protocols::task_operations::ResidueProbDesignOperation Class Reference

A TaskOperation that allows amino acids at designable positions through a set of aa probabilities (aa profile). More...

#include <ResidueProbDesignOperation.hh>

Inheritance diagram for protocols::task_operations::ResidueProbDesignOperation:

Public Member Functions
	ResidueProbDesignOperation ()
	ResidueProbDesignOperation (ResidueProbDesignOperation const &src)
	~ResidueProbDesignOperation () override
void	apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
void	parse_tag (TagCOP tag, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. More...
void	set_aa_probability_set (PerResidueAAProbSet per_res_aa_probs)
	Sets the whole aa probability set. More...
void	set_aa_probabilities (core::Size const resnum, AAProbabilities aa_probs)
	Sets aa probabilities for a particular resnum. More...
void	set_aa_probabilities_from_file (const std::string &weights_file)
	Reads weights for each posenum and residue type. Format for each line in the file is: POSENUM RESIDUETYPE WEIGHT. With weight as a real between 0 and 1. More...
void	set_overall_aa_probabilities (AAProbabilities aa_probs)
	Set the probability for a particular aa @ a particular resnum. More...
void	set_no_probability (bool no_probability)
	Set to sample all available AAs per position instead of sampling based on weights Used to increase diversity and for testing purposes. More...
void	clear_prob_set ()
	Clears the probability matrix. More...
void	clear_overall_prob_set ()
	Clears the overall probabilities if any are set. More...
void	set_include_native_restype (bool include)
	Include current residuetype in packer in addition to selected mutation. Default is true. More...
bool	include_native_restype () const
void	set_sample_zero_probs_at (core::Real const probability)
	Sample any zero probabilities at this probability instead of not using them. More...
core::Real	sample_zero_probs_at () const
void	set_picking_rounds (core::Size picking_rounds)
	Max number of times to sample from the probability distribution. Default is once. More...
core::Size	picking_rounds () const
bool	resnum_exists_in_set (core::Size const resnum) const
core::pack::task::operation::TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...
void	set_defaults ()
Public Member Functions inherited from core::pack::task::operation::TaskOperation
	~TaskOperation () override
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
static std::string	keyname ()

Private Types
typedef std::map < core::chemical::AA, core::Real >	AAProbabilities
typedef std::map< core::Size, AAProbabilities >	PerResidueAAProbSet

Private Member Functions
void	init_for_equal_operator_and_copy_constructor (ResidueProbDesignOperation &lhs, ResidueProbDesignOperation const &rhs)
utility::vector1< core::Real >	get_weights (AAProbabilities &aa_prob_set) const
	Create full weight set for all amino acids from a probability set. More...
bool	aa_exists (core::chemical::AA amino_acid, AAProbabilities const &aa_prob_set) const

Private Attributes
PerResidueAAProbSet	prob_set_
AAProbabilities	overall_prob_set_
bool	include_native_restype_
core::Real	zero_probs_overwrite_
core::Size	picking_rounds_
bool	no_probability_ = false

Additional Inherited Members
Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP	TagCOP
typedef basic::datacache::DataMap	DataMap
typedef pose::Pose	Pose

Detailed Description

A TaskOperation that allows amino acids at designable positions through a set of aa probabilities (aa profile).

Each time a task is generated, it will choose one amino acid from the set for that position and add it to (or replace) the set of packable residues chosen for that position. Decreases number of rotamers for packing and the space for design. Instead of using energy for profiles, we use selection of residues through probabilities at each task generation. If picking rounds is higher can result in more than one additional residue in the task from the native.

Default is for the TaskOp to control the allowed amino acids only if the class has probabilities to use for that resnum. If no probabilities were set in general, it will not do anything. Probabilities should add to one, but if not, they will act as weights. Does NOT control which positions are set to design or repack, only what can be designed into.

If probabilities/weights for a particular residue are not present in the map, will not modify that residues task.

Member Typedef Documentation

typedef std::map< core::chemical::AA, core::Real > protocols::task_operations::ResidueProbDesignOperation::AAProbabilities

private

typedef std::map< core::Size, AAProbabilities > protocols::task_operations::ResidueProbDesignOperation::PerResidueAAProbSet

private

Constructor & Destructor Documentation

protocols::task_operations::ResidueProbDesignOperation::ResidueProbDesignOperation

(

)

References set_defaults().

protocols::task_operations::ResidueProbDesignOperation::ResidueProbDesignOperation

(

ResidueProbDesignOperation const &

src

)

References init_for_equal_operator_and_copy_constructor().

protocols::task_operations::ResidueProbDesignOperation::~ResidueProbDesignOperation ( )

overridedefault

Member Function Documentation

bool protocols::task_operations::ResidueProbDesignOperation::aa_exists ( core::chemical::AA  amino_acid, AAProbabilities const &  aa_prob_set  ) const

private

Referenced by get_weights().

void protocols::task_operations::ResidueProbDesignOperation::apply ( core::pose::Pose const &  , core::pack::task::PackerTask &    ) const

overridevirtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements core::pack::task::operation::TaskOperation.

References protocols::cluster::calibur::aa, core::pack::task::PackerTask::designing_residues(), core::chemical::first_l_aa, core::pack::task::ResidueLevelTask::get_original_residue(), get_weights(), include_native_restype_, no_probability_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, overall_prob_set_, picking_rounds_, prob_set_, resnum_exists_in_set(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::scoring::rg, core::pose::Pose::size(), core::pose::Pose::total_residue(), and protocols::task_operations::TR().

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply().

void protocols::task_operations::ResidueProbDesignOperation::clear_overall_prob_set

(

)

Clears the overall probabilities if any are set.

References overall_prob_set_.

void protocols::task_operations::ResidueProbDesignOperation::clear_prob_set

(

)

Clears the probability matrix.

References prob_set_.

core::pack::task::operation::TaskOperationOP protocols::task_operations::ResidueProbDesignOperation::clone ( ) const

overridevirtual

Create another task operation of the type matching the most-derived version of the class.

Implements core::pack::task::operation::TaskOperation.

vector1< Real > protocols::task_operations::ResidueProbDesignOperation::get_weights ( AAProbabilities &  aa_prob_set ) const

private

Create full weight set for all amino acids from a probability set.

References aa_exists(), and zero_probs_overwrite_.

Referenced by apply().

bool protocols::task_operations::ResidueProbDesignOperation::include_native_restype

(

)

const

References include_native_restype_.

void protocols::task_operations::ResidueProbDesignOperation::init_for_equal_operator_and_copy_constructor ( ResidueProbDesignOperation &  lhs, ResidueProbDesignOperation const &  rhs  )

private

References include_native_restype_, no_probability_, overall_prob_set_, picking_rounds_, prob_set_, and zero_probs_overwrite_.

Referenced by ResidueProbDesignOperation().

static std::string protocols::task_operations::ResidueProbDesignOperation::keyname ( )

inlinestatic

Referenced by protocols::task_operations::ResidueProbDesignOperationCreator::keyname(), and provide_xml_schema().

void protocols::task_operations::ResidueProbDesignOperation::parse_tag ( TagCOP  tag, DataMap &    )

overridevirtual

Used to parse an xml-like tag to load parameters and properties.

Reimplemented from core::pack::task::operation::TaskOperation.

References no_probability_, set_aa_probabilities_from_file(), set_include_native_restype(), set_no_probability(), set_picking_rounds(), and set_sample_zero_probs_at().

Size protocols::task_operations::ResidueProbDesignOperation::picking_rounds

(

)

const

References picking_rounds_.

Referenced by set_picking_rounds().

void protocols::task_operations::ResidueProbDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::task_operations::ResidueProbDesignOperationCreator::provide_xml_schema().

bool protocols::task_operations::ResidueProbDesignOperation::resnum_exists_in_set

(

core::Size const

resnum

)

const

References prob_set_.

Referenced by apply().

Real protocols::task_operations::ResidueProbDesignOperation::sample_zero_probs_at

(

)

const

References zero_probs_overwrite_.

void protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities	(	core::Size const	resnum,
		AAProbabilities	aa_probs
	)

Sets aa probabilities for a particular resnum.

References prob_set_.

void protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file

(

const std::string &

weights_file

)

Reads weights for each posenum and residue type. Format for each line in the file is: POSENUM RESIDUETYPE WEIGHT. With weight as a real between 0 and 1.

References protocols::cluster::calibur::aa, core::chemical::aa_from_one_or_three(), set_aa_probability_set(), protocols::sparta::split(), and protocols::task_operations::TR().

Referenced by parse_tag().

void protocols::task_operations::ResidueProbDesignOperation::set_aa_probability_set

(

PerResidueAAProbSet

per_res_aa_probs

)

Sets the whole aa probability set.

References prob_set_.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), and set_aa_probabilities_from_file().

void protocols::task_operations::ResidueProbDesignOperation::set_defaults

(

)

References set_include_native_restype(), set_picking_rounds(), and set_sample_zero_probs_at().

Referenced by ResidueProbDesignOperation().

void protocols::task_operations::ResidueProbDesignOperation::set_include_native_restype

(

bool

include

)

Include current residuetype in packer in addition to selected mutation. Default is true.

References include_native_restype_.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), parse_tag(), and set_defaults().

void protocols::task_operations::ResidueProbDesignOperation::set_no_probability

(

bool

no_probability

)

Set to sample all available AAs per position instead of sampling based on weights Used to increase diversity and for testing purposes.

References no_probability_.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), and parse_tag().

void protocols::task_operations::ResidueProbDesignOperation::set_overall_aa_probabilities

(

AAProbabilities

aa_probs

)

Set the probability for a particular aa @ a particular resnum.

Sets aa probabilities for all positions not given specifically. All designable residues will use these probabilities this if not specified through other functions.

References overall_prob_set_.

void protocols::task_operations::ResidueProbDesignOperation::set_picking_rounds

(

core::Size

picking_rounds

)

Max number of times to sample from the probability distribution. Default is once.

This is to increase variability. Too many rounds will even out the distribution. Can also run the PackRotamers mover or equivalent multiple times for sampling.

References picking_rounds(), and picking_rounds_.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), parse_tag(), and set_defaults().

void protocols::task_operations::ResidueProbDesignOperation::set_sample_zero_probs_at

(

core::Real const

probability

)

Sample any zero probabilities at this probability instead of not using them.

References protocols::simple_moves::bb_sampler::probability, and zero_probs_overwrite_.

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperation::apply(), parse_tag(), and set_defaults().

Member Data Documentation

bool protocols::task_operations::ResidueProbDesignOperation::include_native_restype_

private

Referenced by apply(), include_native_restype(), init_for_equal_operator_and_copy_constructor(), and set_include_native_restype().

bool protocols::task_operations::ResidueProbDesignOperation::no_probability_ = false

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), parse_tag(), and set_no_probability().

AAProbabilities protocols::task_operations::ResidueProbDesignOperation::overall_prob_set_

private

Referenced by apply(), clear_overall_prob_set(), init_for_equal_operator_and_copy_constructor(), and set_overall_aa_probabilities().

core::Size protocols::task_operations::ResidueProbDesignOperation::picking_rounds_

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), picking_rounds(), and set_picking_rounds().

PerResidueAAProbSet protocols::task_operations::ResidueProbDesignOperation::prob_set_

private

Referenced by apply(), clear_prob_set(), init_for_equal_operator_and_copy_constructor(), resnum_exists_in_set(), set_aa_probabilities(), and set_aa_probability_set().

core::Real protocols::task_operations::ResidueProbDesignOperation::zero_probs_overwrite_

private

Referenced by get_weights(), init_for_equal_operator_and_copy_constructor(), sample_zero_probs_at(), and set_sample_zero_probs_at().

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

• src/protocols/task_operations/ResidueProbDesignOperation.hh
• src/protocols/task_operations/ResidueProbDesignOperation.cc