#include <SeqprofConsensusOperation.hh>

Inheritance diagram for protocols::task_operations::SeqprofConsensusOperation:

[legend]

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef TaskOperation	parent

typedef utility::tag::TagCOP	TagCOP

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef pose::Pose	Pose

Public Member Functions
	SeqprofConsensusOperation ()
	default constructor More...

	~SeqprofConsensusOperation () override
	destructor More...

TaskOperationOP	clone () const override
	make clone More...

void	parse_tag (TagCOP tag, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. More...

void	apply (Pose const &pose, PackerTask &task) const override
	apply More...

core::sequence::SequenceProfileOP	parse_profile_from_pose (Pose const &pose) const

void	aa_probability_filter (Pose const &pose, utility::vector1< Real > const &pos_profile, core::Real const position_min_prob, core::Size const aa_idx, utility::vector1< bool > &keep_aas) const

core::sequence::SequenceProfileCOP	seqprof () const

void	set_ignore_pose_profile_length_mismatch (bool const setting)

void	set_seqprof (core::sequence::SequenceProfileOP seqprof, bool reweight=false)
	Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first. More...

void	convert_scores_to_probabilities (bool const c)

bool	convert_scores_to_probabilities () const

RestrictToAlignedSegmentsOperationOP	restrict_to_aligned_segments () const

void	restrict_to_aligned_segments (RestrictToAlignedSegmentsOperationOP rtas)

core::Real	conservation_cutoff_aligned_segments () const

void	conservation_cutoff_aligned_segments (core::Real const c)

ProteinInterfaceDesignOperationOP	protein_interface_design () const

void	protein_interface_design (ProteinInterfaceDesignOperationOP pido)

core::Real	conservation_cutoff_protein_interface_design () const

void	conservation_cutoff_protein_interface_design (core::Real const c)

void	debug (bool const b)

bool	debug () const

core::Size	chain_num () const

void	chain_num (core::Size const d)

bool	keep_native () const

void	keep_native (bool const b)

bool	use_occurrence_data () const

void	use_occurrence_data (bool const b)

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	aa_occurrence_filter (utility::vector1< Real > const &pos_occurance, core::Real const pos_min_occurance, utility::vector1< bool > &keep_aas)

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static utility::tag::XMLSchemaComplexTypeGeneratorOP	create_complex_type_generator (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

Private Attributes
std::string	seqprof_filename_

core::sequence::SequenceProfileOP	seqprof_

core::Real	min_aa_probability_
	mininum probability that an aa must have in the sequence profile to be considered More...

bool	prob_larger_current_
	whether probability of a given aa to be included needs to be higher than the probability of the aa in the input pose More...

bool	ignore_pose_profile_length_mismatch_

bool	convert_scores_to_probabilities_

RestrictToAlignedSegmentsOperationOP	restrict_to_aligned_segments_

core::Real	conservation_cutoff_aligned_segments_

ProteinInterfaceDesignOperationOP	protein_interface_design_

core::Real	conservation_cutoff_protein_interface_design_

bool	debug_

bool	keep_native_

core::Size	chain_num_

bool	restrict_to_repacking_

bool	use_occurrence_data_

Member Typedef Documentation

◆ PackerTask

typedef core::pack::task::PackerTask protocols::task_operations::SeqprofConsensusOperation::PackerTask

◆ parent

typedef TaskOperation protocols::task_operations::SeqprofConsensusOperation::parent

◆ Pose

typedef core::pose::Pose protocols::task_operations::SeqprofConsensusOperation::Pose

◆ Real

typedef core::Real protocols::task_operations::SeqprofConsensusOperation::Real

◆ String

typedef std::string protocols::task_operations::SeqprofConsensusOperation::String

◆ TagCOP

typedef utility::tag::TagCOP protocols::task_operations::SeqprofConsensusOperation::TagCOP

◆ TaskOperation

typedef core::pack::task::operation::TaskOperation protocols::task_operations::SeqprofConsensusOperation::TaskOperation

◆ TaskOperationOP

typedef core::pack::task::operation::TaskOperationOP protocols::task_operations::SeqprofConsensusOperation::TaskOperationOP

Constructor & Destructor Documentation

◆ SeqprofConsensusOperation()

protocols::task_operations::SeqprofConsensusOperation::SeqprofConsensusOperation ( )

default constructor

References seqprof(), seqprof_, seqprof_filename_, and use_occurrence_data_.

◆ ~SeqprofConsensusOperation()

protocols::task_operations::SeqprofConsensusOperation::~SeqprofConsensusOperation ( )

overridedefault

destructor

Member Function Documentation

◆ aa_occurrence_filter()

void protocols::task_operations::SeqprofConsensusOperation::aa_occurrence_filter	(	utility::vector1< Real > const &	pos_occurance,
		core::Real const	pos_min_occurance,
		utility::vector1< bool > &	keep_aas
	)

static

References protocols::cluster::calibur::aa, core::chemical::aa_ala, and core::chemical::num_canonical_aas.

Referenced by apply().

◆ aa_probability_filter()

void protocols::task_operations::SeqprofConsensusOperation::aa_probability_filter	(	Pose const &	pose,
		utility::vector1< Real > const &	pos_profile,
		core::Real const	position_min_prob,
		core::Size const	aa_idx,
		utility::vector1< bool > &	keep_aas
	)		const

References core::chemical::ResidueTypeBase::aa(), protocols::cluster::calibur::aa, core::chemical::aa_ala, keep_native_, core::chemical::num_canonical_aas, prob_larger_current_, and core::pose::Pose::residue_type().

Referenced by apply().

◆ apply()

void protocols::task_operations::SeqprofConsensusOperation::apply	(	Pose const &	pose,
		PackerTask &	task
	)		const

overridevirtual

apply

all AA that have a higher probability in the seqprofile than the native residue are allowed. probability also needs to be higher than min_aa_probability_

NOTE ON SYMMETRIC POSE BEHAVIOR: pssm files are usually for one chain only, therefore this task operation will only set the residue behavior for the first chain/asymetric unit. it could be possible to handle the symmetry setup here, i.e. set up the residue level task for every symmetric copy, but it's prolly better to let the symmetry machinery deal with that mode of packer task symmetrization should be intersection

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

Reimplemented in protocols::task_operations::RestrictConservedLowDdgOperation.

References core::chemical::ResidueTypeBase::aa(), protocols::cluster::calibur::aa, core::chemical::aa_ala, aa_occurrence_filter(), aa_probability_filter(), core::conformation::Residue::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chain_num_, core::pose::Pose::conformation(), conservation_cutoff_aligned_segments(), conservation_cutoff_protein_interface_design(), debug(), ignore_pose_profile_length_mismatch_, core::chemical::ResidueTypeBase::is_protein(), core::pose::symmetry::is_symmetric(), keep_native_, min_aa_probability_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, parse_profile_from_pose(), protein_interface_design(), protein_interface_design_, core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), restrict_to_aligned_segments(), restrict_to_aligned_segments_, core::pack::task::ResidueLevelTask::restrict_to_repacking(), restrict_to_repacking_, seqprof(), seqprof_, core::pose::Pose::size(), tr(), and use_occurrence_data_.

Referenced by protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task().

◆ chain_num() [1/2]

core::Size protocols::task_operations::SeqprofConsensusOperation::chain_num ( ) const

inline

References chain_num_.

◆ chain_num() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::chain_num ( core::Size const d )

inline

References chain_num_.

◆ clone()

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

overridevirtual

make clone

clone

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

Reimplemented in protocols::task_operations::RestrictConservedLowDdgOperation.

◆ conservation_cutoff_aligned_segments() [1/2]

core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments ( ) const

inline

References conservation_cutoff_aligned_segments_.

Referenced by apply(), and parse_tag().

◆ conservation_cutoff_aligned_segments() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments ( core::Real const c )

inline

References conservation_cutoff_aligned_segments_.

◆ conservation_cutoff_protein_interface_design() [1/2]

core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design ( ) const

inline

References conservation_cutoff_protein_interface_design_.

Referenced by apply(), and parse_tag().

◆ conservation_cutoff_protein_interface_design() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design ( core::Real const c )

inline

References conservation_cutoff_protein_interface_design_.

◆ convert_scores_to_probabilities() [1/2]

bool protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities ( ) const

inline

References convert_scores_to_probabilities_.

Referenced by parse_tag().

◆ convert_scores_to_probabilities() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities ( bool const c )

inline

References convert_scores_to_probabilities_.

◆ create_complex_type_generator()

XMLSchemaComplexTypeGeneratorOP protocols::task_operations::SeqprofConsensusOperation::create_complex_type_generator ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide the complete, but changable, XML Schema for the base class so that derived classes may ammend it (by changing the element name, and possibly adding attributes)

References core::pack::task::operation::complex_type_name_for_task_op(), protocols::task_operations::ProteinInterfaceDesignOperation::keyname(), protocols::task_operations::RestrictToAlignedSegmentsOperation::keyname(), keyname(), protocols::task_operations::ProteinInterfaceDesignOperation::provide_xml_schema(), and protocols::task_operations::RestrictToAlignedSegmentsOperation::provide_xml_schema().

Referenced by protocols::task_operations::RestrictConservedLowDdgOperation::create_complex_type_generator(), and provide_xml_schema().

◆ debug() [1/2]

bool protocols::task_operations::SeqprofConsensusOperation::debug ( ) const

inline

References debug_.

Referenced by apply(), and parse_tag().

◆ debug() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::debug ( bool const b )

inline

References protocols::match::upstream::b, and debug_.

◆ keep_native() [1/2]

bool protocols::task_operations::SeqprofConsensusOperation::keep_native ( ) const

inline

References keep_native_.

◆ keep_native() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::keep_native ( bool const b )

inline

References protocols::match::upstream::b, and keep_native_.

◆ keyname()

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

inlinestatic

Referenced by create_complex_type_generator(), and protocols::task_operations::SeqprofConsensusOperationCreator::keyname().

◆ parse_profile_from_pose()

core::sequence::SequenceProfileOP protocols::task_operations::SeqprofConsensusOperation::parse_profile_from_pose ( Pose const & pose ) const

References chain_num_, core::pose::Pose::constraint_set(), seqprof(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), tr(), and use_occurrence_data_.

Referenced by apply().

◆ parse_tag()

void protocols::task_operations::SeqprofConsensusOperation::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.

Reimplemented in protocols::task_operations::RestrictConservedLowDdgOperation.

References chain_num_, conservation_cutoff_aligned_segments(), conservation_cutoff_protein_interface_design(), convert_scores_to_probabilities(), debug(), ignore_pose_profile_length_mismatch_, keep_native_, min_aa_probability_, prob_larger_current_, protein_interface_design_, restrict_to_aligned_segments_, restrict_to_repacking_, seqprof(), seqprof_, seqprof_filename_, tr(), and use_occurrence_data_.

Referenced by protocols::task_operations::RestrictConservedLowDdgOperation::parse_tag().

◆ protein_interface_design() [1/2]

ProteinInterfaceDesignOperationOP protocols::task_operations::SeqprofConsensusOperation::protein_interface_design ( ) const

References protein_interface_design_.

Referenced by apply().

◆ protein_interface_design() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::protein_interface_design ( ProteinInterfaceDesignOperationOP pido )

References protein_interface_design_.

◆ provide_xml_schema()

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

static

References create_complex_type_generator().

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

◆ restrict_to_aligned_segments() [1/2]

RestrictToAlignedSegmentsOperationOP protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments ( ) const

References restrict_to_aligned_segments_.

Referenced by apply().

◆ restrict_to_aligned_segments() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments ( RestrictToAlignedSegmentsOperationOP rtas )

References restrict_to_aligned_segments_.

◆ seqprof()

core::sequence::SequenceProfileCOP protocols::task_operations::SeqprofConsensusOperation::seqprof ( ) const

References seqprof_.

Referenced by apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), parse_profile_from_pose(), parse_tag(), protocols::task_operations::RestrictConservedLowDdgOperation::position_untouchable(), protocols::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(), SeqprofConsensusOperation(), and set_seqprof().

◆ set_ignore_pose_profile_length_mismatch()

void protocols::task_operations::SeqprofConsensusOperation::set_ignore_pose_profile_length_mismatch ( bool const setting )

inline

References ignore_pose_profile_length_mismatch_.

Referenced by protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task().

◆ set_seqprof()

void protocols::task_operations::SeqprofConsensusOperation::set_seqprof	(	core::sequence::SequenceProfileOP	seqprof,
		bool	reweight = `false`
	)

Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first.

References seqprof(), and seqprof_.

◆ use_occurrence_data() [1/2]

bool protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data ( ) const

inline

References use_occurrence_data_.

◆ use_occurrence_data() [2/2]

void protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data ( bool const b )

inline

References protocols::match::upstream::b, and use_occurrence_data_.

Member Data Documentation

◆ chain_num_

core::Size protocols::task_operations::SeqprofConsensusOperation::chain_num_

private

Referenced by apply(), chain_num(), parse_profile_from_pose(), and parse_tag().

◆ conservation_cutoff_aligned_segments_

core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments_

private

Referenced by conservation_cutoff_aligned_segments().

◆ conservation_cutoff_protein_interface_design_

core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design_

private

Referenced by conservation_cutoff_protein_interface_design().

◆ convert_scores_to_probabilities_

bool protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities_

private

Referenced by convert_scores_to_probabilities().

◆ debug_

bool protocols::task_operations::SeqprofConsensusOperation::debug_

private

Referenced by debug().

◆ ignore_pose_profile_length_mismatch_

bool protocols::task_operations::SeqprofConsensusOperation::ignore_pose_profile_length_mismatch_

private

@default false. if true, every pose seqpos that is bigger than the size of the sequence_profile will be set to repacking allows using this taskop in situations where one wants to do consensus design on one chain of a protein/protein interface

Referenced by apply(), parse_tag(), and set_ignore_pose_profile_length_mismatch().

◆ keep_native_

bool protocols::task_operations::SeqprofConsensusOperation::keep_native_

private

Referenced by aa_probability_filter(), apply(), keep_native(), and parse_tag().

◆ min_aa_probability_

core::Real protocols::task_operations::SeqprofConsensusOperation::min_aa_probability_

private

mininum probability that an aa must have in the sequence profile to be considered

Referenced by apply(), and parse_tag().

◆ prob_larger_current_

bool protocols::task_operations::SeqprofConsensusOperation::prob_larger_current_

private

whether probability of a given aa to be included needs to be higher than the probability of the aa in the input pose

Referenced by aa_probability_filter(), and parse_tag().

◆ protein_interface_design_

ProteinInterfaceDesignOperationOP protocols::task_operations::SeqprofConsensusOperation::protein_interface_design_

private

Referenced by apply(), parse_tag(), and protein_interface_design().

◆ restrict_to_aligned_segments_

RestrictToAlignedSegmentsOperationOP protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments_

private

Referenced by apply(), parse_tag(), and restrict_to_aligned_segments().

◆ restrict_to_repacking_

bool protocols::task_operations::SeqprofConsensusOperation::restrict_to_repacking_

private

Referenced by apply(), and parse_tag().

◆ seqprof_

core::sequence::SequenceProfileOP protocols::task_operations::SeqprofConsensusOperation::seqprof_

private

Stored as a per-position probability weighted value

Referenced by apply(), parse_tag(), seqprof(), SeqprofConsensusOperation(), and set_seqprof().

◆ seqprof_filename_

std::string protocols::task_operations::SeqprofConsensusOperation::seqprof_filename_

private

Referenced by parse_tag(), and SeqprofConsensusOperation().

◆ use_occurrence_data_

bool protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data_

private

Referenced by apply(), parse_profile_from_pose(), parse_tag(), SeqprofConsensusOperation(), and use_occurrence_data().

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

src/protocols/task_operations/SeqprofConsensusOperation.hh
src/protocols/task_operations/SeqprofConsensusOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Member Typedef Documentation

◆ PackerTask

◆ parent

◆ Pose

◆ Real

◆ String

◆ TagCOP

◆ TaskOperation

◆ TaskOperationOP

Constructor & Destructor Documentation

◆ SeqprofConsensusOperation()

◆ ~SeqprofConsensusOperation()

Member Function Documentation

◆ aa_occurrence_filter()

◆ aa_probability_filter()

◆ apply()

◆ chain_num() [1/2]

◆ chain_num() [2/2]

◆ clone()

◆ conservation_cutoff_aligned_segments() [1/2]

◆ conservation_cutoff_aligned_segments() [2/2]

◆ conservation_cutoff_protein_interface_design() [1/2]

◆ conservation_cutoff_protein_interface_design() [2/2]

◆ convert_scores_to_probabilities() [1/2]

◆ convert_scores_to_probabilities() [2/2]

◆ create_complex_type_generator()

◆ debug() [1/2]

◆ debug() [2/2]

◆ keep_native() [1/2]

◆ keep_native() [2/2]

◆ keyname()

◆ parse_profile_from_pose()

◆ parse_tag()

◆ protein_interface_design() [1/2]

◆ protein_interface_design() [2/2]

◆ provide_xml_schema()

◆ restrict_to_aligned_segments() [1/2]

◆ restrict_to_aligned_segments() [2/2]

◆ seqprof()

◆ set_ignore_pose_profile_length_mismatch()

◆ set_seqprof()

◆ use_occurrence_data() [1/2]

◆ use_occurrence_data() [2/2]

Member Data Documentation

◆ chain_num_

◆ conservation_cutoff_aligned_segments_

◆ conservation_cutoff_protein_interface_design_

◆ convert_scores_to_probabilities_

◆ debug_

◆ ignore_pose_profile_length_mismatch_

◆ keep_native_

◆ min_aa_probability_

◆ prob_larger_current_

◆ protein_interface_design_

◆ restrict_to_aligned_segments_

◆ restrict_to_repacking_

◆ seqprof_

◆ seqprof_filename_

◆ use_occurrence_data_