protocols::jd3::full_model_inputters::PDBFullModelInputter Class Reference

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

#include <PDBFullModelInputter.hh>

Inheritance diagram for protocols::jd3::full_model_inputters::PDBFullModelInputter:

Public Member Functions
	PDBFullModelInputter ()
	~PDBFullModelInputter () 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 &, utility::options::OptionCollection const &, utility::tag::TagCOP tag) override
	Takes a FullModelInputSource object previously initialized in the call to initialize_full_model_input_sources() 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 .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 FullModelInputter, which reads from -s/-l and PDB files.

Constructor & Destructor Documentation

PDBFullModelInputter()

protocols::jd3::full_model_inputters::PDBFullModelInputter::PDBFullModelInputter ( )

default

~PDBFullModelInputter()

protocols::jd3::full_model_inputters::PDBFullModelInputter::~PDBFullModelInputter ( )

overridedefault

Member Function Documentation

full_model_from_input_source()

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

overridevirtual

Takes a FullModelInputSource object previously initialized in the call to initialize_full_model_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::full_model_inputters::FullModelInputter.

References core::chemical::FA_STANDARD, protocols::abinitio::filename(), core::import_pose::get_pdb_and_cleanup(), core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses(), and protocols::jd3::full_model_inputters::FullModelInputSource::string_string_map().

full_model_input_sources_from_command_line()

FullModelInputSources protocols::jd3::full_model_inputters::PDBFullModelInputter::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 protocols::jd2::input_pdb_files_from_command_line(), and keyname().

full_model_input_sources_from_tag()

FullModelInputSources protocols::jd3::full_model_inputters::PDBFullModelInputter::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 keyname().

job_available_on_command_line()

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

overridevirtual

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

keyname()

std::string protocols::jd3::full_model_inputters::PDBFullModelInputter::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 full_model_input_sources_from_command_line(), full_model_input_sources_from_tag(), protocols::jd3::full_model_inputters::PDBFullModelInputterCreator::keyname(), and provide_xml_schema().

list_options_read()

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

static

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

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

provide_xml_schema()

void protocols::jd3::full_model_inputters::PDBFullModelInputter::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::full_model_inputters::full_model_inputter_xsd_type_definition_w_attributes(), and keyname().

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

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

• src/protocols/jd3/full_model_inputters/PDBFullModelInputter.hh
• src/protocols/jd3/full_model_inputters/PDBFullModelInputter.cc