Rosetta 3.4
Public Member Functions
protocols::contact_map::ContactMap Class Reference

#include <ContactMap.hh>

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List of all members.

Public Member Functions

 ContactMap ()
 Default constructor.
 ContactMap (ContactMap const &)
 Copy constructor.
 ~ContactMap ()
 Destructor.
virtual moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
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).
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.
virtual void apply (Pose &pose)
 Process supplied pose.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
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
void set_output_prefix (std::string prefix)
 Setter functions for private class variables.
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
void reset ()
 Resets the movers n_poses_ variable and the counts of all contacts to 0.
void write_to_file (std::string filename="")
 Output function that writes the ContactMap to the specified file.

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().

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 datamap,
protocols::filters::Filters_map const &  ,
moves::Movers_map const &  ,
Pose const &  pose 
) [virtual]

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

Reimplemented from protocols::moves::Mover.

References core::pose::Pose::n_residue(), parse_region_string(), set_distance_cutoff(), and set_output_prefix().

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.

Referenced by apply().

void protocols::contact_map::ContactMap::set_distance_cutoff ( core::Real  cutoff) [inline]

Referenced by parse_my_tag().

void protocols::contact_map::ContactMap::set_output_prefix ( std::string  prefix) [inline]

Setter functions for private class variables.

Referenced by parse_my_tag().

virtual void protocols::contact_map::ContactMap::test_move ( Pose pose) [inline, virtual]

: 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.

Referenced by apply().


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