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protocols::toolbox::task_operations::JointSequenceOperation Class Reference

#include <JointSequenceOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::JointSequenceOperation:
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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::TagPtr TagPtr
 
- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr TagPtr
 
typedef pose::Pose Pose
 

Public Member Functions

 JointSequenceOperation ()
 default constructor More...
 
 ~JointSequenceOperation ()
 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...
 
void parse_def (utility::lua::LuaObject const &def)
 
virtual void apply (Pose const &pose, PackerTask &task) const
 apply More...
 
void add_pdb (std::string filename)
 Add the sequence from the given filename to the set of allowed aas. More...
 
void add_pose (Pose const &pose)
 Add the sequence from the given pose to the set of allowed aas. More...
 
void add_native_pdb (std::string filename)
 Add the sequence from the given filename to the set of allowed aas and add the rotamers to the set of possible rotamers. More...
 
void add_native_pose (core::pose::PoseCOP posecop)
 Add the sequence from the given pose to the set of allowed aas and add the rotamers to the set of possible rotamers. More...
 
void use_current_pose (bool ucp)
 Should the current pose (pose supplied to apply) be used in addition to the other ones? More...
 
void use_natro (bool unr)
 Should the rotamers for the native poses be used? More...
 
void set_chain (core::Size chain)
 Return which chain to operate on with 0 meaning all. More...
 
void add_native_fasta (std::string fasta_file)
 Add the sequence from the given fasta filename to the set of allowed aas. More...
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual ~TaskOperation ()
 

Private Attributes

bool use_current_pose_
 
bool use_natro_
 
bool use_fasta_
 
core::pack::rotamer_set::UnboundRotamersOperationOP ubr_
 
std::vector
< core::sequence::SequenceOP
sequences_
 
core::Size chain_
 Which chain to operate on. More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::toolbox::task_operations::JointSequenceOperation::JointSequenceOperation ( )

default constructor

Referenced by clone().

protocols::toolbox::task_operations::JointSequenceOperation::~JointSequenceOperation ( )

destructor

Member Function Documentation

void protocols::toolbox::task_operations::JointSequenceOperation::add_native_fasta ( std::string  fasta_file)

Add the sequence from the given fasta filename to the set of allowed aas.

Read native as a FASTA file.

References sequences_.

Referenced by parse_def(), and parse_tag().

void protocols::toolbox::task_operations::JointSequenceOperation::add_native_pdb ( std::string  filename)

Add the sequence from the given filename to the set of allowed aas and add the rotamers to the set of possible rotamers.

Add the sequence from the given filename to the set of allowed aas and add the rotamers to the set of possible rotamers (if use_natro_ is set)

References add_native_pose(), and core::import_pose::pose_from_pdb().

Referenced by parse_def(), and parse_tag().

void protocols::toolbox::task_operations::JointSequenceOperation::add_native_pose ( core::pose::PoseCOP  posecop)

Add the sequence from the given pose to the set of allowed aas and add the rotamers to the set of possible rotamers.

References add_pose(), ubr_, and use_natro_.

Referenced by add_native_pdb(), parse_def(), and parse_tag().

void protocols::toolbox::task_operations::JointSequenceOperation::add_pdb ( std::string  filename)

Add the sequence from the given filename to the set of allowed aas.

References add_pose(), chain_, core::import_pose::pose_from_pdb(), core::pose::Pose::split_by_chain(), and protocols::TR().

Referenced by parse_def(), and parse_tag().

void protocols::toolbox::task_operations::JointSequenceOperation::add_pose ( Pose const &  pose)

Add the sequence from the given pose to the set of allowed aas.

References core::pose::Pose::pdb_info(), core::pose::Pose::sequence(), and sequences_.

Referenced by add_native_pose(), and add_pdb().

void protocols::toolbox::task_operations::JointSequenceOperation::apply ( Pose const &  pose,
PackerTask task 
) const
virtual
core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::JointSequenceOperation::clone ( ) const
virtual

make clone

clone

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

References JointSequenceOperation().

void protocols::toolbox::task_operations::JointSequenceOperation::parse_def ( utility::lua::LuaObject const &  def)
virtual
void protocols::toolbox::task_operations::JointSequenceOperation::parse_tag ( TagPtr  tag)
virtual
void protocols::toolbox::task_operations::JointSequenceOperation::set_chain ( core::Size  chain)

Return which chain to operate on with 0 meaning all.

which chain should be considered

References chain_.

void protocols::toolbox::task_operations::JointSequenceOperation::use_current_pose ( bool  ucp)

Should the current pose (pose supplied to apply) be used in addition to the other ones?

References use_current_pose_.

Referenced by parse_def(), and parse_tag().

void protocols::toolbox::task_operations::JointSequenceOperation::use_natro ( bool  unr)

Should the rotamers for the native poses be used?

References ubr_, and use_natro_.

Referenced by parse_def(), and parse_tag().

Member Data Documentation

core::Size protocols::toolbox::task_operations::JointSequenceOperation::chain_
private

Which chain to operate on.

Referenced by add_pdb(), apply(), parse_def(), parse_tag(), and set_chain().

std::vector<core::sequence::SequenceOP> protocols::toolbox::task_operations::JointSequenceOperation::sequences_
private

Referenced by add_native_fasta(), add_pose(), and apply().

core::pack::rotamer_set::UnboundRotamersOperationOP protocols::toolbox::task_operations::JointSequenceOperation::ubr_
private

Referenced by add_native_pose(), apply(), and use_natro().

bool protocols::toolbox::task_operations::JointSequenceOperation::use_current_pose_
private

Referenced by apply(), and use_current_pose().

bool protocols::toolbox::task_operations::JointSequenceOperation::use_fasta_
private
bool protocols::toolbox::task_operations::JointSequenceOperation::use_natro_
private

Referenced by add_native_pose(), apply(), and use_natro().


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