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protocols::jd3::pose_inputters::PDBPoseInputter Class Reference

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:
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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
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
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: