Reading the xml file and generating the mover. More...

#include <RosettaScriptsParser.hh>

Public Member Functions
	RosettaScriptsParser ()

virtual	~RosettaScriptsParser ()

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

MoverOP	generate_mover_for_protocol (Pose &pose, bool &modified_pose, utility::tag::TagCOP protocol_tag)

MoverOP	parse_protocol_tag (Pose &pose, utility::tag::TagCOP protocol_tag)

MoverOP	parse_protocol_tag (utility::tag::TagCOP protocol_tag)

void	register_factory_prototypes ()
	Factories avoid requiring compiler dependencies for all possible constructible derived classes, by allowing runtime registration of derived class prototypes. However, this requires pre-registration of a derived type with the factory prior to asking the factory to return an instance of that type. This method registers those additional derived classes that are available for construction in the RosettaScriptsParser context. TO-DO: replace this manual factory registration system with a load-time-initialized singleton scheme (see r32404 for example) More...

void	instantiate_filter (utility::tag::TagCOP const &tag_ptr, basic::datacache::DataMap &data, protocols::filters::Filters_map &filters, protocols::moves::Movers_map &movers, core::pose::Pose &pose)
	Instantiate a new filter and add it to the list of defined filters for this ROSETTASCRIPTS block. More...

void	instantiate_mover (utility::tag::TagCOP const &tag_ptr, basic::datacache::DataMap &data, protocols::filters::Filters_map &filters, protocols::moves::Movers_map &movers, core::pose::Pose &pose)
	Instantiate a new mover and add it to the list of defined movers for this ROSETTASCRIPTS block. More...

void	instantiate_taskoperation (utility::tag::TagCOP const &tag_ptr, basic::datacache::DataMap &data, protocols::filters::Filters_map &filters, protocols::moves::Movers_map &movers, core::pose::Pose &pose)
	Instantiate a new task operation (used in IMPORT tag) More...

utility::tag::TagCOP	find_rosettascript_tag (utility::tag::TagCOP rootTag, const std::string &section_name, const std::string &option_name, const std::string &option_value)
	Recursively find a specific tag by option name and valie in any ROSETTASCRIPTS tag that's a child of rootTag. More...

void	import_tags (std::set< ImportTagName > &import_tag_names, utility::tag::TagCOP &my_tag, basic::datacache::DataMap &data, protocols::filters::Filters_map &filters, protocols::moves::Movers_map &movers, core::pose::Pose &pose)
	Import filters, movers, ... specified in the IMPORT tag in the order they were originally defined elsewhere in the script. More...

Public Member Functions inherited from protocols::jd2::Parser
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...

Private Member Functions
int	process_includes (utility::tag::TagCOP root_tag, int &processed_includes)

void	process_include_xml (utility::tag::TagCOP tag, utility::vector0< utility::tag::TagOP > &tags_from_includes, int &processed_includes)
	Process a single XML include file. More...

Static Private Member Functions
static void	substitute_variables_in_stream (std::istream &in, utility::options::StringVectorOption const &script_vars, std::stringstream &out)
	Create a variable substituted version of the input stream, given a StringVectorOption formated list of variables to substitiute. Each item in script_vars should be in the form of "variable=value", where "value" is the string to substitiute into the input stream whereever the string "%%variable%%" is found in the input. More...

Detailed Description

Reading the xml file and generating the mover.

Member Typedef Documentation

typedef std::pair<std::string, std::string> protocols::rosetta_scripts::RosettaScriptsParser::ImportTagName

typedef protocols::moves::MoverFactory protocols::rosetta_scripts::RosettaScriptsParser::MoverFactory

typedef protocols::moves::MoverFactoryOP protocols::rosetta_scripts::RosettaScriptsParser::MoverFactoryOP

typedef utility::vector0< utility::tag::TagCOP > protocols::rosetta_scripts::RosettaScriptsParser::TagCOPs

Constructor & Destructor Documentation

protocols::rosetta_scripts::RosettaScriptsParser::RosettaScriptsParser ( )

References register_factory_prototypes().

protocols::rosetta_scripts::RosettaScriptsParser::~RosettaScriptsParser ( )

virtual

Member Function Documentation

TagCOP protocols::rosetta_scripts::RosettaScriptsParser::find_rosettascript_tag	(	utility::tag::TagCOP	rootTag,
		const std::string &	section_name,
		const std::string &	option_name,
		const std::string &	option_value
	)

Recursively find a specific tag by option name and valie in any ROSETTASCRIPTS tag that's a child of rootTag.

Referenced by protocols::pose_reporters::FilterReporter::parse_my_tag(), and protocols::pose_selectors::Filter::parse_my_tag().

MoverOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol	(	Pose &	pose,
		bool &	modified_pose,
		utility::tag::TagCOP	protocol_tag
	)

bool protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_from_pose	(	protocols::jd2::JobCOP	job,
		core::pose::Pose &	pose,
		protocols::moves::MoverOP &	mover,
		bool	new_input,
		std::string const	xml_fname
	)

virtual

Uses the Tag interface to the xml reader library in boost to parse an xml file that contains design protocol information. A sample protocol file can be found in src/pilot/apps/sarel/dock_design.protocol. INCLUDES allows inclusion of additional module files (in XML format). SCOREFXNS provides a way to define scorefunctions as they are defined in the rosetta database, using the weights/patch convenctions. Several default scorefunctions are preset and can be used without defining them explicitly. FILTERS defines a set of filters that can be used together with the dockdesign movers to prune out poses that don't meet certain criteria MOVERS defines the movers that will be used PROTOCOLS is the only order-sensitive section where subsequent movers and filters are expected to be defined. These movers and filters were defined in the previous two sections. The order in which the protocols are specified by the user will be maintained by the DockDesign mover. APPLY_TO_POSE This section allows for certain movers to be applied to the pose prior to starting the DockDesign protocol. For instance, these movers could set constraints, such as favor_native_residue. In this case, for example, the weights of res_type_constraint in all of the scorefunctions that are defined in SCOREFXNS or by default are set to 1.0, but can be changed by the user globally (in the definition of the weight on the constraint), or in particular for each of the scorefunctions by changing the relevant term (which is set by default to the global value). OUTPUT is a section which allows the XML control of how things are output Notice that the order of the sections by which the protocol is written doesn't matter, BUT the order of the mover-filter pairs in PROTOCOLS section does matter.

Implements protocols::jd2::Parser.

References utility::io::izstream::close(), utility::tag::Tag::create(), generate_mover_for_protocol(), utility::io::izstream::good(), utility::io::izstream::open(), option, runtime_assert, substitute_variables_in_stream(), tag, protocols::rosetta_scripts::TR, user, and utility_exit_with_message.

Referenced by protocols::rpc::JSON_RPC::run().

void protocols::rosetta_scripts::RosettaScriptsParser::import_tags	(	std::set< ImportTagName > &	import_tag_names,
		utility::tag::TagCOP &	my_tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map &	filters,
		protocols::moves::Movers_map &	movers,
		core::pose::Pose &	pose
	)

Import filters, movers, ... specified in the IMPORT tag in the order they were originally defined elsewhere in the script.

References instantiate_filter(), instantiate_mover(), instantiate_taskoperation(), key, tag, and protocols::rosetta_scripts::TR.

Referenced by generate_mover_for_protocol().

void protocols::rosetta_scripts::RosettaScriptsParser::instantiate_filter	(	utility::tag::TagCOP const &	tag_ptr,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map &	filters,
		protocols::moves::Movers_map &	movers,
		core::pose::Pose &	pose
	)

Instantiate a new filter and add it to the list of defined filters for this ROSETTASCRIPTS block.

References protocols::filters::FilterFactory::get_instance(), runtime_assert, protocols::rosetta_scripts::TR, and type.

Referenced by generate_mover_for_protocol(), and import_tags().

void protocols::rosetta_scripts::RosettaScriptsParser::instantiate_mover	(	utility::tag::TagCOP const &	tag_ptr,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map &	filters,
		protocols::moves::Movers_map &	movers,
		core::pose::Pose &	pose
	)

Instantiate a new mover and add it to the list of defined movers for this ROSETTASCRIPTS block.

References protocols::moves::MoverFactory::get_instance(), runtime_assert, protocols::rosetta_scripts::TR, and type.

