#include <SilentFileFullModelInputter.hh>

Inheritance diagram for protocols::jd3::full_model_inputters::SilentFileFullModelInputter:

Public Member Functions
	SilentFileFullModelInputter ()

	~SilentFileFullModelInputter () override

bool	job_available_on_command_line () const override

FullModelInputSources	full_model_input_sources_from_command_line () override
	Constructs a list of FullModelInputSource objects reading from the -s or -l command line flags. This stores the names of the PDBs that are to be read in, and it initializes the input tags based on the pdb names, stripping the path and the extension from the file name. More...

FullModelInputSources	full_model_input_sources_from_tag (utility::options::OptionCollection const &opts, utility::tag::TagCOP tag) override
	Construct a list of FullModelInputSource objects from a Tag object that will be used by the JobQueen to construct a list of LarvalJobs. More...

core::pose::PoseOP	full_model_from_input_source (FullModelInputSource const &input_source, utility::options::OptionCollection const &options, utility::tag::TagCOP tag) override
	this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb More...

core::io::silent::SilentFileData const &	silent_file_data () const
	this function returns the SilentStruct that belongs to the given job More...

Public Member Functions inherited from protocols::jd3::full_model_inputters::FullModelInputter
	FullModelInputter ()

	~FullModelInputter () override

Static Public Member Functions
static std::string	keyname ()
	returns the name for the element that will be used in a job-definition file for a structure originating from a silent file: "Silent" More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	returns the schema for the PDB element used in a job-definition file including all options that govern how a silent struct is loaded. More...

static void	list_options_read (utility::options::OptionKeyList &read_options)

Private Member Functions
void	initialize_sfd_from_options_and_tag (utility::options::OptionCollection const &options, utility::tag::TagCOP tag)

void	initialize_sfd_from_files_and_tags (utility::vector1< utility::file::FileName > const &silent_files, utility::vector1< std::string > const &tags)

Private Attributes
core::io::silent::SilentFileOptionsOP	sf_opts_

core::io::silent::SilentFileDataOP	sfd_

Constructor & Destructor Documentation

protocols::jd3::full_model_inputters::SilentFileFullModelInputter::SilentFileFullModelInputter ( )

References tr().

protocols::jd3::full_model_inputters::SilentFileFullModelInputter::~SilentFileFullModelInputter ( )

overridedefault

Member Function Documentation

core::pose::PoseOP protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source	(	FullModelInputSource const &	input_source,
		utility::options::OptionCollection const &	options,
		utility::tag::TagCOP	tag
	)

overridevirtual

this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb

This function will first see if the pose already exists in the Job. If not, it will read it into the pose reference, and hand a COP cloned from that pose to the Job. If the pose pre-exists it just copies the COP's pose into it.

Implements protocols::jd3::full_model_inputters::FullModelInputter.

References core::io::silent::SilentFileData::begin(), core::chemical::FA_STANDARD, protocols::abinitio::filename(), core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses(), initialize_sfd_from_options_and_tag(), core::io::silent::SilentFileData::read_file(), sfd_, silent_file_data(), and protocols::jd3::full_model_inputters::FullModelInputSource::string_string_map().

FullModelInputSources protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_input_sources_from_command_line ( )

overridevirtual

Constructs a list of FullModelInputSource objects reading from the -s or -l command line flags. This stores the names of the PDBs that are to be read in, and it initializes the input tags based on the pdb names, stripping the path and the extension from the file name.

Implements protocols::jd3::full_model_inputters::FullModelInputter.

References initialize_sfd_from_options_and_tag(), keyname(), sfd_, and tr().

FullModelInputSources protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_input_sources_from_tag	(	utility::options::OptionCollection const &	opts,
		utility::tag::TagCOP
	)

overridevirtual

Construct a list of FullModelInputSource objects from a Tag object that will be used by the JobQueen to construct a list of LarvalJobs.

Implements protocols::jd3::full_model_inputters::FullModelInputter.

References initialize_sfd_from_options_and_tag(), keyname(), and sfd_.

void protocols::jd3::full_model_inputters::SilentFileFullModelInputter::initialize_sfd_from_files_and_tags	(	utility::vector1< utility::file::FileName > const &	silent_files,
		utility::vector1< std::string > const &	tags
	)

private

References sfd_, and tr().

Referenced by initialize_sfd_from_options_and_tag().

void protocols::jd3::full_model_inputters::SilentFileFullModelInputter::initialize_sfd_from_options_and_tag	(	utility::options::OptionCollection const &	options,
		utility::tag::TagCOP	tag
	)

private

References protocols::abinitio::filename(), initialize_sfd_from_files_and_tags(), sf_opts_, and sfd_.

Referenced by full_model_from_input_source(), full_model_input_sources_from_command_line(), and full_model_input_sources_from_tag().

bool protocols::jd3::full_model_inputters::SilentFileFullModelInputter::job_available_on_command_line ( ) const

overridevirtual

Implements protocols::jd3::full_model_inputters::FullModelInputter.

std::string protocols::jd3::full_model_inputters::SilentFileFullModelInputter::keyname ( )

static

returns the name for the element that will be used in a job-definition file for a structure originating from a silent file: "Silent"

Referenced by full_model_input_sources_from_command_line(), full_model_input_sources_from_tag(), protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator::keyname(), and provide_xml_schema().

void protocols::jd3::full_model_inputters::SilentFileFullModelInputter::list_options_read ( utility::options::OptionKeyList & read_options )

static

References core::io::silent::SilentFileOptions::list_read_options().

Referenced by protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator::list_options_read().

void protocols::jd3::full_model_inputters::SilentFileFullModelInputter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

returns the schema for the PDB element used in a job-definition file including all options that govern how a silent struct is loaded.

returns the schema for the PDB element used in a job-definition file including all options that govern how a PDB is loaded.

References core::io::silent::SilentFileOptions::append_attributes_for_tag_parsing(), protocols::jd3::full_model_inputters::full_model_inputter_xsd_type_definition_w_attributes(), and keyname().

Referenced by protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator::provide_xml_schema().

core::io::silent::SilentFileData const& protocols::jd3::full_model_inputters::SilentFileFullModelInputter::silent_file_data ( ) const

inline

this function returns the SilentStruct that belongs to the given job

References sfd_.

Referenced by full_model_from_input_source().

Member Data Documentation

core::io::silent::SilentFileOptionsOP protocols::jd3::full_model_inputters::SilentFileFullModelInputter::sf_opts_

private

Referenced by initialize_sfd_from_options_and_tag().

core::io::silent::SilentFileDataOP protocols::jd3::full_model_inputters::SilentFileFullModelInputter::sfd_

private

Referenced by full_model_from_input_source(), full_model_input_sources_from_command_line(), full_model_input_sources_from_tag(), initialize_sfd_from_files_and_tags(), initialize_sfd_from_options_and_tag(), and silent_file_data().

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

src/protocols/jd3/full_model_inputters/SilentFileFullModelInputter.hh
src/protocols/jd3/full_model_inputters/SilentFileFullModelInputter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation