protocols::jd2::EnsembleJobInputter Class Reference

A Job Inputter for distributing a job based on a set of input structures that make up an ensemble Two modes. Seed Ensemble and Grid Ensemble. More...

#include <EnsembleJobInputter.hh>

Inheritance diagram for protocols::jd2::EnsembleJobInputter:

Public Member Functions
	EnsembleJobInputter ()
	~EnsembleJobInputter () override
void	fill_jobs (JobsContainer &jobs) override
	this function determines what jobs exist from -s/-l More...
Public Member Functions inherited from protocols::jd2::PDBJobInputter
	PDBJobInputter ()
	~PDBJobInputter () override
void	pose_from_job (core::pose::Pose &pose, JobOP job) 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...
void	fill_jobs (JobsContainer &jobs) override
	this function determines what jobs exist from -s/-l More...
JobInputterInputSource::Enum	input_source () const override
	Return the type of input source that the PDBJobInputter is currently using. More...
Public Member Functions inherited from protocols::jd2::JobInputter
	~JobInputter () override
JobInputterCOP	get_self_ptr () const
	Get self const owning pointers. More...
JobInputterOP	get_self_ptr ()
	Get self owning pointers. More...
JobInputterCAP	get_self_weak_ptr () const
	Get self const weak pointers. More...
JobInputterAP	get_self_weak_ptr ()
	Get self weak pointers. More...
virtual void	update_jobs_list (JobsContainerOP jobs)
	This function is only called by certain JobInputters to update the jobs list after it has already been created. More...
virtual bool	updates_jobs_list () const
	Does this type of JobInputter update the jobs list? More...

Private Member Functions
utility::vector1< core::Real >	read_get_weights (std::string const &filename, utility::vector1< std::string > const &inputs) const

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd2::JobInputter
static std::string	job_inputter_input_source_to_string (JobInputterInputSource::Enum source)
	call this with input_source() to get the input source of a particular job inputter More...
Protected Member Functions inherited from protocols::jd2::JobInputter
void	load_pose_into_job (core::pose::Pose const &pose, JobOP job)
	this function modifies the InnerJob's pose. Access to that pose is via friendship. More...
void	load_pose_into_job (core::pose::PoseCOP pose, JobOP job)
	this function modifies the InnerJob's pose. Access to that pose is via friendship. More...
virtual core::Size	get_nstruct () const
	this code is here to restrict the use of inner_job_nonconst (this class is a friend class and can do it) More...

Detailed Description

A Job Inputter for distributing a job based on a set of input structures that make up an ensemble Two modes. Seed Ensemble and Grid Ensemble.

Seed Ensemble

Randomly choose the starting files using the list of structures given by -s and -l

-jd2:seed_ensemble_weights (RealVector)

• Will give weights to the input PDBs and trigger seed_ensemble mode and the JI. We then use the weighted sampler to choose the input pdb for each nstruct. The weights could be the size of the cluster, the energy, that you like some structure better, etc. Must match number of inputs.

-jd2:seed_ensemble_weight_file (File)

• A file specifying weights to use for each input structure. Enables seed_ensemble mode and the JI. Two columns. basename with extension (or relative path or full path), weight. Any not given in file will be set to 0 by default. Can give a line that is [ALL weight] to set all input pdbs to a given weight. Used for example, to upweight a specific structure:

Example:

#name weight ALL 1 awesome_model.pdb 3

-jd2:seed_ensemble (Bool)

• Enable seed ensemble mode, but simply randomly choose the input pdb for each nstruct. For seed ensemble mode, the number of input pdbs can be larger than nstruct.

Grid Ensemble

Use the input files given in -s and -l and nstruct to cover a grid.

-in:jd2:grid_ensemble (Bool)

• Will enable the basic component of the JI. Here, instead of sampling nstruct for every input pdb, we only sample nstruct no matter the number of input PDBs (with nstruct split as evenly as possible over the input PDBs).

Constructor & Destructor Documentation

protocols::jd2::EnsembleJobInputter::EnsembleJobInputter

(

)

References protocols::jd2::TR().

protocols::jd2::EnsembleJobInputter::~EnsembleJobInputter ( )

overridedefault

Member Function Documentation

void protocols::jd2::EnsembleJobInputter::fill_jobs ( JobsContainer &  jobs )

overridevirtual

this function determines what jobs exist from -s/-l

this function determines what jobs exist from -s/-l

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobsContainer::clear(), protocols::jd2::JobsContainer::push_back(), core::scoring::rg, core::id::to_string(), and protocols::jd2::TR().

utility::vector1< core::Real > protocols::jd2::EnsembleJobInputter::read_get_weights ( std::string const &  filename, utility::vector1< std::string > const &  inputs  ) const

private

References protocols::jd2::TR().

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

• src/protocols/jd2/EnsembleJobInputter.hh
• src/protocols/jd2/EnsembleJobInputter.cc