Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Private Attributes | List of all members
protocols::toolbox::task_operations::SeqprofConsensusOperation Class Reference

#include <SeqprofConsensusOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::SeqprofConsensusOperation:
Inheritance graph
[legend]
Collaboration diagram for protocols::toolbox::task_operations::SeqprofConsensusOperation:
Collaboration graph
[legend]

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

Public Member Functions

 SeqprofConsensusOperation ()
 default constructor More...
 
 ~SeqprofConsensusOperation ()
 destructor More...
 
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...
 
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 seqprof_filename_
 
core::sequence::SequenceProfileCOP 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_
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

default constructor

References protocols::swa::rna::file_exists(), seqprof(), seqprof_, and seqprof_filename_.

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, core::pose::Pose::conformation(), ignore_pose_profile_length_mismatch_, core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), min_aa_probability_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, prob_larger_current_, core::pack::task::PackerTask::request_symmetrize_by_intersection(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), seqprof_, core::io::serialization::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::toolbox::tr().

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

core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::SeqprofConsensusOperation::clone ( ) const
virtual
void protocols::toolbox::task_operations::SeqprofConsensusOperation::parse_tag ( TagPtr  tag)
virtual
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::SequenceProfileCOP  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

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().

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().

core::sequence::SequenceProfileCOP 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: