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protocols::jd3::pose_inputters Namespace Reference

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  PoseInputterFactory
 
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  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

typedef utility::pointer::shared_ptr< PDBPoseInputter const > protocols::jd3::pose_inputters::PDBPoseInputterCOP
typedef utility::pointer::shared_ptr< PDBPoseInputter > protocols::jd3::pose_inputters::PDBPoseInputterOP
typedef utility::pointer::shared_ptr< PoseInputSource const > protocols::jd3::pose_inputters::PoseInputSourceCOP
typedef utility::pointer::shared_ptr< PoseInputSource > protocols::jd3::pose_inputters::PoseInputSourceOP
typedef utility::pointer::shared_ptr< PoseInputter const > protocols::jd3::pose_inputters::PoseInputterCOP
typedef utility::pointer::shared_ptr< PoseInputterCreator const > protocols::jd3::pose_inputters::PoseInputterCreatorCOP
typedef utility::pointer::shared_ptr< PoseInputter > protocols::jd3::pose_inputters::PoseInputterOP

Function Documentation

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