Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
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

Constructor & Destructor Documentation

protocols::toolbox::task_operations::SeqprofConsensusOperation::SeqprofConsensusOperation ( )
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
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
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 
)
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)
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)
core::sequence::SequenceProfileCOP protocols::toolbox::task_operations::SeqprofConsensusOperation::seqprof ( ) const
void protocols::toolbox::task_operations::SeqprofConsensusOperation::set_ignore_pose_profile_length_mismatch ( bool const  setting)
inline
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
RestrictToAlignedSegmentsOperationOP protocols::toolbox::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments_
private
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

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