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protocols::contact_map::ContactMap Class Reference

#include <ContactMap.hh>

Inheritance diagram for protocols::contact_map::ContactMap:
Inheritance graph
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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 &) 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 set_models_per_file (core::Size setting)
 
void set_row_format (bool setting)
 
void set_distance_matrix (bool setting)
 
void set_regions (core::select::residue_selector::ResidueSelectorCOP region1, core::select::residue_selector::ResidueSelectorCOP region2=nullptr)
 
void set_region2_all_atom (bool setting)
 
void set_reference_pose (core::pose::PoseCOP setting)
 
core::select::residue_selector::ResidueSelectorCOP parse_region_string (std::string const &) 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::select::residue_selector::ResidueSelector const &region, Pose const &pose)
 Initializes ContactMap within a single region. More...
 
void fill_contacts (core::select::residue_selector::ResidueSelector const &region1, core::select::residue_selector::ResidueSelector const &region2, Pose const &pose)
 Initializes ContactMap between two separate regions. More...
 
void fill_contacts_all_atom2 (core::select::residue_selector::ResidueSelector const &region1, core::select::residue_selector::ResidueSelector const &region2, Pose const &pose)
 Initializes ContactMap between a single region and all atoms of a ligand. 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 Stringsinfo ()
 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< Contactcontacts_
 Container for all AtomPairs included in the ContactMap. More...
 
utility::vector1< core::Sizeoutput_matrix_
 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. 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_
 
core::pose::PoseCOP reference_pose_
 
core::select::residue_selector::ResidueSelectorCOP region1_
 
core::select::residue_selector::ResidueSelectorCOP region2_
 
bool region2_all_atom_ = false
 

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 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
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::select::residue_selector::ResidueSelector const &  region,
Pose const &  pose 
)
void protocols::contact_map::ContactMap::fill_contacts ( core::select::residue_selector::ResidueSelector const &  region1,
core::select::residue_selector::ResidueSelector const &  region2,
Pose const &  pose 
)
void protocols::contact_map::ContactMap::fill_contacts_all_atom2 ( core::select::residue_selector::ResidueSelector const &  region1,
core::select::residue_selector::ResidueSelector const &  region2,
Pose const &  pose 
)
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
void protocols::contact_map::ContactMap::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
core::select::residue_selector::ResidueSelectorCOP protocols::contact_map::ContactMap::parse_region_string ( std::string const &  region_def) const

: Parses region 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')

Referenced by parse_my_tag().

void protocols::contact_map::ContactMap::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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_distance_matrix ( bool  setting)
inline

References distance_matrix_.

void protocols::contact_map::ContactMap::set_models_per_file ( core::Size  setting)
inline

References models_per_file_.

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::set_reference_pose ( core::pose::PoseCOP  setting)
inline

References reference_pose_.

void protocols::contact_map::ContactMap::set_region2_all_atom ( bool  setting)
inline

References region2_all_atom_.

void protocols::contact_map::ContactMap::set_regions ( core::select::residue_selector::ResidueSelectorCOP  region1,
core::select::residue_selector::ResidueSelectorCOP  region2 = nullptr 
)
inline

References region1_, and region2_.

void protocols::contact_map::ContactMap::set_row_format ( bool  setting)
inline

References row_format_.

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)

Member Data Documentation

utility::vector1<std::string> protocols::contact_map::ContactMap::column_names_
private
utility::vector1<Contact> protocols::contact_map::ContactMap::contacts_
private

Container for all AtomPairs included in the ContactMap.

Referenced by apply(), fill_contacts(), fill_contacts_all_atom2(), get_contact(), reset(), and write_to_stream().

core::Real protocols::contact_map::ContactMap::distance_cutoff_
private
bool protocols::contact_map::ContactMap::distance_matrix_
private
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(), parse_my_tag(), and set_models_per_file().

core::Size protocols::contact_map::ContactMap::n_poses_
private
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(), fill_contacts_all_atom2(), and get_contact().

std::string protocols::contact_map::ContactMap::output_prefix_
private
core::pose::PoseCOP protocols::contact_map::ContactMap::reference_pose_
private
core::select::residue_selector::ResidueSelectorCOP protocols::contact_map::ContactMap::region1_
private

Referenced by apply(), parse_my_tag(), and set_regions().

core::select::residue_selector::ResidueSelectorCOP protocols::contact_map::ContactMap::region2_
private

Referenced by apply(), parse_my_tag(), and set_regions().

bool protocols::contact_map::ContactMap::region2_all_atom_ = false
private
bool protocols::contact_map::ContactMap::reset_count_
private

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

Referenced by apply(), and parse_my_tag().

bool protocols::contact_map::ContactMap::row_format_
private
utility::vector1<std::string> protocols::contact_map::ContactMap::row_names_
private

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