#include <ContactMap.hh>

Inheritance diagram for protocols::contact_map::ContactMap:

Public Member Functions
	ContactMap ()
	Default constructor. More...

	ContactMap (ContactMap const &)
	Copy constructor. More...

	~ContactMap () override
	Destructor. More...

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &) override
	Processes options specified in xml-file and sets up the ContactMap. More...

void	apply (Pose &pose) override
	Process supplied pose. More...

void	test_move (Pose &pose) override
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	set_output_prefix (std::string prefix)
	Setter functions for private class variables. More...

void	set_distance_cutoff (core::Real cutoff)

void	parse_region_string (std::string, core::Size &, core::Size &, Pose const &)
	: Parses region string end sets the boundaries accordingly More...

void	reset ()
	Resets the movers n_poses_ variable and the counts of all contacts to 0. More...

void	write_to_file (std::string filename="")
	Output function that writes the ContactMap to the specified file. More...

void	write_to_stream (std::ostream &output_stream)

void	fill_contacts (core::Size region_begin, core::Size region_end, Pose const &pose)
	Initializes ContactMap within a single region. More...

void	fill_contacts (core::Size region_begin, core::Size region_end, core::Size seqpos_ligand, Pose const &pose)
	Initializes ContactMap between a single region and a ligand. More...

void	fill_contacts (core::Size region1_begin, core::Size region1_end, core::Size region2_begin, core::Size region2_end, Pose const &pose)
	Initializes ContactMap between two separate regions. More...

Contact const &	get_contact (core::Size row, core::Size col)
	Get the contact for a particular row and column The identity contact (the contact of a residue with itself) is shared between all identity contacts. (The last identity contact in region.) More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Attributes
utility::vector1< Contact >	contacts_
	Container for all AtomPairs included in the ContactMap. More...

utility::vector1< core::Size >	output_matrix_
	Vector that maps the matrix position to the index of the contact in contacts_ Vector of size columnsrows with field(row, column) stored at (row-1)[#columns] + column. More...

utility::vector1< std::string >	column_names_

utility::vector1< std::string >	row_names_

std::string	output_prefix_

core::Size	n_poses_

core::Real	distance_cutoff_

core::Size	models_per_file_
	int value after how many models an output file will be generated More...

bool	reset_count_
	bool value indicating whether the reset function will be called after file output More...

bool	row_format_

bool	distance_matrix_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

protocols::contact_map::ContactMap::ContactMap ( )

Default constructor.

protocols::contact_map::ContactMap::ContactMap ( ContactMap const & )

default

Copy constructor.

protocols::contact_map::ContactMap::~ContactMap ( )

overridedefault

Destructor.

Member Function Documentation

void protocols::contact_map::ContactMap::apply ( Pose & pose )

overridevirtual

Process supplied pose.

Implements protocols::moves::Mover.

References contacts_, protocols::jd2::current_input_tag(), protocols::jd2::current_output_name(), core::kinematics::distance(), distance_cutoff_, distance_matrix_, models_per_file_, n_poses_, output_prefix_, reset(), reset_count_, core::pose::Pose::residue(), write_to_file(), and protocols::kinmatch::xyz().

Referenced by test_move().

moves::MoverOP protocols::contact_map::ContactMap::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

void protocols::contact_map::ContactMap::fill_contacts	(	core::Size	region_begin,
		core::Size	region_end,
		Pose const &	pose
	)

Initializes ContactMap within a single region.

References column_names_, contacts_, core::sequence::end, core::chemical::ResidueTypeBase::name1(), core::conformation::Residue::name3(), output_matrix_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), row_names_, and protocols::contact_map::ContactPartner::string_rep().

Referenced by parse_my_tag().

void protocols::contact_map::ContactMap::fill_contacts	(	core::Size	region_begin,
		core::Size	region_end,
		core::Size	seqpos_ligand,
		Pose const &	pose
	)

Initializes ContactMap between a single region and a ligand.

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), core::conformation::Residue::atoms(), column_names_, contacts_, core::sequence::end, core::chemical::ResidueTypeBase::name1(), core::conformation::Residue::name3(), output_matrix_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), row_names_, and protocols::contact_map::ContactPartner::string_rep().

void protocols::contact_map::ContactMap::fill_contacts	(	core::Size	region1_begin,
		core::Size	region1_end,
		core::Size	region2_begin,
		core::Size	region2_end,
		Pose const &	pose
	)

Initializes ContactMap between two separate regions.

References column_names_, contacts_, core::chemical::ResidueTypeBase::name1(), core::conformation::Residue::name3(), output_matrix_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), row_names_, and protocols::contact_map::ContactPartner::string_rep().

moves::MoverOP protocols::contact_map::ContactMap::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Contact const & protocols::contact_map::ContactMap::get_contact	(	core::Size	row,
		core::Size	col
	)

Get the contact for a particular row and column The identity contact (the contact of a residue with itself) is shared between all identity contacts. (The last identity contact in region.)

References column_names_, contacts_, and output_matrix_.

Referenced by write_to_stream().

std::string protocols::contact_map::ContactMap::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::contact_map::ContactMap::mover_name ( )

static

Referenced by get_name(), protocols::contact_map::ContactMapCreator::keyname(), and provide_xml_schema().

void protocols::contact_map::ContactMap::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	,
		protocols::filters::Filters_map const &	,
		moves::Movers_map const &	,
		Pose const &	pose
	)

overridevirtual

Processes options specified in xml-file and sets up the ContactMap.

Reimplemented from protocols::moves::Mover.

References distance_cutoff_, distance_matrix_, fill_contacts(), models_per_file_, output_prefix_, parse_region_string(), reset_count_, row_format_, set_distance_cutoff(), set_output_prefix(), and core::pose::Pose::size().

void protocols::contact_map::ContactMap::parse_region_string	(	std::string	region_def,
		core::Size &	region_begin,
		core::Size &	region_end,
		Pose const &	pose
	)

: Parses region string end sets the boundaries accordingly

Parses region definition string end sets the boundaries accordingly.

: Possible formats for the region definition are "<int seqpos>" (e.g '12'), "<int begin>-<int end>" (e.g. '1-10') or "<char chainID>"(e.g. 'A')

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::get_chain_id_from_chain(), and core::pose::Pose::size().

Referenced by parse_my_tag().

void protocols::contact_map::ContactMap::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::contact_map::ContactMapCreator::provide_xml_schema().

void protocols::contact_map::ContactMap::reset ( void )

Resets the movers n_poses_ variable and the counts of all contacts to 0.

References contacts_, and n_poses_.

Referenced by apply().

void protocols::contact_map::ContactMap::set_distance_cutoff ( core::Real cutoff )

inline

References distance_cutoff_.

Referenced by parse_my_tag().

void protocols::contact_map::ContactMap::set_output_prefix ( std::string prefix )

inline

Setter functions for private class variables.

References output_prefix_.

Referenced by parse_my_tag().

void protocols::contact_map::ContactMap::test_move ( Pose & pose )

inlineoverridevirtual

: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying

Reimplemented from protocols::moves::Mover.

References apply().

void protocols::contact_map::ContactMap::write_to_file ( std::string filename = "" )

Output function that writes the ContactMap to the specified file.

References n_poses_, core::conformation::membrane::out, output_prefix_, and write_to_stream().

Referenced by apply().

void protocols::contact_map::ContactMap::write_to_stream ( std::ostream & output_stream )

References column_names_, contacts_, distance_cutoff_, get_contact(), n_poses_, row_format_, row_names_, and protocols::contact_map::Contact::string_rep().

Referenced by write_to_file().

Member Data Documentation

utility::vector1<std::string> protocols::contact_map::ContactMap::column_names_

private

Referenced by fill_contacts(), get_contact(), and write_to_stream().

utility::vector1<Contact> protocols::contact_map::ContactMap::contacts_

private

Container for all AtomPairs included in the ContactMap.

Referenced by apply(), fill_contacts(), get_contact(), reset(), and write_to_stream().

core::Real protocols::contact_map::ContactMap::distance_cutoff_

private

Referenced by apply(), parse_my_tag(), set_distance_cutoff(), and write_to_stream().

bool protocols::contact_map::ContactMap::distance_matrix_

private

Referenced by apply(), and parse_my_tag().

core::Size protocols::contact_map::ContactMap::models_per_file_

private

int value after how many models an output file will be generated

Referenced by apply(), and parse_my_tag().

core::Size protocols::contact_map::ContactMap::n_poses_

private

Referenced by apply(), reset(), write_to_file(), and write_to_stream().

utility::vector1<core::Size> protocols::contact_map::ContactMap::output_matrix_

private

Vector that maps the matrix position to the index of the contact in contacts_ Vector of size columns*rows with field(row, column) stored at (row-1)*[#columns] + column.

Referenced by fill_contacts(), and get_contact().

std::string protocols::contact_map::ContactMap::output_prefix_

private

Referenced by apply(), parse_my_tag(), set_output_prefix(), and write_to_file().