Classes
class	PDBPoseInputter
	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...

class	PDBPoseInputterCreator

class	PoseInputSource
	The PoseInputSource is a small class for holding data about the starting Pose for a Job and where it comes from (i.e. which of the PoseInputters claims responsibility for creating a Pose for this instance). The "input_tag" is a string description of the input source and will be used as the "job_tag" to control output – the input tag should not include the file extension. It is perfectly reasonable for complex PoseInputters to subclass from PoseInputSource to tuck more complex data in the PoseInputSource, though, the string-string map ought to provide considerable flexibility in storing data without deriving new subclasses. More...

class	PoseInputter
	The PoseInputter is responsible for reading from the command line a set of structures that are each to be run through a protocol, where each input struture will be the starting point for some number of jobs (where that number is at the JobQueen's discretion). The PoseInputter is responsible for two things: More...

class	PoseInputterCreator

class	PoseInputterRegistrator
	This templated class will register an instance of an PoseInputterCreator (class T) with the PoseInputterFactory. It will ensure that no PoseInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	PoseInputterFactory

class	SilentFilePoseInputter

class	SilentFilePoseInputterCreator

Typedefs
typedef utility::pointer::shared_ptr< PDBPoseInputter >	PDBPoseInputterOP

typedef utility::pointer::shared_ptr< PDBPoseInputter const >	PDBPoseInputterCOP

typedef utility::pointer::shared_ptr< PoseInputSource >	PoseInputSourceOP

typedef utility::pointer::shared_ptr< PoseInputSource const >	PoseInputSourceCOP

typedef utility::vector1< PoseInputSourceOP >	PoseInputSources

typedef utility::pointer::shared_ptr< PoseInputter >	PoseInputterOP

typedef utility::pointer::shared_ptr< PoseInputter const >	PoseInputterCOP

typedef utility::vector1< std::pair< PoseInputSourceOP, PoseInputterOP > >	PoseInputSourcesAndInputters

typedef utility::pointer::shared_ptr< PoseInputterCreator >	PoseInputterCreatorOP

typedef utility::pointer::shared_ptr< PoseInputterCreator const >	PoseInputterCreatorCOP

typedef utility::pointer::shared_ptr< SilentFilePoseInputter >	SilentFilePoseInputterOP

typedef utility::pointer::shared_ptr< SilentFilePoseInputter const >	SilentFilePoseInputterCOP

Functions
static basic::Tracer	TR ("protocols.jd3.pose_inputter.PDBPoseInputter")

void	pose_inputter_xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &inputter_type, std::string const &description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a PoseInputter that contains no subtags but may contain any number of attributes (aka options). More...

static basic::Tracer	TR ("protocols.jd3.pose_inputters.PoseInputterFactory")

Typedef Documentation

◆ PDBPoseInputterCOP

typedef utility::pointer::shared_ptr< PDBPoseInputter const > protocols::jd3::pose_inputters::PDBPoseInputterCOP

◆ PDBPoseInputterOP

typedef utility::pointer::shared_ptr< PDBPoseInputter > protocols::jd3::pose_inputters::PDBPoseInputterOP

◆ PoseInputSourceCOP

typedef utility::pointer::shared_ptr< PoseInputSource const > protocols::jd3::pose_inputters::PoseInputSourceCOP

◆ PoseInputSourceOP

typedef utility::pointer::shared_ptr< PoseInputSource > protocols::jd3::pose_inputters::PoseInputSourceOP

◆ PoseInputSources

typedef utility::vector1< PoseInputSourceOP > protocols::jd3::pose_inputters::PoseInputSources

◆ PoseInputSourcesAndInputters

typedef utility::vector1< std::pair< PoseInputSourceOP, PoseInputterOP > > protocols::jd3::pose_inputters::PoseInputSourcesAndInputters

◆ PoseInputterCOP

typedef utility::pointer::shared_ptr< PoseInputter const > protocols::jd3::pose_inputters::PoseInputterCOP

◆ PoseInputterCreatorCOP

typedef utility::pointer::shared_ptr< PoseInputterCreator const > protocols::jd3::pose_inputters::PoseInputterCreatorCOP

◆ PoseInputterCreatorOP

typedef utility::pointer::shared_ptr< PoseInputterCreator > protocols::jd3::pose_inputters::PoseInputterCreatorOP

◆ PoseInputterOP

typedef utility::pointer::shared_ptr< PoseInputter > protocols::jd3::pose_inputters::PoseInputterOP

◆ SilentFilePoseInputterCOP

typedef utility::pointer::shared_ptr< SilentFilePoseInputter const> protocols::jd3::pose_inputters::SilentFilePoseInputterCOP

◆ SilentFilePoseInputterOP

typedef utility::pointer::shared_ptr< SilentFilePoseInputter > protocols::jd3::pose_inputters::SilentFilePoseInputterOP

Function Documentation

◆ pose_inputter_xsd_type_definition_w_attributes()

void protocols::jd3::pose_inputters::pose_inputter_xsd_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	inputter_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Define the XML schema definition for a PoseInputter that contains no subtags but may contain any number of attributes (aka options).

References protocols::jd3::pose_inputters::PoseInputterFactory::complex_type_name_for_pose_inputter().

Referenced by protocols::jd3::pose_inputters::PDBPoseInputter::provide_xml_schema(), and protocols::jd3::pose_inputters::SilentFilePoseInputter::provide_xml_schema().

◆ TR() [1/2]

static basic::Tracer protocols::jd3::pose_inputters::TR ( "protocols.jd3.pose_inputter.PDBPoseInputter" )

static

Referenced by protocols::jd3::pose_inputters::PoseInputterFactory::new_pose_inputter(), and protocols::jd3::pose_inputters::PDBPoseInputter::pose_from_input_source().

◆ TR() [2/2]

static basic::Tracer protocols::jd3::pose_inputters::TR ( "protocols.jd3.pose_inputters.PoseInputterFactory" )