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protocols::jd3::pose_inputters::SilentFilePoseInputter Class Reference

#include <SilentFilePoseInputter.hh>

Inheritance diagram for protocols::jd3::pose_inputters::SilentFilePoseInputter:
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Public Member Functions

 SilentFilePoseInputter ()
 
 ~SilentFilePoseInputter () 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 &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::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 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::pose_inputters::SilentFilePoseInputter::SilentFilePoseInputter ( )

References tr().

protocols::jd3::pose_inputters::SilentFilePoseInputter::~SilentFilePoseInputter ( )
overridedefault

Member Function Documentation

void protocols::jd3::pose_inputters::SilentFilePoseInputter::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::pose_inputters::SilentFilePoseInputter::initialize_sfd_from_options_and_tag ( utility::options::OptionCollection const &  options,
utility::tag::TagCOP  tag 
)
private
bool protocols::jd3::pose_inputters::SilentFilePoseInputter::job_available_on_command_line ( ) const
overridevirtual
std::string protocols::jd3::pose_inputters::SilentFilePoseInputter::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 protocols::jd3::pose_inputters::SilentFilePoseInputterCreator::keyname(), pose_input_sources_from_command_line(), pose_input_sources_from_tag(), and provide_xml_schema().

void protocols::jd3::pose_inputters::SilentFilePoseInputter::list_options_read ( utility::options::OptionKeyList &  read_options)
static
core::pose::PoseOP protocols::jd3::pose_inputters::SilentFilePoseInputter::pose_from_input_source ( PoseInputSource 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::pose_inputters::PoseInputter.

References core::io::silent::SilentStruct::fill_pose(), initialize_sfd_from_options_and_tag(), protocols::jd3::InputSource::input_tag(), and sfd_.

PoseInputSources protocols::jd3::pose_inputters::SilentFilePoseInputter::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 initialize_sfd_from_options_and_tag(), keyname(), sfd_, and tr().

PoseInputSources protocols::jd3::pose_inputters::SilentFilePoseInputter::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 initialize_sfd_from_options_and_tag(), keyname(), and sfd_.

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

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

core::io::silent::SilentFileData const& protocols::jd3::pose_inputters::SilentFilePoseInputter::silent_file_data ( ) const
inline

this function returns the SilentStruct that belongs to the given job

References sfd_.

Member Data Documentation

core::io::silent::SilentFileOptionsOP protocols::jd3::pose_inputters::SilentFilePoseInputter::sf_opts_
private
core::io::silent::SilentFileDataOP protocols::jd3::pose_inputters::SilentFilePoseInputter::sfd_
private

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