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:

[legend]

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< bool >	no_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

Add restrictions for non-CDR positions and residue types according to options.

References ab_info_, protocols::antibody::antigen_region, design_antigen_, design_framework_, design_framework_conserved_res_, design_h3_stem_, design_proline_, protocols::antibody::design::disable_conserved_framework_positions(), protocols::antibody::design::disable_design_region(), disable_disallowed_aa(), protocols::antibody::design::disable_h3_stem_positions(), disable_proline_design(), and protocols::antibody::framework_region.

Referenced by generate_tf_seq_design(), and generate_tf_seq_design_graft_design().

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

References core::chemical::aa_from_one_or_three(), ab_info_, cdr_design_options_, core::chemical::name_from_aa(), and protocols::antibody::TR().

Referenced by add_extra_restrict_operations().

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

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by add_extra_restrict_operations().

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

Get a LoopsOP for CDRs set to design.

References ab_info_, cdr_design_options_, protocols::antibody::CDRNameEnum_proto_total, protocols::antibody::get_cdr_loops(), and protocols::antibody::TR().

Referenced by generate_task_op_cdr_design(), and get_design_cdr_loops_with_stem().

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

References ab_info_, protocols::antibody::framework_region, protocols::antibody::design::get_native_sequence(), protocols::antibody::design::has_native_sequence(), core::pose::Pose::size(), and protocols::antibody::TR().

Referenced by generate_tf_seq_design(), and generate_tf_seq_design_graft_design().

protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodySeqDesignTFCreator::get_general_loop_task_op	(	protocols::loops::LoopsOP	loops,
		bool	design_neighbors = `true`
	)		const

private

References neighbor_dis_.

Referenced by generate_task_op_all_cdr_design(), and generate_task_op_cdr_design().

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

References design_antigen_, design_framework_, design_framework_conservative_, design_framework_conserved_res_, design_h3_stem_, neighbor_detection_dis(), no_probability_, profile_picking_rounds_, set_probability_data_cutoff(), use_outliers_, and zero_prob_weight_.

Referenced by AntibodySeqDesignTFCreator().

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

References ab_info_, cdr_design_options_, design_antigen_, design_framework_, design_proline_, and no_data_cdrs_.

Referenced by AntibodySeqDesignTFCreator().

Member Data Documentation

utility::pointer::DeepCopyOP< AntibodyInfo const > protocols::antibody::design::AntibodySeqDesignTFCreator::ab_info_

private

Referenced by add_extra_restrict_operations(), disable_design_for_non_designing_cdrs(), disable_disallowed_aa(), generate_task_op_all_cdr_design(), generate_task_op_cdr_design(), generate_task_op_cdr_profiles(), generate_tf_seq_design_graft_design(), get_design_cdr_loops(), get_framework_conservative_op(), set_cdr_design_options(), and setup_default_options().

utility::vector1< utility::pointer::DeepCopyOP< CDRSeqDesignOptions > > protocols::antibody::design::AntibodySeqDesignTFCreator::cdr_design_options_

private

Referenced by AntibodySeqDesignTFCreator(), disable_design_for_non_designing_cdrs(), disable_disallowed_aa(), generate_task_op_cdr_profiles(), generate_tf_seq_design_graft_design(), get_cdr_design_options(), get_design_cdr_loops(), set_cdr_design_options(), and setup_default_options().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_antigen_

private

Referenced by add_extra_restrict_operations(), design_antigen(), read_command_line_options(), and setup_default_options().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework_

private

Referenced by add_extra_restrict_operations(), design_framework(), generate_tf_seq_design_graft_design(), read_command_line_options(), and setup_default_options().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework_conservative_

private

Referenced by generate_tf_seq_design(), generate_tf_seq_design_graft_design(), read_command_line_options(), and set_design_framework_conservative().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_framework_conserved_res_

private

Referenced by add_extra_restrict_operations(), read_command_line_options(), and set_design_framework_conserved_res().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_h3_stem_

private

Referenced by add_extra_restrict_operations(), read_command_line_options(), and set_design_H3_stem().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::design_proline_

private

Referenced by add_extra_restrict_operations(), design_proline(), and setup_default_options().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::force_north_paper_db_

private

Referenced by generate_task_op_cdr_profiles().

core::Real protocols::antibody::design::AntibodySeqDesignTFCreator::neighbor_dis_

private

Referenced by get_general_loop_task_op(), and neighbor_detection_dis().

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

Referenced by generate_task_op_cdr_profiles(), read_command_line_options(), and set_no_probability().

core::Size protocols::antibody::design::AntibodySeqDesignTFCreator::prob_cutoff_

private

Referenced by generate_task_op_cdr_profiles(), and set_probability_data_cutoff().

core::Size protocols::antibody::design::AntibodySeqDesignTFCreator::profile_picking_rounds_

private

Referenced by generate_task_op_cdr_profiles(), and read_command_line_options().

core::Size protocols::antibody::design::AntibodySeqDesignTFCreator::stem_size_

private

Referenced by AntibodySeqDesignTFCreator(), generate_task_op_all_cdr_design(), generate_task_op_cdr_design(), and get_design_cdr_loops_with_stem().

bool protocols::antibody::design::AntibodySeqDesignTFCreator::use_outliers_

private

Referenced by generate_task_op_cdr_profiles(), and read_command_line_options().

core::Real protocols::antibody::design::AntibodySeqDesignTFCreator::zero_prob_weight_

private

Referenced by generate_task_op_cdr_profiles(), read_command_line_options(), and set_zero_prob_weight_at().

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

src/protocols/antibody/design/AntibodySeqDesignTFCreator.hh
src/protocols/antibody/design/AntibodySeqDesignTFCreator.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation