protocols::rosetta_scripts::RosettaScriptsParser Class Reference

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

#include <RosettaScriptsParser.hh>

Inheritance diagram for protocols::rosetta_scripts::RosettaScriptsParser:

Public Types
typedef utility::vector0 < utility::tag::TagCOP >	TagCOPs
typedef utility::tag::TagCOP	TagCOP
typedef moves::MoverOP	MoverOP
typedef std::pair< std::string, std::string >	ImportTagName

Public Member Functions
	RosettaScriptsParser ()
	~RosettaScriptsParser () override
ParsedProtocolOP	generate_mover (std::string const &xml_fname, std::string const &current_input_name="", std::string const &current_output_name="")
	Convenience function to construct a ParsedProtocol from a file. More...
ParsedProtocolOP	generate_mover (std::string const &xml_fname, utility::vector1< std::string > const &script_vars, std::string const &current_input_name="", std::string const &current_output_name="")
	Convenience function to construct a ParsedProtocol from a file. More...
ParsedProtocolOP	generate_mover (utility::options::OptionCollection const &options, std::string const &current_input_name, std::string const &current_output_name, basic::resource_manager::ResourceManagerOP resource_manager)
	Convenience function to construct a ParsedProtocol from a file. More...
ParsedProtocolOP	generate_mover (utility::options::OptionCollection const &options, std::string const &xml_fname, std::string const &current_input_name="", std::string const &current_output_name="", XmlObjectsOP xml_objects=nullptr, basic::resource_manager::ResourceManagerOP resource_manager=nullptr)
	Convenience function to construct a ParsedProtocol from a file. More...
ParsedProtocolOP	generate_mover_xml_string (utility::options::OptionCollection const &options, std::string const &xml_text, std::string const &current_input_name, std::string const &current_output_name, XmlObjectsOP xml_objects)
	Convenience function to construct a ParsedProtocol from a string. More...
ParsedProtocolOP	generate_mover (utility::options::OptionCollectionCOP options, std::string const &current_input_name, std::string const &current_output_name, basic::resource_manager::ResourceManagerOP resource_manager)
	Convenience function to construct a ParsedProtocol from a file. More...
ParsedProtocolOP	generate_mover (utility::options::OptionCollectionCOP options, std::string const &xml_fname, std::string const &current_input_name="", std::string const &current_output_name="", XmlObjectsOP xml_objects=nullptr, basic::resource_manager::ResourceManagerOP resource_manager=nullptr)
	Convenience function to construct a ParsedProtocol from a file. More...
ParsedProtocolOP	generate_mover_xml_string (utility::options::OptionCollectionCOP options, std::string const &xml_text, std::string const &current_input_name, std::string const &current_output_name, XmlObjectsOP xml_objects)
	Convenience function to construct a ParsedProtocol from a string. More...
TagCOP	create_tag_from_xml (std::string const &xml_fname, utility::options::OptionCollection const &options)
	Create a tag from an XML file. Read from Script Vars options from a local options collection. More...
TagCOP	create_tag_from_xml (std::string const &xml_fname, utility::vector1< std::string > const &script_vars)
	Create a tag from an XML file. Use Script Vars bariable to do any substitutions. Script Var String: "xx=yy" for xx% replacement in XML script. More...
TagCOP	create_tag_from_xml_string (std::string const &xml_text, utility::options::OptionCollection const &options)
	Create a tag from an XML string. Read from Script Vars options from a local options collection. More...
TagCOP	create_tag_from_xml_string (std::string const &xml_text, utility::vector1< std::string > const &script_vars)
	Create a tag from an XML string. Use Script Vars bariable to do any substitutions. Script Var String: "xx=yy" for xx% replacement in XML script. More...
ParsedProtocolOP	parse_protocol_tag (utility::tag::TagCOP protocol_tag, utility::options::OptionCollection const &options)
	Create the ParsedProtocolMover for the protocol using a tag. More...
ParsedProtocolOP	generate_mover_for_protocol (utility::tag::TagCOP protocol_tag, utility::options::OptionCollection const &options, std::string const &current_input_name="", std::string const &current_output_name="", XmlObjectsOP xml_objects=nullptr, basic::resource_manager::ResourceManagerOP resource_manager=nullptr)
	Create the ParsedProtocolMover for the protocol using a tag. More...
ParsedProtocolOP	generate_mover_for_protocol (utility::tag::TagCOP protocol_tag, basic::datacache::DataMap &data, utility::options::OptionCollection const &options, XmlObjectsOP xml_objects=nullptr, basic::resource_manager::ResourceManagerOP resource_manager=nullptr)
	Create the ParsedProtocolMover for the protocol using a tag. More...
ParsedProtocolOP	generate_mover_for_protocol (core::pose::Pose &, bool &, utility::tag::TagCOP protocol_tag, utility::options::OptionCollection const &options, std::string const &current_input_name="", std::string const &current_output_name="", XmlObjectsOP xml_objects=nullptr, basic::resource_manager::ResourceManagerOP resource_manager=nullptr)
	Create the ParsedProtocolMover for the protocol using a tag. More...
void	initialize_data_map (basic::datacache::DataMap &data, utility::options::OptionCollection const &options)
	Initialize the passed datamap with the standard set of pre-defined RosettaScripts objects. More...
void	read_in_and_recursively_replace_includes (std::string const &filename, std::string &substituted_contents, utility::vector1< std::string > filenames_encountered, core::Size const recursion_level, bool const do_not_recurse=false, std::string const &xml_text_for_top_level="") const
	Actually read in the XML file. Called recursively to read in XML files that this XML file includes. At the end of this operation, substituted_contents contains the contents of the XML file, with all xi:includes replaced with the contents of included XML files. Files are opened and closed here. More...
void	parse_resources_tag (utility::tag::TagCOP resources_tag, basic::datacache::DataMap &data, basic::resource_manager::ResourceManagerOP resource_manager) const
void	parse_apply_to_pose_tag (utility::tag::TagCOP apply_tag, basic::datacache::DataMap &data) const
void	instantiate_filter (utility::tag::TagCOP const &tag_ptr, basic::datacache::DataMap &data) const
	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) const
	Instantiate a new mover and add it to the list of defined movers for this ROSETTASCRIPTS block. More...
void	instantiate_packer_palette (utility::tag::TagCOP const &tag_ptr, basic::datacache::DataMap &data) const
	Instantiate a PackerPalette object. More...
void	instantiate_taskoperation (utility::tag::TagCOP const &tag_ptr, basic::datacache::DataMap &data) const
	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	parse_import_tag (utility::tag::TagCOP import_tag, basic::datacache::DataMap &data) const
void	import_tags (std::set< ImportTagName > &import_tag_names, utility::tag::TagCOP my_tag, basic::datacache::DataMap &data) const
	Import filters, movers, ... specified in the IMPORT tag in the order they were originally defined elsewhere in the script. More...
void	validate_input_script_against_xsd (std::string const &fname, std::stringstream const &input_xml) const
void	set_recursion_limit (utility::options::OptionCollection const &options)
void	generate_mover (MoverOP &mover, bool new_input, std::string const &xml_file, std::string const &current_input_name="", std::string const &current_output_name="", bool guarantee_new_mover=false)
	Original, JD2-compatible mover generating function. More...
bool	protocol_option_set (utility::options::OptionCollection const &options) const
	Checks the LOCAL options collection to see if a protocol has been set. More...

Static Public Member Functions
static 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...
static std::string	xsd_for_rosetta_scripts ()
static void	write_ROSETTASCRIPTS_complex_type (utility::tag::XMLSchemaDefinition &)
static std::string	rosetta_scripts_element_name ()
static std::string	rosetta_scripts_complex_type_naming_func (std::string const &element_name)
static void	list_options_read (utility::options::OptionKeyList &read_options)
	List the command-line options used by this class. More...
static void	substitute_variables_in_stream (std::istream &in, utility::vector1< std::string > const &script_vars, std::stringstream &out)
	Substitute xx==yy using the XML syntax %xx%%. / script_vars is a list of strings of "xx==yy". More...

Private Member Functions
bool	has_slash_at_end (std::string const &str, core::Size const endpos) const
	Is the current tag one with a slash at the end? More...
bool	has_double_percent_signs (std::string const &str, core::Size const endpos) const
	Is the current tag one with something that will be replaced by variable replacement? More...
TagCOP	finish_creating_tag (std::string const &xml_fname, utility::vector1< std::string > const &script_vars, std::string const &substituted_contents) const
	To be called after the full xml tree has been loaded into a string from create_tag_from_xml*. More...
void	load_native (std::string const &fname)
	Load a native into this class, which will be placed into the datamap as a resource upon generating mover(s). More...

Private Attributes
utility::tag::XMLSchemaValidatorOP	validator_
	The object used to validate XML input files against the schema. More...
core::Size	recursion_limit_
	The depth of the rabbit hole one can find oneself in by including XML files that include XML files. Defaults to 8. More...
core::pose::PoseOP	native_pose_ = nullptr
utility::options::OptionCollectionCOP	local_options_ = nullptr

Detailed Description

Reading the xml file and generating the mover.

Uses the Tag interface to the xml reader library in boost to parse an xml file that contains design protocol information.

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 – DEPRECATED/Removed. This section used to allow for applying certain movers to the pose prior to protocol start. This functionality has been removed. Anything other than an empty APPLY_TO_POSE section will raise an error.

xi:include statements can be placed anywhere to trigger read-in of another RosettaScripts XML file. Contents of the file replace the xi:include statement.

Member Typedef Documentation

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

typedef moves::MoverOP protocols::rosetta_scripts::RosettaScriptsParser::MoverOP

typedef utility::tag::TagCOP protocols::rosetta_scripts::RosettaScriptsParser::TagCOP

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

Constructor & Destructor Documentation

protocols::rosetta_scripts::RosettaScriptsParser::RosettaScriptsParser

(

)

References register_factory_prototypes(), and set_recursion_limit().

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

overridedefault

Member Function Documentation

TagCOP protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml	(	std::string const &	xml_fname,
		utility::options::OptionCollection const &	options
	)

Create a tag from an XML file. Read from Script Vars options from a local options collection.

Create a tag from an XML file. Read from a local options collection.

Referenced by generate_mover().

TagCOP protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml	(	std::string const &	xml_fname,
		utility::vector1< std::string > const &	script_vars
	)

Create a tag from an XML file. Use Script Vars bariable to do any substitutions. Script Var String: "xx=yy" for xx% replacement in XML script.

References finish_creating_tag(), and read_in_and_recursively_replace_includes().

TagCOP protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml_string	(	std::string const &	xml_text,
		utility::options::OptionCollection const &	options
	)

Create a tag from an XML string. Read from Script Vars options from a local options collection.

Create a tag from an XML string. Read from a local options collection.

Referenced by generate_mover_xml_string().

TagCOP protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml_string	(	std::string const &	xml_text,
		utility::vector1< std::string > const &	script_vars
	)

Create a tag from an XML string. Use Script Vars bariable to do any substitutions. Script Var String: "xx=yy" for xx% replacement in XML script.

References finish_creating_tag(), and read_in_and_recursively_replace_includes().

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().

TagCOP protocols::rosetta_scripts::RosettaScriptsParser::finish_creating_tag ( std::string const &  xml_fname, utility::vector1< std::string > const &  script_vars, std::string const &  substituted_contents  ) const

private

To be called after the full xml tree has been loaded into a string from create_tag_from_xml*.

xml_fname only used for tracer output.

References substitute_variables_in_stream(), protocols::rosetta_scripts::TR(), and validate_input_script_against_xsd().

Referenced by create_tag_from_xml(), and create_tag_from_xml_string().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	std::string const &	xml_fname,
		std::string const &	current_input_name = "",
		std::string const &	current_output_name = ""
	)

Convenience function to construct a ParsedProtocol from a file.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

References create_tag_from_xml(), and generate_mover_for_protocol().

Referenced by protocols::rosetta_scripts::XmlObjects::create_from_file(), generate_mover(), protocols::jd2::VectorPoseJobDistributor::go_serial(), and protocols::rpc::JSON_RPC::run().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	std::string const &	xml_fname,
		utility::vector1< std::string > const &	script_vars,
		std::string const &	current_input_name = "",
		std::string const &	current_output_name = ""
	)

Convenience function to construct a ParsedProtocol from a file.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

References create_tag_from_xml(), and generate_mover_for_protocol().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	utility::options::OptionCollection const &	options,
		std::string const &	current_input_name,
		std::string const &	current_output_name,
		basic::resource_manager::ResourceManagerOP	resource_manager
	)

Convenience function to construct a ParsedProtocol from a file.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects. Any Resources requested in the RESOURCES block will be retrieved from the ResourceManager and placed in the DataMap.

References generate_mover().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	utility::options::OptionCollection const &	options,
		std::string const &	xml_fname,
		std::string const &	current_input_name = "",
		std::string const &	current_output_name = "",
		XmlObjectsOP	xml_objects = nullptr,
		basic::resource_manager::ResourceManagerOP	resource_manager = nullptr
	)

Convenience function to construct a ParsedProtocol from a file.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

References create_tag_from_xml(), and generate_mover_for_protocol().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	utility::options::OptionCollectionCOP	options,
		std::string const &	current_input_name,
		std::string const &	current_output_name,
		basic::resource_manager::ResourceManagerOP	resource_manager
	)

Convenience function to construct a ParsedProtocol from a file.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects. Any Resources requested in the RESOURCES block will be retrieved from the ResourceManager and placed in the DataMap.

Places an OptionCollectionCOP into the datamap for local option parsing.

References generate_mover(), and local_options_.

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	utility::options::OptionCollectionCOP	options,
		std::string const &	xml_fname,
		std::string const &	current_input_name = "",
		std::string const &	current_output_name = "",
		XmlObjectsOP	xml_objects = nullptr,
		basic::resource_manager::ResourceManagerOP	resource_manager = nullptr
	)

Convenience function to construct a ParsedProtocol from a file.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

Places an OptionCollectionCOP into the datamap for local option parsing.

References generate_mover(), and local_options_.

void protocols::rosetta_scripts::RosettaScriptsParser::generate_mover	(	moves::MoverOP &	in_mover,
		bool	new_input,
		std::string const &	xml_fname,
		std::string const &	current_input_name = "",
		std::string const &	current_output_name = "",
		bool	guarantee_new_mover = false
	)

Original, JD2-compatible mover generating function.

NOT accessible in PyRosetta. For general use and PyRosetta, use mover-returning generate_mover() functions. READS FROM GLOBAL OPTIONS.

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.

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 – DEPRECATED/Removed. This section used to allow for applying certain movers to the pose prior to protocol start. This functionality has been removed. Anything other than an empty APPLY_TO_POSE section will raise an error.

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.

xi:include statements can be placed anywhere to trigger read-in of another RosettaScripts XML file. Contents of the file replace the xi:include statement.

References create_tag_from_xml(), generate_mover_for_protocol(), and protocols::rosetta_scripts::TR().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol	(	utility::tag::TagCOP	protocol_tag,
		utility::options::OptionCollection const &	options,
		std::string const &	current_input_name = "",
		std::string const &	current_output_name = "",
		XmlObjectsOP	xml_objects = nullptr,
		basic::resource_manager::ResourceManagerOP	resource_manager = nullptr
	)

Create the ParsedProtocolMover for the protocol using a tag.

Load the datamap with the predefined object, then go through tags, generating object and the ParsedProtocol Mover. READS from LOCAL OptionCollection.

References protocols::jd2::current_output_name(), and initialize_data_map().

Referenced by generate_mover(), generate_mover_for_protocol(), generate_mover_xml_string(), and parse_protocol_tag().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol	(	utility::tag::TagCOP	protocol_tag,
		basic::datacache::DataMap &	data,
		utility::options::OptionCollection const &	options,
		XmlObjectsOP	xml_objects = nullptr,
		basic::resource_manager::ResourceManagerOP	resource_manager = nullptr
	)

Create the ParsedProtocolMover for the protocol using a tag.

Uses the passed DataMap for passing to parse_my_tag. This function does the heavy lifting.

Does not add any predefined objects to the data map (though in-tag defined objects will be added.)

References instantiate_filter(), instantiate_mover(), native_pose_, parse_apply_to_pose_tag(), parse_import_tag(), parse_resources_tag(), core::scoring::parse_score_function(), and protocols::rosetta_scripts::TR().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol ( core::pose::Pose &  , bool &  , utility::tag::TagCOP  protocol_tag, utility::options::OptionCollection const &  options, std::string const &  current_input_name = "", std::string const &  current_output_name = "", XmlObjectsOP  xml_objects = nullptr, basic::resource_manager::ResourceManagerOP  resource_manager = nullptr  )

inline

Create the ParsedProtocolMover for the protocol using a tag.

This interface is preserved for (PyRosetta) backwards compatibility only. The Pose and bool (modified_pose) parameters are now unused.

References protocols::jd2::current_output_name(), and generate_mover_for_protocol().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_xml_string	(	utility::options::OptionCollection const &	options,
		std::string const &	xml_text,
		std::string const &	current_input_name,
		std::string const &	current_output_name,
		XmlObjectsOP	xml_objects
	)

Convenience function to construct a ParsedProtocol from a string.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

References create_tag_from_xml_string(), and generate_mover_for_protocol().

Referenced by protocols::rosetta_scripts::XmlObjects::create_from_string(), and generate_mover_xml_string().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_xml_string	(	utility::options::OptionCollectionCOP	options,
		std::string const &	xml_text,
		std::string const &	current_input_name,
		std::string const &	current_output_name,
		XmlObjectsOP	xml_objects
	)

Convenience function to construct a ParsedProtocol from a string.

Reads in an RosettaScript from file, replaces script_vars if present, Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

Places an OptionCollectionCOP into the datamap for local option parsing.

References generate_mover_xml_string(), and local_options_.

bool protocols::rosetta_scripts::RosettaScriptsParser::has_double_percent_signs ( std::string const &  str, core::Size const  endpos  ) const

private

Is the current tag one with something that will be replaced by variable replacement?

Starting from endpos, crawl backward until we hit a '<' or ''. Return 'false' if the former is preceded by a percent sign and 'true' if we hit the latter.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Starting from endpos, crawl backward until we hit a '<' or ''. Return 'false' if the former and 'true' if the latter.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

bool protocols::rosetta_scripts::RosettaScriptsParser::has_slash_at_end ( std::string const &  str, core::Size const  endpos  ) const

private

Is the current tag one with a slash at the end?

Starting from endpos, crawl backward until we hit a '/' or a non-whitespace character. Return true if and only if it's a slash, false otherwise.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

void protocols::rosetta_scripts::RosettaScriptsParser::import_tags	(	std::set< ImportTagName > &	import_tag_names,
		utility::tag::TagCOP	my_tag,
		basic::datacache::DataMap &	data
	)		const

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_packer_palette(), instantiate_taskoperation(), and protocols::rosetta_scripts::TR().

Referenced by parse_import_tag().

void protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map	(	basic::datacache::DataMap &	data,
		utility::options::OptionCollection const &	options
	)

Initialize the passed datamap with the standard set of pre-defined RosettaScripts objects.

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::DOCK_PATCH, core::scoring::get_score_function(), load_native(), local_options_, native_pose_, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, core::scoring::REF_2015, core::scoring::SCORE12_PATCH, core::scoring::SOFT_REP_DESIGN_WTS, core::scoring::TALARIS_2013, and core::scoring::TALARIS_2014.

Referenced by generate_mover_for_protocol().

void protocols::rosetta_scripts::RosettaScriptsParser::instantiate_filter	(	utility::tag::TagCOP const &	tag_ptr,
		basic::datacache::DataMap &	data
	)		const

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

References protocols::rosetta_scripts::TR().

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
	)		const

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

References protocols::rosetta_scripts::TR().

Referenced by generate_mover_for_protocol(), and import_tags().

void protocols::rosetta_scripts::RosettaScriptsParser::instantiate_packer_palette	(	utility::tag::TagCOP const &	tag_ptr,
		basic::datacache::DataMap &	data
	)		const

Instantiate a PackerPalette object.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References protocols::rosetta_scripts::TR().

Referenced by import_tags().

void protocols::rosetta_scripts::RosettaScriptsParser::instantiate_taskoperation	(	utility::tag::TagCOP const &	tag_ptr,
		basic::datacache::DataMap &	data
	)		const

Instantiate a new task operation (used in IMPORT tag)

References protocols::rosetta_scripts::TR().

Referenced by import_tags().

void protocols::rosetta_scripts::RosettaScriptsParser::list_options_read ( utility::options::OptionKeyList &  read_options )

static

List the command-line options used by this class.

References core::scoring::list_read_options_in_get_score_function().

Referenced by protocols::rosetta_scripts::RosettaScriptsJobQueen::RosettaScriptsJobQueen().

void protocols::rosetta_scripts::RosettaScriptsParser::load_native ( std::string const &  fname )

private

Load a native into this class, which will be placed into the datamap as a resource upon generating mover(s).

References native_pose_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::rosetta_scripts::TR().

Referenced by initialize_data_map().

void protocols::rosetta_scripts::RosettaScriptsParser::parse_apply_to_pose_tag	(	utility::tag::TagCOP	apply_tag,
		basic::datacache::DataMap &	data
	)		const

References protocols::rosetta_scripts::TR().

Referenced by generate_mover_for_protocol().

void protocols::rosetta_scripts::RosettaScriptsParser::parse_import_tag	(	utility::tag::TagCOP	import_tag,
		basic::datacache::DataMap &	data
	)		const

References import_tags().

Referenced by generate_mover_for_protocol().

ParsedProtocolOP protocols::rosetta_scripts::RosettaScriptsParser::parse_protocol_tag	(	utility::tag::TagCOP	protocol_tag,
		utility::options::OptionCollection const &	options
	)

Create the ParsedProtocolMover for the protocol using a tag.

Creates mover via standard parsing machinery

References generate_mover_for_protocol().

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

void protocols::rosetta_scripts::RosettaScriptsParser::parse_resources_tag	(	utility::tag::TagCOP	resources_tag,
		basic::datacache::DataMap &	data,
		basic::resource_manager::ResourceManagerOP	resource_manager
	)		const

References protocols::rosetta_scripts::TR().

Referenced by generate_mover_for_protocol().

bool protocols::rosetta_scripts::RosettaScriptsParser::protocol_option_set

(

utility::options::OptionCollection const &

options

)

const

Checks the LOCAL options collection to see if a protocol has been set.

void protocols::rosetta_scripts::RosettaScriptsParser::read_in_and_recursively_replace_includes	(	std::string const &	filename,
		std::string &	substituted_contents,
		utility::vector1< std::string >	filenames_encountered,
		core::Size const	recursion_level,
		bool const	do_not_recurse = false,
		std::string const &	xml_text_for_top_level = ""
	)		const

Actually read in the XML file. Called recursively to read in XML files that this XML file includes. At the end of this operation, substituted_contents contains the contents of the XML file, with all xi:includes replaced with the contents of included XML files. Files are opened and closed here.

Note that filenames_encountered is passed by copy rather than by reference DELIBERATELY. This is so that it remains a list of parent files, so that only circular dependencies (attempts to include one's own parent, grandparent, etc.) are detected. If xml_text_for_top_level is set the filename passed will not be read and instead xml_text_for_top_level will be used as though it was the contents of the first file.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)

References recursion_limit_, and protocols::rosetta_scripts::TR().

Referenced by create_tag_from_xml(), and create_tag_from_xml_string().

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

static

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 protocols::multistage_rosetta_scripts::MRSJobQueen::MRSJobQueen(), and RosettaScriptsParser().

std::string protocols::rosetta_scripts::RosettaScriptsParser::rosetta_scripts_complex_type_naming_func ( std::string const &  element_name )

static

Referenced by protocols::rosetta_scripts::MultipleOutputWrapper::provide_xml_schema(), protocols::rosetta_scripts::MultiplePoseMover::provide_xml_schema(), write_ROSETTASCRIPTS_complex_type(), and xsd_for_rosetta_scripts().

std::string protocols::rosetta_scripts::RosettaScriptsParser::rosetta_scripts_element_name ( )

static

Referenced by protocols::rosetta_scripts::MultipleOutputWrapper::provide_xml_schema(), protocols::rosetta_scripts::MultiplePoseMover::provide_xml_schema(), write_ROSETTASCRIPTS_complex_type(), and xsd_for_rosetta_scripts().

void protocols::rosetta_scripts::RosettaScriptsParser::set_recursion_limit

(

utility::options::OptionCollection const &

options

)

References recursion_limit_.

Referenced by RosettaScriptsParser().

void protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream ( std::istream &  instream, utility::vector1< std::string > const &  script_vars, std::stringstream &  out  )

static

Substitute xx==yy using the XML syntax %xx%%. / script_vars is a list of strings of "xx==yy".

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 core::sequence::end, and protocols::rosetta_scripts::TR().

Referenced by finish_creating_tag(), and protocols::jd3::standard::perform_variable_substitution().

void protocols::rosetta_scripts::RosettaScriptsParser::validate_input_script_against_xsd	(	std::string const &	fname,
		std::stringstream const &	input_xml
	)		const

References protocols::rosetta_scripts::TR(), validator_, and xsd_for_rosetta_scripts().

Referenced by finish_creating_tag().

void protocols::rosetta_scripts::RosettaScriptsParser::write_ROSETTASCRIPTS_complex_type ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::scoring::attributes_for_parse_score_function(), protocols::moves::complex_type_name_for_mover(), protocols::parser::DataLoaderFactory::data_loader_ct_namer(), protocols::filters::FilterFactory::filter_xml_schema_group_name(), protocols::rosetta_scripts::ParsedProtocol::mover_name(), protocols::moves::MoverFactory::mover_xml_schema_group_name(), rosetta_scripts_complex_type_naming_func(), and rosetta_scripts_element_name().

Referenced by protocols::rosetta_scripts::MultipleOutputWrapper::provide_xml_schema(), protocols::rosetta_scripts::MultiplePoseMover::provide_xml_schema(), and xsd_for_rosetta_scripts().

std::string protocols::rosetta_scripts::RosettaScriptsParser::xsd_for_rosetta_scripts ( )

static

References rosetta_scripts_complex_type_naming_func(), rosetta_scripts_element_name(), protocols::rosetta_scripts::TR(), and write_ROSETTASCRIPTS_complex_type().

Referenced by protocols::rosetta_scripts::save_schema(), and validate_input_script_against_xsd().

Member Data Documentation

utility::options::OptionCollectionCOP protocols::rosetta_scripts::RosettaScriptsParser::local_options_ = nullptr

private

Referenced by generate_mover(), generate_mover_xml_string(), and initialize_data_map().

core::pose::PoseOP protocols::rosetta_scripts::RosettaScriptsParser::native_pose_ = nullptr

private

Referenced by generate_mover_for_protocol(), initialize_data_map(), and load_native().

core::Size protocols::rosetta_scripts::RosettaScriptsParser::recursion_limit_

private

The depth of the rabbit hole one can find oneself in by including XML files that include XML files. Defaults to 8.

Referenced by read_in_and_recursively_replace_includes(), and set_recursion_limit().

utility::tag::XMLSchemaValidatorOP protocols::rosetta_scripts::RosettaScriptsParser::validator_

private

The object used to validate XML input files against the schema.

Referenced by validate_input_script_against_xsd().

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

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