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protocols::task_operations::SeqprofConsensusOperation Class Reference

#include <SeqprofConsensusOperation.hh>

Inheritance diagram for protocols::task_operations::SeqprofConsensusOperation:
Inheritance graph
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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 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

 SeqprofConsensusOperation ()
 default constructor More...
 
 ~SeqprofConsensusOperation () override
 destructor More...
 
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...
 
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 ()
 

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 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_
 
bool debug_
 
bool keep_native_
 
core::Size chain_num_
 
bool restrict_to_repacking_
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

default constructor

References seqprof(), seqprof_, and seqprof_filename_.

protocols::task_operations::SeqprofConsensusOperation::~SeqprofConsensusOperation ( )
overridedefault

destructor

Member Function Documentation

void protocols::task_operations::SeqprofConsensusOperation::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

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

Reimplemented in protocols::task_operations::RestrictConservedLowDdgOperation.

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::aa(), core::chemical::aa_ala, core::pack::dunbrack::c, 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(), debug(), ignore_pose_profile_length_mismatch_, core::chemical::ResidueTypeBase::is_protein(), core::pose::symmetry::is_symmetric(), keep_native_, min_aa_probability_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, prob_larger_current_, protein_interface_design(), protein_interface_design_, 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(), restrict_to_repacking_, seqprof(), seqprof_, core::pose::Pose::size(), core::pose::Pose::split_by_chain(), and tr().

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

core::Size protocols::task_operations::SeqprofConsensusOperation::chain_num ( ) const
inline

References chain_num_.

void protocols::task_operations::SeqprofConsensusOperation::chain_num ( core::Size const  d)
inline

References chain_num_.

core::pack::task::operation::TaskOperationOP protocols::task_operations::SeqprofConsensusOperation::clone ( ) const
overridevirtual
core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments ( ) const
inline
void protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments ( core::Real const  c)
inline
core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design ( ) const
inline
void protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design ( core::Real const  c)
inline
void protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities ( bool const  c)
inline
bool protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities ( ) const
inline

References convert_scores_to_probabilities_.

Referenced by parse_tag().

XMLSchemaComplexTypeGeneratorOP protocols::task_operations::SeqprofConsensusOperation::create_complex_type_generator ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::SeqprofConsensusOperation::debug ( bool const  b)
inline
bool protocols::task_operations::SeqprofConsensusOperation::debug ( ) const
inline

References debug_.

Referenced by apply(), and parse_tag().

bool protocols::task_operations::SeqprofConsensusOperation::keep_native ( ) const
inline

References keep_native_.

void protocols::task_operations::SeqprofConsensusOperation::keep_native ( bool const  b)
inline
static std::string protocols::task_operations::SeqprofConsensusOperation::keyname ( )
inlinestatic
void protocols::task_operations::SeqprofConsensusOperation::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual
ProteinInterfaceDesignOperationOP protocols::task_operations::SeqprofConsensusOperation::protein_interface_design ( ) const

References protein_interface_design_.

Referenced by apply().

void protocols::task_operations::SeqprofConsensusOperation::protein_interface_design ( ProteinInterfaceDesignOperationOP  pido)
void protocols::task_operations::SeqprofConsensusOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
RestrictToAlignedSegmentsOperationOP protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments ( ) const

References restrict_to_aligned_segments_.

Referenced by apply().

void protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments ( RestrictToAlignedSegmentsOperationOP  rtas)
core::sequence::SequenceProfileCOP protocols::task_operations::SeqprofConsensusOperation::seqprof ( ) const
void protocols::task_operations::SeqprofConsensusOperation::set_ignore_pose_profile_length_mismatch ( bool const  setting)
inline
void protocols::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::task_operations::SeqprofConsensusOperation::chain_num_
private

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

core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments_
private
core::Real protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design_
private
bool protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities_
private
bool protocols::task_operations::SeqprofConsensusOperation::debug_
private

Referenced by debug().

bool protocols::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(), parse_tag(), and set_ignore_pose_profile_length_mismatch().

bool protocols::task_operations::SeqprofConsensusOperation::keep_native_
private

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

core::Real protocols::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::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::task_operations::SeqprofConsensusOperation::protein_interface_design_
private
RestrictToAlignedSegmentsOperationOP protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments_
private
bool protocols::task_operations::SeqprofConsensusOperation::restrict_to_repacking_
private

Referenced by apply(), and parse_tag().

core::sequence::SequenceProfileOP protocols::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::task_operations::SeqprofConsensusOperation::seqprof_filename_
private

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