#include <JointSequenceOperation.hh>

Inheritance diagram for protocols::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::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
	JointSequenceOperation ()
	default constructor More...

	~JointSequenceOperation () 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...

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
	~TaskOperation () override

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

Private Attributes
bool	use_current_pose_

bool	use_natro_

core::pack::rotamer_set::UnboundRotamersOperationOP	ubr_

std::vector < core::sequence::SequenceOP >	sequences_

core::Size	chain_
	Which chain to operate on. More...

core::Size	use_chain_
	from which chain to extract the sequence information More...

Member Typedef Documentation

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

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

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

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

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

typedef utility::tag::TagCOP protocols::task_operations::JointSequenceOperation::TagCOP

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

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

Constructor & Destructor Documentation

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

default constructor

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

overridedefault

destructor

Member Function Documentation

void protocols::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_tag().

void protocols::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(), core::import_pose::PDB_file, and core::import_pose::pose_from_file().

Referenced by parse_tag().

void protocols::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(), and parse_tag().

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

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

References add_pose(), core::import_pose::PDB_file, and core::import_pose::pose_from_file().

Referenced by parse_tag().

void protocols::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(), sequences_, core::pose::Pose::split_by_chain(), protocols::task_operations::TR(), and use_chain_.

Referenced by add_native_pose(), and add_pdb().

void protocols::task_operations::JointSequenceOperation::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_

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

References protocols::cluster::calibur::aa, 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::ResidueTypeBase::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_, core::pose::Pose::size(), protocols::loops::start, core::pose::symmetry::symmetry_info(), protocols::task_operations::TR(), ubr_, use_current_pose_, and use_natro_.

TaskOperationOP protocols::task_operations::JointSequenceOperation::clone ( ) const

overridevirtual

make clone

clone

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

static std::string protocols::task_operations::JointSequenceOperation::keyname ( )

inlinestatic

Referenced by protocols::task_operations::JointSequenceOperationCreator::keyname(), and provide_xml_schema().

void protocols::task_operations::JointSequenceOperation::parse_tag	(	TagCOP	tag,
		DataMap &
	)

overridevirtual

Used to parse an xml-like tag to load parameters and properties.

Reimplemented from core::pack::task::operation::TaskOperation.

References add_native_fasta(), add_native_pdb(), add_native_pose(), add_pdb(), chain_, protocols::jd2::get_current_jobs_starting_pose(), core::sequence::read_fasta_file_str(), protocols::task_operations::TR(), use_chain_, use_current_pose(), and use_natro().

void protocols::task_operations::JointSequenceOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::task_operations::JointSequenceOperationCreator::provide_xml_schema().

void protocols::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::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_tag().

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

Should the rotamers for the native poses be used?

References ubr_, and use_natro_.

Referenced by parse_tag().

Member Data Documentation

core::Size protocols::task_operations::JointSequenceOperation::chain_

private

Which chain to operate on.

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

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

private

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

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

private

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

core::Size protocols::task_operations::JointSequenceOperation::use_chain_

private

from which chain to extract the sequence information

Referenced by add_pose(), and parse_tag().

bool protocols::task_operations::JointSequenceOperation::use_current_pose_

private

Referenced by apply(), and use_current_pose().

bool protocols::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:

src/protocols/task_operations/JointSequenceOperation.hh
src/protocols/task_operations/JointSequenceOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation