This is the simplest implementation of PoseInputter, which reads from -s/-l and PDB files. These can be any Protein Data Bank file type: .pdb, .cif, .mmtf. More...

#include <PDBPoseInputter.hh>

Inheritance diagram for protocols::jd3::pose_inputters::PDBPoseInputter:

[legend]

Public Member Functions
	PDBPoseInputter ()

	~PDBPoseInputter () override

bool	job_available_on_command_line () const override

PoseInputSources	pose_input_sources_from_command_line () override
	Constructs a list of PoseInputSource 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...

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

core::pose::PoseOP	pose_from_input_source (PoseInputSource const &, utility::options::OptionCollection const &, utility::tag::TagCOP tag) override
	Takes a PoseInputSource object previously initialized in the call to initialize_pose_input_sources() More...

Public Member Functions inherited from protocols::jd3::pose_inputters::PoseInputter
	PoseInputter ()

	~PoseInputter () 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 PoseInputter, which reads from -s/-l and PDB files. These can be any Protein Data Bank file type: .pdb, .cif, .mmtf.

Constructor & Destructor Documentation

protocols::jd3::pose_inputters::PDBPoseInputter::PDBPoseInputter ( )

default

protocols::jd3::pose_inputters::PDBPoseInputter::~PDBPoseInputter ( )

overridedefault

Member Function Documentation

bool protocols::jd3::pose_inputters::PDBPoseInputter::job_available_on_command_line ( ) const

overridevirtual

Implements protocols::jd3::pose_inputters::PoseInputter.

std::string protocols::jd3::pose_inputters::PDBPoseInputter::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 protocols::jd3::pose_inputters::PDBPoseInputterCreator::keyname(), pose_input_sources_from_command_line(), pose_input_sources_from_tag(), and provide_xml_schema().

void protocols::jd3::pose_inputters::PDBPoseInputter::list_options_read ( utility::options::OptionKeyList & read_options )

static

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

Referenced by protocols::jd3::pose_inputters::PDBPoseInputterCreator::list_options_read().

core::pose::PoseOP protocols::jd3::pose_inputters::PDBPoseInputter::pose_from_input_source	(	PoseInputSource const &	input_source,
		utility::options::OptionCollection const &	options,
		utility::tag::TagCOP	tag
	)

overridevirtual

Takes a PoseInputSource object previously initialized in the call to initialize_pose_input_sources()

This is only a stub implementation – the logic here ought to be robust enough to handle non-fullatom poses, but it currently isn't. This will improve. One thought is that the options that control how poses are loaded from disk could be included in the per-job option set, and then passed into this function via an OptionCollection...

Implements protocols::jd3::pose_inputters::PoseInputter.

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::import_pose::ImportPoseOptions::read_fold_tree(), protocols::jd3::InputSource::source_id(), and protocols::jd3::pose_inputters::PoseInputSource::string_string_map().

PoseInputSources protocols::jd3::pose_inputters::PDBPoseInputter::pose_input_sources_from_command_line ( )

overridevirtual

Constructs a list of PoseInputSource 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::pose_inputters::PoseInputter.

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

PoseInputSources protocols::jd3::pose_inputters::PDBPoseInputter::pose_input_sources_from_tag	(	utility::options::OptionCollection const &	opts,
		utility::tag::TagCOP
	)

overridevirtual

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

Implements protocols::jd3::pose_inputters::PoseInputter.

References keyname().

void protocols::jd3::pose_inputters::PDBPoseInputter::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 keyname(), and protocols::jd3::pose_inputters::pose_inputter_xsd_type_definition_w_attributes().

Referenced by protocols::jd3::pose_inputters::PDBPoseInputterCreator::provide_xml_schema().

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

src/protocols/jd3/pose_inputters/PDBPoseInputter.hh
src/protocols/jd3/pose_inputters/PDBPoseInputter.cc

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation