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protocols::task_operations::RestrictConservedLowDdgOperation Class Reference

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:
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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::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)
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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 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

Constructor & Destructor Documentation

protocols::task_operations::RestrictConservedLowDdgOperation::RestrictConservedLowDdgOperation ( )
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
static std::string protocols::task_operations::RestrictConservedLowDdgOperation::keyname ( )
inlinestatic
void protocols::task_operations::RestrictConservedLowDdgOperation::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual
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
void protocols::task_operations::RestrictConservedLowDdgOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::chemical::AA protocols::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa ( core::Size  seqpos) const
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
std::map< core::Size, core::io::PositionDdGInfo::PositionDdGInfoOP > protocols::task_operations::RestrictConservedLowDdgOperation::position_ddGs_
private
bool protocols::task_operations::RestrictConservedLowDdgOperation::verbose_
private

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