#include <SeqprofConsensusOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::SeqprofConsensusOperation:

Collaboration diagram for protocols::toolbox::task_operations::SeqprofConsensusOperation:

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::TagPtr	TagPtr

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

typedef pose::Pose	Pose

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

	~SeqprofConsensusOperation ()
	destructor More...

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

void	parse_tag (TagPtr tag)
	Used to parse an xml-like tag to load parameters and properties. More...

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

core::sequence::SequenceProfileCOP	seqprof () const

void	set_ignore_pose_profile_length_mismatch (bool const setting)

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

Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

virtual void	parse_def (utility::lua::LuaObject const &def)

Private Attributes
std::string	seqprof_filename_

core::sequence::SequenceProfileCOP	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_

Member Typedef Documentation

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

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

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

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

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

typedef utility::tag::TagPtr protocols::toolbox::task_operations::SeqprofConsensusOperation::TagPtr

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

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

Constructor & Destructor Documentation

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

default constructor

References protocols::swa::rna::file_exists(), seqprof(), seqprof_, and seqprof_filename_.

Referenced by clone().

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

destructor

Member Function Documentation

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

virtual

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::toolbox::task_operations::RestrictConservedLowDdgOperation.

References core::chemical::ResidueType::aa(), core::chemical::aa_ala, core::pose::Pose::conformation(), ignore_pose_profile_length_mismatch_, core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), min_aa_probability_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, prob_larger_current_, core::pack::task::PackerTask::request_symmetrize_by_intersection(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), seqprof_, core::io::serialization::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::toolbox::tr().

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

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

virtual

make clone

clone

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

Reimplemented in protocols::toolbox::task_operations::RestrictConservedLowDdgOperation.

References SeqprofConsensusOperation().

void protocols::toolbox::task_operations::SeqprofConsensusOperation::parse_tag ( TagPtr tag)

virtual

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

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

Reimplemented in protocols::toolbox::task_operations::RestrictConservedLowDdgOperation.

References ignore_pose_profile_length_mismatch_, min_aa_probability_, prob_larger_current_, seqprof(), seqprof_, and seqprof_filename_.

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

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

References seqprof_.

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

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

inline

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

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

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

References seqprof(), and seqprof_.

Member Data Documentation

bool protocols::toolbox::task_operations::SeqprofConsensusOperation::ignore_pose_profile_length_mismatch_

private

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(), and parse_tag().

core::Real protocols::toolbox::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().

bool protocols::toolbox::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 apply(), and parse_tag().

core::sequence::SequenceProfileCOP protocols::toolbox::task_operations::SeqprofConsensusOperation::seqprof_

private

Stored as a per-position probability weighted value

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

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

private

Referenced by parse_tag(), and SeqprofConsensusOperation().

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

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

Public Types

Public Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation