Rosetta 3.4
Public Member Functions
protocols::comparative_modeling::hybridize::HybridizeProtocol Class Reference

#include <HybridizeProtocol.hh>

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List of all members.

Public Member Functions

 HybridizeProtocol ()
 HybridizeProtocol (std::string template_list_file)
void init ()
void read_template_structures (utility::file::FileName template_list)
void read_template_structures (utility::vector1< utility::file::FileName > const &template_filenames)
void add_template (std::string template_fn, std::string cst_fn, core::Real weight=1., core::Size cluster_id=1, utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0))
core::Real get_gdtmm (core::pose::Pose &pose)
void pick_starting_template (core::Size &initial_template_index, core::Size &initial_template_index_icluster, utility::vector1< core::Size > &template_index_icluster, utility::vector1< core::pose::PoseOP > &templates_icluster, utility::vector1< core::Real > &weights_icluster, utility::vector1< protocols::loops::Loops > &template_chunks_icluster, utility::vector1< protocols::loops::Loops > &template_contigs_icluster)
void initialize_and_sample_loops (core::pose::Pose &pose, core::pose::PoseOP chosen_templ, protocols::loops::Loops template_contigs_icluster, core::scoring::ScoreFunctionOP scorefxn)
virtual void apply (Pose &)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
virtual protocols::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, DataMap &, Filters_map const &, Movers_map const &, Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Constructor & Destructor Documentation

protocols::comparative_modeling::hybridize::HybridizeProtocol::HybridizeProtocol ( )

References init(), and read_template_structures().

Referenced by clone(), and fresh_instance().

protocols::comparative_modeling::hybridize::HybridizeProtocol::HybridizeProtocol ( std::string  template_list_file)

Member Function Documentation

void protocols::comparative_modeling::hybridize::HybridizeProtocol::add_template ( std::string  template_fn,
std::string  cst_fn,
core::Real  weight = 1.,
core::Size  cluster_id = 1,
utility::vector1< core::Size cst_reses = utility::vector1<core::Size>(0) 
)
void protocols::comparative_modeling::hybridize::HybridizeProtocol::apply ( Pose pose) [virtual]
protocols::moves::MoverOP protocols::comparative_modeling::hybridize::HybridizeProtocol::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 HybridizeProtocol().

protocols::moves::MoverOP protocols::comparative_modeling::hybridize::HybridizeProtocol::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 HybridizeProtocol().

core::Real protocols::comparative_modeling::hybridize::HybridizeProtocol::get_gdtmm ( core::pose::Pose pose)
std::string protocols::comparative_modeling::hybridize::HybridizeProtocol::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

void protocols::comparative_modeling::hybridize::HybridizeProtocol::init ( void  )
void protocols::comparative_modeling::hybridize::HybridizeProtocol::initialize_and_sample_loops ( core::pose::Pose pose,
core::pose::PoseOP  chosen_templ,
protocols::loops::Loops  template_contigs_icluster,
core::scoring::ScoreFunctionOP  scorefxn 
)
void protocols::comparative_modeling::hybridize::HybridizeProtocol::parse_my_tag ( TagPtr const  tag,
moves::DataMap data,
filters::Filters_map const &  filters,
moves::Movers_map const &  movers,
Pose const &  pose 
) [virtual]

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References add_template(), protocols::moves::DataMap::get(), protocols::rosetta_scripts::get_resnum_list_ordered(), core::fragment::FragmentIO::read_data(), and read_template_structures().

void protocols::comparative_modeling::hybridize::HybridizeProtocol::pick_starting_template ( core::Size initial_template_index,
core::Size initial_template_index_icluster,
utility::vector1< core::Size > &  template_index_icluster,
utility::vector1< core::pose::PoseOP > &  templates_icluster,
utility::vector1< core::Real > &  weights_icluster,
utility::vector1< protocols::loops::Loops > &  template_chunks_icluster,
utility::vector1< protocols::loops::Loops > &  template_contigs_icluster 
)

References protocols::comparative_modeling::RG().

Referenced by apply().

void protocols::comparative_modeling::hybridize::HybridizeProtocol::read_template_structures ( utility::file::FileName  template_list)
void protocols::comparative_modeling::hybridize::HybridizeProtocol::read_template_structures ( utility::vector1< utility::file::FileName > const &  template_filenames)

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