protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter Class Reference

This is the simplest implementation of ChunkLibraryInputter, which reads from -s/-l and PDB files. More...

#include <PDBChunkLibraryInputter.hh>

Inheritance diagram for protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter:

Public Member Functions
	PDBChunkLibraryInputter ()
	~PDBChunkLibraryInputter () override
bool	job_available_on_command_line () const override
ChunkLibraryInputSources	chunk_library_input_sources_from_command_line () override
	Constructs a list of ChunkLibraryInputSource 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...
ChunkLibraryInputSources	chunk_library_input_sources_from_tag (utility::options::OptionCollection const &opts, utility::tag::TagCOP tag) override
	Construct a list of ChunkLibraryInputSource objects from a Tag object that will be used by the JobQueen to construct a list of LarvalJobs. More...
core::pose::PoseOP	chunk_library_from_input_source (ChunkLibraryInputSource const &, utility::options::OptionCollection const &, utility::tag::TagCOP tag) override
	Takes a ChunkLibraryInputSource object previously initialized in the call to initialize_chunk_library_input_sources() More...
Public Member Functions inherited from protocols::jd3::chunk_library_inputters::ChunkLibraryInputter
	ChunkLibraryInputter ()
	~ChunkLibraryInputter () 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 .pdb file: "PDB" 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 PDB is loaded. More...
static void	list_options_read (utility::options::OptionKeyList &read_options)

Detailed Description

This is the simplest implementation of ChunkLibraryInputter, which reads from -s/-l and PDB files.

Constructor & Destructor Documentation

PDBChunkLibraryInputter()

protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::PDBChunkLibraryInputter

(

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~PDBChunkLibraryInputter()

protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::~PDBChunkLibraryInputter ( )

override

Member Function Documentation

chunk_library_from_input_source()

core::pose::PoseOP protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::chunk_library_from_input_source ( ChunkLibraryInputSource const &  input_source, utility::options::OptionCollection const &  options, utility::tag::TagCOP  tag  )

overridevirtual

Takes a ChunkLibraryInputSource object previously initialized in the call to initialize_chunk_library_input_sources()

Implements protocols::jd3::chunk_library_inputters::ChunkLibraryInputter.

References protocols::jd3::chunk_library_inputters::ChunkLibraryInputSource::string_string_map().

chunk_library_input_sources_from_command_line()

ChunkLibraryInputSources protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::chunk_library_input_sources_from_command_line ( )

overridevirtual

Constructs a list of ChunkLibraryInputSource 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::chunk_library_inputters::ChunkLibraryInputter.

References protocols::jd2::input_pdb_files_from_command_line(), and keyname().

chunk_library_input_sources_from_tag()

ChunkLibraryInputSources protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::chunk_library_input_sources_from_tag ( utility::options::OptionCollection const &  opts, utility::tag::TagCOP    )

overridevirtual

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

Implements protocols::jd3::chunk_library_inputters::ChunkLibraryInputter.

References keyname().

job_available_on_command_line()

bool protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::job_available_on_command_line ( ) const

overridevirtual

Implements protocols::jd3::chunk_library_inputters::ChunkLibraryInputter.

keyname()

std::string protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::keyname ( )

static

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

Referenced by chunk_library_input_sources_from_command_line(), chunk_library_input_sources_from_tag(), protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator::keyname(), and provide_xml_schema().

list_options_read()

void protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::list_options_read ( utility::options::OptionKeyList &  read_options )

static

References core::import_pose::ImportPoseOptions::list_options_read().

Referenced by protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator::list_options_read().

provide_xml_schema()

void protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::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 PDB is loaded.

References protocols::jd3::chunk_library_inputters::chunk_library_inputter_xsd_type_definition_w_attributes(), and keyname().

Referenced by protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator::provide_xml_schema().

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

• src/protocols/jd3/chunk_library_inputters/PDBChunkLibraryInputter.hh
• src/protocols/jd3/chunk_library_inputters/PDBChunkLibraryInputter.cc