Rosetta 3.4
Public Member Functions
protocols::ligand_docking::LigandDockProtocol Class Reference

#include <LigandDockProtocol.hh>

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List of all members.

Public Member Functions

 LigandDockProtocol ()
 LigandDockProtocol (std::string const protocol, bool const minimize_ligand, bool const minimize_backbone, bool const tether_ligand, bool const mutate_same_name3, core::Real const ligand_chi_stddev_deg, core::Real const protein_CA_stddev_Ang, core::Real const ligand_tether_stddev_Ang_=-1, core::Size const ligand_shear_moves=0)
virtual ~LigandDockProtocol ()
void add_start_from (core::Real x, core::Real y, core::Real z)
virtual void apply (core::pose::Pose &pose)
 Creates a new hierarchy of Movers for each Pose passed in.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void append_ligand_docking_scores (core::pose::Pose const &before, core::pose::Pose const &after, core::scoring::ScoreFunctionCOP scorefxn, std::map< std::string, core::Real > &scores, protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io=NULL) const
 Scores to be output that aren't normal scorefunction terms.

Constructor & Destructor Documentation

protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( )
protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( std::string const  protocol,
bool const  minimize_ligand,
bool const  minimize_backbone,
bool const  tether_ligand,
bool const  mutate_same_name3,
core::Real const  ligand_chi_stddev_deg,
core::Real const  protein_CA_stddev_Ang,
core::Real const  ligand_tether_stddev_Ang_ = -1,
core::Size const  ligand_shear_moves = 0 
)
protocols::ligand_docking::LigandDockProtocol::~LigandDockProtocol ( ) [virtual]

Member Function Documentation

void protocols::ligand_docking::LigandDockProtocol::add_start_from ( core::Real  x,
core::Real  y,
core::Real  z 
)
void protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores ( core::pose::Pose const &  before,
core::pose::Pose const &  after,
core::scoring::ScoreFunctionCOP  scorefxn,
std::map< std::string, core::Real > &  scores,
protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP  constraint_io = NULL 
) const
void protocols::ligand_docking::LigandDockProtocol::apply ( core::pose::Pose pose) [virtual]

Creates a new hierarchy of Movers for each Pose passed in.

Some Movers (e.g. repack) require knowledge of the Pose to create, and are only valid for that Pose and other conformations of it (i.e. poses with the same number of residues, jumps, etc). In general, we expect each Pose coming in here to be from a different PDB file. The cost of creating these objects anew should be minimal compared to the processing work they do.

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Reimplemented in protocols::ligand_docking::LigandDockMain.

References protocols::docking::FaDockingSlideIntoContact::apply(), protocols::ligand_docking::LigandBaseProtocol::bb_interface_cutoff_, core::pose::Pose::fold_tree(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id(), protocols::ligand_docking::LigandBaseProtocol::hard_scorefxn_, core::pack::dunbrack::load_unboundrot(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), core::pose::Pose::remove_constraint(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding_, protocols::ligand_docking::LigandBaseProtocol::scorefxn_, protocols::ligand_docking::LigandBaseProtocol::setup_bbmin_foldtree(), protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn_, and protocols::ligand_docking::LigandBaseProtocol::use_soft_rep_.

std::string protocols::ligand_docking::LigandDockProtocol::get_name ( ) const [virtual]

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

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Reimplemented in protocols::ligand_docking::LigandDockMain.


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