will create a TF including CDRs you are minimizing and any neighbors. It will then use settings in your Options classes and class settings such as framework or antigen design to create the TF, disabling CDRs that are not allowed to design as well as framework or antigen regions.

Optionally design any neighbor framework residues Optionally design any neighbor antigen residues Optionally disable framework conservative residues

References ab_info_, add_extra_restrict_operations(), cdr_design_options_, protocols::antibody::CDRNameEnum_proto_total, design_framework_, design_framework_conservative_, protocols::antibody::design::disable_design_cdr(), generate_task_op_cdr_design(), generate_task_op_cdr_profiles(), and get_framework_conservative_op().

utility::vector1< CDRSeqDesignOptionsOP > protocols::antibody::design::AntibodySeqDesignTFCreator::get_cdr_design_options ( )

Get modifiable options.

References cdr_design_options_.

CDRSeqDesignOptionsOP protocols::antibody::design::AntibodySeqDesignTFCreator::get_cdr_design_options ( CDRNameEnum  cdr)

Get modifiable options.

References cdr_design_options_.

protocols::loops::LoopsOP protocols::antibody::design::AntibodySeqDesignTFCreator::get_design_cdr_loops ( core::pose::Pose const &  pose,
core::Size  stem_size = 0 
) const
private
protocols::loops::LoopsOP protocols::antibody::design::AntibodySeqDesignTFCreator::get_design_cdr_loops_with_stem ( core::pose::Pose const &  pose) const
private

Explicitly get design cdr loops with stem.

References get_design_cdr_loops(), and stem_size_.

ConservativeDesignOperationOP protocols::antibody::design::AntibodySeqDesignTFCreator::get_framework_conservative_op ( core::pose::Pose const &  pose)
private
protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodySeqDesignTFCreator::get_general_loop_task_op ( protocols::loops::LoopsOP  loops,
bool  design_neighbors = true 
) const
private
void protocols::antibody::design::AntibodySeqDesignTFCreator::neighbor_detection_dis ( core::Real const  neighbor_distance)

Create a TaskOp for profile-based design of CDRs according to SeqDesign options.

Create a TaskOp for conservative-based design of CDRs according to SeqDesign options. Repack neighbors of CDR's being designed within this distance.

References neighbor_dis_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodySeqDesignTFCreator::read_command_line_options ( )
private
void protocols::antibody::design::AntibodySeqDesignTFCreator::set_cdr_design_options ( CDRNameEnum  cdr,
CDRSeqDesignOptionsCOP  design_options 
)

Set design options for single CDR.

References ab_info_, and cdr_design_options_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_cdr_design_options ( utility::vector1< CDRSeqDesignOptionsOP > const  design_options)

Set design options for All CDRs.

References ab_info_, and cdr_design_options_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_design_framework_conservative ( bool  design_framework_conservative)

Use the Conservative Design TaskOP if designing Framework residues. Default true. Recommended.

References design_framework_conservative_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_design_framework_conserved_res ( bool  design_framework_conserved_res)

Enable design of 100% conserved framework positions during TF generation. Default false. Will be expanded.

References design_framework_conserved_res_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_design_H3_stem ( bool  design_H3_stem)

Enable design of the first 2 and last 3 residues of the H3 loop. These are off by default as to help hinder the transition from extended to kinked and vice versa during sequence design.

References design_h3_stem_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_no_probability ( bool  no_probability)

Set to sample all available AAs per position instead of sampling based on weights.

Set to sample all available AAs per position at a weight of 1.0 instead of sampling based on weights.

References no_probability_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_probability_data_cutoff ( core::Size const  cutoff)

Use conservative mutations (or alternative method) instead of using cluster sequence probabilities for design if the number of sequences in the particular CDR's cluster probability data is lower than this cutoff. Default is 10. This is why we try and stay in type 1 lengths during graft.

References prob_cutoff_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodySeqDesignTFCreator::set_zero_prob_weight_at ( core::Real const  weight)

Use these weights during probabilistic design for data that is normally zero.

References zero_prob_weight_.

void protocols::antibody::design::AntibodySeqDesignTFCreator::setup_default_options ( )
private

Member Data Documentation

utility::pointer::DeepCopyOP< AntibodyInfo const > protocols::antibody::design::AntibodySeqDesignTFCreator::ab_info_
private
utility::vector1< utility::pointer::DeepCopyOP< CDRSeqDesignOptions > > protocols::antibody::design::AntibodySeqDesignTFCreator::cdr_design_options_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_antigen_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework_conservative_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework_conserved_res_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_h3_stem_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_proline_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::force_north_paper_db_
private
core::Real protocols::antibody::design::AntibodySeqDesignTFCreator::neighbor_dis_
private
utility::vector1<bool> protocols::antibody::design::AntibodySeqDesignTFCreator::no_data_cdrs_
private

Referenced by setup_default_options().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::no_probability_ = false
private
core::Size protocols::antibody::design::AntibodySeqDesignTFCreator::prob_cutoff_
private
core::Size protocols::antibody::design::AntibodySeqDesignTFCreator::profile_picking_rounds_
private
core::Size protocols::antibody::design::AntibodySeqDesignTFCreator::stem_size_
private
bool protocols::antibody::design::AntibodySeqDesignTFCreator::use_outliers_
private
core::Real protocols::antibody::design::AntibodySeqDesignTFCreator::zero_prob_weight_
private

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