protocols::jd2::Parser Class Reference

#include <Parser.hh>

Public Types
typedef core::pose::Pose	Pose
typedef protocols::moves::Mover	Mover
typedef protocols::moves::MoverOP	MoverOP

Public Member Functions
virtual	~Parser ()
void	generate_mover_from_job (JobOP job, MoverOP &mover, bool new_input)
	generate_mover_from_job is the function called by the job distributor to request a mover. It is defined in the base class (this class) and handles unpackaging the job and passes the work to generate_mover_from_pose. The pose is repackaged into the JobOP so that jobs starting off that pose are properly modified. More...
virtual bool	generate_mover_from_pose (JobCOP job, Pose &pose, MoverOP &mover, bool new_input, std::string const xml_file)=0
	generate_mover_from_pose is overloaded by derived classes to parse as desired. The pose is passed by nonconst reference - the function is thus allowed to modify this pose (preferably not at all, but by adding constraints if necessary). This pose will stay modified for jobs starting off that pose. The function is expected to use its return bool to signal whether the pose has changed or not (and thus whether it needs to be repackaged back into the InnerJob). This function should return IMMEDIATELY with false if it chooses not to modify the mover or pose. More...

Detailed Description

the Parser class can create a protocol (made of Movers) from an XML file. This interface class describes its functionality for the August 08 job distributor.

Member Typedef Documentation

typedef protocols::moves::Mover protocols::jd2::Parser::Mover

typedef protocols::moves::MoverOP protocols::jd2::Parser::MoverOP

typedef core::pose::Pose protocols::jd2::Parser::Pose

Constructor & Destructor Documentation

protocols::jd2::Parser::~Parser ( )

virtual

Member Function Documentation

void protocols::jd2::Parser::generate_mover_from_job	(	JobOP	job,
		MoverOP &	mover,
		bool	new_input
	)

generate_mover_from_job is the function called by the job distributor to request a mover. It is defined in the base class (this class) and handles unpackaging the job and passes the work to generate_mover_from_pose. The pose is repackaged into the JobOP so that jobs starting off that pose are properly modified.

Parameters

[in]	JobOP	job this is the job we're working on (contains the input pose)
	[in/out]	mover this is a mover; the function can choose to overwrite the input with a new mover
[in]	bool	new_input true if this is different input (a different pose) from the last job distributor cycle

the impetus for this function is that Parser is a friend of the InnerJob class and can modify the pose - actual mover generation/pose updating is handled by derived classes.

References protocols::jd2::Job::get_pose(), protocols::jd2::Job::inner_job_nonconst(), protocols::jd2::Job::input_tag(), runtime_assert_string_msg, and core::pose::Pose::total_residue().

virtual bool protocols::jd2::Parser::generate_mover_from_pose ( JobCOP  job, Pose &  pose, MoverOP &  mover, bool  new_input, std::string const  xml_file  )

pure virtual

generate_mover_from_pose is overloaded by derived classes to parse as desired. The pose is passed by nonconst reference - the function is thus allowed to modify this pose (preferably not at all, but by adding constraints if necessary). This pose will stay modified for jobs starting off that pose. The function is expected to use its return bool to signal whether the pose has changed or not (and thus whether it needs to be repackaged back into the InnerJob). This function should return IMMEDIATELY with false if it chooses not to modify the mover or pose.

Parameters

[in]	JobOP	job this is the job we're working on (contains the input pose's name)
	[in/out]	pose this is the "starting pose" for a series of jobs; the function is allowed to modify it by adding constraints if necessary
	[in/out]	mover this is a mover; the function can choose to overwrite the input with a new mover
[in]	bool	new_input true if this is different input (a different pose) from the last job distributor cycle
[out]	bool	the return value states whether or not the pose has been changed - it will be repackaged into the InnerJob only as necessary

Implemented in protocols::rosetta_scripts::RosettaScriptsParser.

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

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