Referenced by generate_mover_for_protocol(), and import_tags().

void protocols::rosetta_scripts::RosettaScriptsParser::instantiate_taskoperation	(	utility::tag::TagCOP const &	tag_ptr,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map &	filters,
		protocols::moves::Movers_map &	movers,
		core::pose::Pose &	pose
	)

Instantiate a new task operation (used in IMPORT tag)

References basic::datacache::DataMap::add(), basic::datacache::DataMap::has(), runtime_assert, protocols::rosetta_scripts::TR, and type.

Referenced by import_tags().

MoverOP protocols::rosetta_scripts::RosettaScriptsParser::parse_protocol_tag	(	Pose &	pose,
		utility::tag::TagCOP	protocol_tag
	)

References generate_mover_for_protocol().

Referenced by protocols::rosetta_scripts::MultipleOutputWrapper::generate_pose(), protocols::rosetta_scripts::AdditionalOutputWrapper::generate_pose(), protocols::rosetta_scripts::MultipleOutputWrapper::parse_my_tag(), protocols::rosetta_scripts::AdditionalOutputWrapper::parse_my_tag(), protocols::rosetta_scripts::MultiplePoseMover::parse_my_tag(), and protocols::rosetta_scripts::MultiplePoseMover::process_pose().

MoverOP protocols::rosetta_scripts::RosettaScriptsParser::parse_protocol_tag ( utility::tag::TagCOP protocol_tag )

References generate_mover_for_protocol().

void protocols::rosetta_scripts::RosettaScriptsParser::process_include_xml	(	utility::tag::TagCOP	tag,
		utility::vector0< utility::tag::TagOP > &	tags_from_includes,
		int &	processed_includes
	)

private

Process a single XML include file.

References utility::tag::Tag::create(), filename(), MAX_INCLUDES, utility::io::izstream::open(), option, process_includes(), utility::options::StringVectorOption::push_back(), s, script_vars, utility::options::StringVectorOption::size(), substitute_variables_in_stream(), tag, protocols::rosetta_scripts::TR, and user.

Referenced by process_includes().

int protocols::rosetta_scripts::RosettaScriptsParser::process_includes	(	utility::tag::TagCOP	root_tag,
		int &	processed_includes
	)

private

References utility::pointer::const_pointer_cast(), MAX_INCLUDES, process_include_xml(), tag, and tags.

Referenced by generate_mover_for_protocol(), and process_include_xml().

void protocols::rosetta_scripts::RosettaScriptsParser::register_factory_prototypes ( )

Factories avoid requiring compiler dependencies for all possible constructible derived classes, by allowing runtime registration of derived class prototypes. However, this requires pre-registration of a derived type with the factory prior to asking the factory to return an instance of that type. This method registers those additional derived classes that are available for construction in the RosettaScriptsParser context. TO-DO: replace this manual factory registration system with a load-time-initialized singleton scheme (see r32404 for example)

Referenced by RosettaScriptsParser().

void protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream	(	std::istream &	in,
		utility::options::StringVectorOption const &	script_vars,
		std::stringstream &	out
	)

staticprivate

Create a variable substituted version of the input stream, given a StringVectorOption formated list of variables to substitiute. Each item in script_vars should be in the form of "variable=value", where "value" is the string to substitiute into the input stream whereever the string "%%variable%%" is found in the input.

Having the return value be passed through a parameter is to get around some copy-constructor limitations of C++ streams.

References end, getline(), utility::options::StringVectorOption::size(), and protocols::rosetta_scripts::TR.

Referenced by generate_mover_from_pose(), and process_include_xml().

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

src/protocols/rosetta_scripts/RosettaScriptsParser.hh
src/protocols/rosetta_scripts/RosettaScriptsParser.cc

Public Types
typedef utility::vector0 < utility::tag::TagCOP >	TagCOPs

typedef protocols::moves::MoverFactory	MoverFactory

typedef protocols::moves::MoverFactoryOP	MoverFactoryOP

typedef std::pair< std::string, std::string >	ImportTagName

Public Types inherited from protocols::jd2::Parser
typedef core::pose::Pose	Pose

typedef protocols::moves::Mover	Mover

typedef protocols::moves::MoverOP	MoverOP

Public Types

Public Member Functions

Private Member Functions

Static Private Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation