a Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking. More...

#include <SeqprofConsensusOperation.hh>

Inheritance diagram for protocols::task_operations::RestrictConservedLowDdgOperation:

[legend]

Public Types
typedef SeqprofConsensusOperation	Parent

Public Types inherited from protocols::task_operations::SeqprofConsensusOperation
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
	RestrictConservedLowDdgOperation ()

	~RestrictConservedLowDdgOperation () override

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...

bool	position_untouchable (core::Size seqpos, core::chemical::AA seqprof_wt) const
	returns true if seqpos has a sequence profile frequency > conservation_cutoff_ and an X->A ddG of > ddG_cutoff_ More...

core::chemical::AA	seqprof_wt_aa (core::Size seqpos) const

core::Real	position_ala_ddG (core::Size seqpos) const
	convenience function to query what the ddG is for a to ala mutation at a certain position More...

bool	verbose () const

Public Member Functions inherited from protocols::task_operations::SeqprofConsensusOperation
	SeqprofConsensusOperation ()
	default constructor More...

	~SeqprofConsensusOperation () override
	destructor 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	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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

static std::string	keyname ()

Static Public Member Functions inherited from protocols::task_operations::SeqprofConsensusOperation
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	ddG_predictions_filename_

std::map< core::Size, core::io::PositionDdGInfo::PositionDdGInfoOP >	position_ddGs_

core::Real	conservation_cutoff_

core::Real	ddG_cutoff_

bool	verbose_

Detailed Description

a Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking.

wt ala positions are set to repacking based on seqprof criterion only. If the input pose contains a forbidden (i.e. non wildtype ) residue at an untouchable position, the residue currently in the pose is also allowed.

Member Typedef Documentation

typedef SeqprofConsensusOperation protocols::task_operations::RestrictConservedLowDdgOperation::Parent

Constructor & Destructor Documentation

protocols::task_operations::RestrictConservedLowDdgOperation::RestrictConservedLowDdgOperation ( )

References ddG_predictions_filename_, position_ddGs_, and core::io::PositionDdGInfo::read_ddg_predictions_file().

protocols::task_operations::RestrictConservedLowDdgOperation::~RestrictConservedLowDdgOperation ( )

overridedefault

Member Function Documentation

void protocols::task_operations::RestrictConservedLowDdgOperation::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

Reimplemented from protocols::task_operations::SeqprofConsensusOperation.

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueTypeBase::is_protein(), core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, position_ddGs_, position_untouchable(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), protocols::task_operations::SeqprofConsensusOperation::seqprof(), seqprof_wt_aa(), and core::pose::Pose::size().

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

overridevirtual

make clone

clone

Reimplemented from protocols::task_operations::SeqprofConsensusOperation.

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

static

References protocols::task_operations::SeqprofConsensusOperation::create_complex_type_generator(), and keyname().

Referenced by protocols::calc_taskop_filters::ConservedPosMutationFilter::provide_xml_schema(), and provide_xml_schema().

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

inlinestatic

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

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

overridevirtual

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

Reimplemented from protocols::task_operations::SeqprofConsensusOperation.

References conservation_cutoff_, ddG_cutoff_, ddG_predictions_filename_, protocols::task_operations::SeqprofConsensusOperation::parse_tag(), position_ddGs_, core::io::PositionDdGInfo::read_ddg_predictions_file(), and verbose_.

core::Real protocols::task_operations::RestrictConservedLowDdgOperation::position_ala_ddG ( core::Size seqpos ) const

convenience function to query what the ddG is for a to ala mutation at a certain position

References core::chemical::aa_ala, ddG_predictions_filename_, core::io::PositionDdGInfo::PositionDdGInfo::mutation_ddGs(), position_ddGs_, seqprof_wt_aa(), and core::id::to_string().

bool protocols::task_operations::RestrictConservedLowDdgOperation::position_untouchable	(	core::Size	seqpos,
		core::chemical::AA	seqprof_wt
	)		const

returns true if seqpos has a sequence profile frequency > conservation_cutoff_ and an X->A ddG of > ddG_cutoff_

References core::chemical::aa_ala, conservation_cutoff_, ddG_cutoff_, ddG_predictions_filename_, core::io::PositionDdGInfo::PositionDdGInfo::mutation_ddGs(), position_ddGs_, protocols::task_operations::SeqprofConsensusOperation::seqprof(), core::id::to_string(), tr(), verbose_, and core::io::PositionDdGInfo::PositionDdGInfo::wt_aa().

Referenced by apply().

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

static

References create_complex_type_generator().

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

core::chemical::AA protocols::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa ( core::Size seqpos ) const

References core::chemical::aa_from_oneletter_code(), and protocols::task_operations::SeqprofConsensusOperation::seqprof().

Referenced by apply(), and position_ala_ddG().

bool protocols::task_operations::RestrictConservedLowDdgOperation::verbose ( ) const

inline

References verbose_.

Member Data Documentation

core::Real protocols::task_operations::RestrictConservedLowDdgOperation::conservation_cutoff_

private

Referenced by parse_tag(), and position_untouchable().

core::Real protocols::task_operations::RestrictConservedLowDdgOperation::ddG_cutoff_

private

Referenced by parse_tag(), and position_untouchable().

std::string protocols::task_operations::RestrictConservedLowDdgOperation::ddG_predictions_filename_

private

Referenced by parse_tag(), position_ala_ddG(), position_untouchable(), and RestrictConservedLowDdgOperation().

std::map< core::Size, core::io::PositionDdGInfo::PositionDdGInfoOP > protocols::task_operations::RestrictConservedLowDdgOperation::position_ddGs_

private

Referenced by apply(), parse_tag(), position_ala_ddG(), position_untouchable(), and RestrictConservedLowDdgOperation().

bool protocols::task_operations::RestrictConservedLowDdgOperation::verbose_

private

Referenced by parse_tag(), position_untouchable(), and verbose().

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation