protocols::toolbox::task_operations::SeqprofConsensusOperation Class Reference

#include <SeqprofConsensusOperation.hh>

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 Member Functions
	SeqprofConsensusOperation ()
	default constructor More...
	~SeqprofConsensusOperation ()
	destructor More...
virtual TaskOperationOP	clone () const
	make clone More...
void	parse_tag (TagCOP tag, DataMap &)
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::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

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	keep_native_
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_
core::Size	chain_num_
bool	debug_

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::TagCOP protocols::toolbox::task_operations::SeqprofConsensusOperation::TagCOP

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 utility::file::file_exists(), basic::options::option, basic::options::OptionKeys::in::file::pssm, seqprof(), seqprof_, seqprof_filename_, and user.

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, c, 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(), core::pose::Pose::constraint_set(), constraints, debug(), ignore_pose_profile_length_mismatch_, core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), keep_native_, min_aa_probability_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, basic::options::option, prob_larger_current_, profile, protein_interface_design(), protein_interface_design_, core::pack::task::TaskFactory::push_back(), core::pack::task::PackerTask::request_symmetrize_by_intersection(), 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(), runtime_assert, seqprof(), seqprof_, size(), core::pose::Pose::split_by_chain(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), protocols::toolbox::tr, basic::options::OptionKeys::out::file::use_occurrence_data, and utility_exit_with_message.

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().

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

inline

Referenced by apply(), and parse_tag().

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

inline

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

inline

Referenced by apply(), and parse_tag().

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

inline

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

inline

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

inline

Referenced by parse_tag().

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

inline

References protocols::match::upstream::b.

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

inline

Referenced by apply(), and parse_tag().

void protocols::toolbox::task_operations::SeqprofConsensusOperation::parse_tag	(	TagCOP	tag,
		DataMap &	datamap
	)

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_, runtime_assert, seqprof(), seqprof_, seqprof_filename_, protocols::toolbox::tr, and utility_exit_with_message.

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

ProteinInterfaceDesignOperationOP protocols::toolbox::task_operations::SeqprofConsensusOperation::protein_interface_design

(

)

const

References protein_interface_design_.

Referenced by apply().

void protocols::toolbox::task_operations::SeqprofConsensusOperation::protein_interface_design

(

ProteinInterfaceDesignOperationOP

pido

)

References protein_interface_design_.

RestrictToAlignedSegmentsOperationOP protocols::toolbox::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments

(

)

const

References restrict_to_aligned_segments_.

Referenced by apply().

void protocols::toolbox::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments

(

RestrictToAlignedSegmentsOperationOP

rtas

)

References restrict_to_aligned_segments_.

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

(

)

const

References seqprof_.

Referenced by apply(), 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::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_.

Member Data Documentation

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

private

Referenced by apply(), and parse_tag().

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

private

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

private

bool protocols::toolbox::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities_

private

bool protocols::toolbox::task_operations::SeqprofConsensusOperation::debug_

private

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().

bool protocols::toolbox::task_operations::SeqprofConsensusOperation::keep_native_

private

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().

ProteinInterfaceDesignOperationOP protocols::toolbox::task_operations::SeqprofConsensusOperation::protein_interface_design_

private

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

RestrictToAlignedSegmentsOperationOP protocols::toolbox::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments_

private

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

core::sequence::SequenceProfileOP 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().

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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