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::toolbox::task_operations::RestrictConservedLowDdgOperation:

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Collaboration diagram for protocols::toolbox::task_operations::RestrictConservedLowDdgOperation:

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Public Types
typedef SeqprofConsensusOperation	Parent

Public Types inherited from protocols::toolbox::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::TagPtr	TagPtr

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

typedef pose::Pose	Pose

Public Member Functions
	RestrictConservedLowDdgOperation ()

	~RestrictConservedLowDdgOperation ()

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...

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::toolbox::task_operations::SeqprofConsensusOperation
	SeqprofConsensusOperation ()
	default constructor More...

	~SeqprofConsensusOperation ()
	destructor 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	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.

Definition at line 114 of file SeqprofConsensusOperation.hh.

Member Typedef Documentation

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

Definition at line 117 of file SeqprofConsensusOperation.hh.

Constructor & Destructor Documentation

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

Definition at line 185 of file SeqprofConsensusOperation.cc.

References ddG_predictions_filename_, protocols::swa::rna::file_exists(), position_ddGs_, and core::io::PositionDdGInfo::read_ddg_predictions_file().

Referenced by clone().

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

Definition at line 198 of file SeqprofConsensusOperation.cc.

Member Function Documentation

void protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::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

Reimplemented from protocols::toolbox::task_operations::SeqprofConsensusOperation.

Definition at line 222 of file SeqprofConsensusOperation.cc.

References core::chemical::ResidueType::aa(), core::chemical::ResidueType::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::toolbox::task_operations::SeqprofConsensusOperation::seqprof(), seqprof_wt_aa(), and core::pose::Pose::total_residue().

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

virtual

make clone

clone

Reimplemented from protocols::toolbox::task_operations::SeqprofConsensusOperation.

Definition at line 202 of file SeqprofConsensusOperation.cc.

References RestrictConservedLowDdgOperation().

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

virtual

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

Reimplemented from protocols::toolbox::task_operations::SeqprofConsensusOperation.

Definition at line 208 of file SeqprofConsensusOperation.cc.

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

core::Real protocols::toolbox::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

Definition at line 297 of file SeqprofConsensusOperation.cc.

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

bool protocols::toolbox::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_

Definition at line 249 of file SeqprofConsensusOperation.cc.

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

Referenced by apply().

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

Definition at line 291 of file SeqprofConsensusOperation.cc.

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

Referenced by apply(), and position_ala_ddG().

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

inline

Definition at line 150 of file SeqprofConsensusOperation.hh.

Member Data Documentation

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

private

Definition at line 156 of file SeqprofConsensusOperation.hh.

Referenced by parse_tag(), and position_untouchable().

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

private

Definition at line 157 of file SeqprofConsensusOperation.hh.

Referenced by parse_tag(), and position_untouchable().

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

private

Definition at line 154 of file SeqprofConsensusOperation.hh.

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

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

private

Definition at line 155 of file SeqprofConsensusOperation.hh.

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

bool protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::verbose_

private

Definition at line 158 of file SeqprofConsensusOperation.hh.

Referenced by parse_tag(), and position_untouchable().

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation