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protocols::contact_map::ContactMap Class Reference

#include <ContactMap.hh>

Inheritance diagram for protocols::contact_map::ContactMap:
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Collaboration diagram for protocols::contact_map::ContactMap:
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Public Member Functions

 ContactMap ()
 Default constructor. More...
 
 ContactMap (ContactMap const &)
 Copy constructor. More...
 
 ~ContactMap ()
 Destructor. More...
 
virtual moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
virtual void parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)
 Processes options specified in xml-file and sets up the ContactMap. More...
 
virtual void apply (Pose &pose)
 Process supplied pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void test_move (Pose &pose)
 : 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...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

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...
 

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_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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.

Referenced by clone(), and fresh_instance().

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

Copy constructor.

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

Destructor.

Member Function Documentation

void protocols::contact_map::ContactMap::apply ( Pose pose)
virtual
moves::MoverOP protocols::contact_map::ContactMap::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

References ContactMap().

void protocols::contact_map::ContactMap::fill_contacts ( core::Size  region_begin,
core::Size  region_end,
Pose const &  pose 
)
private
void protocols::contact_map::ContactMap::fill_contacts ( core::Size  region_begin,
core::Size  region_end,
core::Size  seqpos_ligand,
Pose const &  pose 
)
private
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 
)
private
moves::MoverOP protocols::contact_map::ContactMap::fresh_instance ( ) const
virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

References ContactMap().

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

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

Implements protocols::moves::Mover.

References protocols::contact_map::ContactMapCreator::mover_name().

void protocols::contact_map::ContactMap::parse_my_tag ( TagPtr const  tag,
moves::DataMap ,
protocols::filters::Filters_map const &  ,
moves::Movers_map const &  ,
Pose const &  pose 
)
virtual
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::n_residue().

Referenced by parse_my_tag().

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().

virtual void protocols::contact_map::ContactMap::test_move ( Pose pose)
inlinevirtual

: 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 column_names_, contacts_, n_poses_, output_matrix_, output_prefix_, row_format_, and row_names_.

Referenced by apply().

Member Data Documentation

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

Referenced by fill_contacts(), and write_to_file().

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

Container for all AtomPairs included in the ContactMap.

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

core::Real protocols::contact_map::ContactMap::distance_cutoff_
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(), and parse_my_tag().

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

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

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 write_to_file().

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

Referenced by parse_my_tag(), and write_to_file().

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

Referenced by fill_contacts(), and write_to_file().


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