Rosetta 3.4
Public Member Functions
protocols::flexpep_docking::FlexPepDockingProtocol Class Reference

#include <FlexPepDockingProtocol.hh>

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List of all members.

Public Member Functions

 FlexPepDockingProtocol (Size const rb_jump_in=1)
 constructor
 FlexPepDockingProtocol (Size const rb_jump_in, bool const fullatom, bool const view=false)
 ~FlexPepDockingProtocol ()
void set_default ()
 setup that is called from constructor
void view (bool view_in)
 setter
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
virtual void apply (core::pose::Pose &pose)
 main flexible peptide docking protocol
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Constructor & Destructor Documentation

protocols::flexpep_docking::FlexPepDockingProtocol::FlexPepDockingProtocol ( Size const  rb_jump_in = 1)
protocols::flexpep_docking::FlexPepDockingProtocol::FlexPepDockingProtocol ( Size const  rb_jump_in,
bool const  fullatom,
bool const  view = false 
)
protocols::flexpep_docking::FlexPepDockingProtocol::~FlexPepDockingProtocol ( )

Member Function Documentation

void protocols::flexpep_docking::FlexPepDockingProtocol::apply ( core::pose::Pose pose) [virtual]

main flexible peptide docking protocol

FlexPepDocking apply

Detailed:
Main function for peptide docking. Includes the following steps: 1) Optional centroid mode docking, with alternating MCM cycles of rigid-body movement and peptide torsion relaxation 2) High-resolution peptide docking, with alternating MCM cycles of rigid-body movement and peptide torsion relaxation with side-chain repacking on-the-fly Prepack mode: prepare a starting structure for later runs OR: Score only mode Minimize only mode

IMPORTANT NOTE: Apply should not change the internal state of this object in a way that will affect the behaviour of subsequent apply() invocations (because, e.g., the job distributor may invoke apply() for multiple decoys, using the same mover object)

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::constraints::add_fa_constraints_from_cmdline(), protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), core::pose::Pose::conformation(), protocols::moves::Mover::get_native_pose(), core::import_pose::pose_from_pdb(), protocols::moves::Mover::set_native_pose(), and protocols::TR().

protocols::moves::MoverOP protocols::flexpep_docking::FlexPepDockingProtocol::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 FlexPepDockingProtocol().

std::string protocols::flexpep_docking::FlexPepDockingProtocol::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

void protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::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 core::import_pose::centroid_pose_from_pdb(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), protocols::rosetta_scripts::parse_score_function(), core::import_pose::pose_from_pdb(), and protocols::moves::Mover::set_native_pose().

void protocols::flexpep_docking::FlexPepDockingProtocol::set_default ( )
void protocols::flexpep_docking::FlexPepDockingProtocol::view ( bool  view_in) [inline]

setter

Referenced by FlexPepDockingProtocol(), and set_default().


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