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Rosetta
2021.16
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Rosetta
2021.16
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#include <SilentFilePoseInputter.hh>
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_ |
| protocols::jd3::pose_inputters::SilentFilePoseInputter::SilentFilePoseInputter | ( | ) |
References tr().
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overridedefault |
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private |
Referenced by initialize_sfd_from_options_and_tag().
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private |
References protocols::abinitio::filename(), initialize_sfd_from_files_and_tags(), sf_opts_, and sfd_.
Referenced by pose_from_input_source(), pose_input_sources_from_command_line(), and pose_input_sources_from_tag().
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overridevirtual |
Implements protocols::jd3::pose_inputters::PoseInputter.
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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().
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static |
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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_.
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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().
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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_.
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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().
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inline |
this function returns the SilentStruct that belongs to the given job
References sfd_.
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private |
Referenced by initialize_sfd_from_options_and_tag().
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private |
1.8.7