#include <JointSequenceOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::JointSequenceOperation:

Collaboration diagram for protocols::toolbox::task_operations::JointSequenceOperation:

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...

Detailed Description

Definition at line 46 of file JointSequenceOperation.hh.

Member Typedef Documentation

typedef core::pack::task::PackerTask protocols::toolbox::task_operations::JointSequenceOperation::PackerTask

Definition at line 52 of file JointSequenceOperation.hh.

typedef TaskOperation protocols::toolbox::task_operations::JointSequenceOperation::parent

Definition at line 55 of file JointSequenceOperation.hh.

typedef core::pose::Pose protocols::toolbox::task_operations::JointSequenceOperation::Pose

Definition at line 51 of file JointSequenceOperation.hh.

typedef core::Real protocols::toolbox::task_operations::JointSequenceOperation::Real

Definition at line 50 of file JointSequenceOperation.hh.

typedef std::string protocols::toolbox::task_operations::JointSequenceOperation::String

Definition at line 49 of file JointSequenceOperation.hh.

typedef utility::tag::TagPtr protocols::toolbox::task_operations::JointSequenceOperation::TagPtr

Definition at line 56 of file JointSequenceOperation.hh.

typedef core::pack::task::operation::TaskOperation protocols::toolbox::task_operations::JointSequenceOperation::TaskOperation

Definition at line 53 of file JointSequenceOperation.hh.

typedef core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::JointSequenceOperation::TaskOperationOP

Definition at line 54 of file JointSequenceOperation.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 59 of file JointSequenceOperation.cc.

Referenced by clone().

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

destructor

Definition at line 70 of file JointSequenceOperation.cc.

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.

Definition at line 315 of file JointSequenceOperation.cc.

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)

Definition at line 272 of file JointSequenceOperation.cc.

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.

Definition at line 281 of file JointSequenceOperation.cc.

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.

Definition at line 241 of file JointSequenceOperation.cc.

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.

Definition at line 260 of file JointSequenceOperation.cc.

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

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_

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

Definition at line 82 of file JointSequenceOperation.cc.

References core::pose::Pose::aa(), core::chemical::aa_from_oneletter_code(), core::pack::task::PackerTask::append_rotamerset_operation(), chain_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::end, core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, core::chemical::oneletter_code_specifies_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), sequences_, protocols::loops::start, core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), protocols::TR(), ubr_, use_current_pose_, and use_natro_.