Rosetta 3.4
Public Types | Public Member Functions
protocols::protein_interface_design::movers::DesignMinimizeHbonds Class Reference

used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined. More...

#include <DesignMinimizeHbonds.hh>

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List of all members.

Public Types

typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
typedef
core::scoring::ScoreFunction 
ScoreFunction
typedef core::pose::Pose Pose

Public Member Functions

 DesignMinimizeHbonds ()
 DesignMinimizeHbonds (ScoreFunctionCOP scorefxn_repack, ScoreFunctionCOP scorefxn_minimize, utility::vector1< core::Size > const target_residues, bool const donors, bool const acceptors, bool const bb_hbond, bool const sc_hbond, core::Real const hbond_energy_threshold, core::Real interface_distance_cutoff=8.0, bool const repack_partner1=true, bool const repack_partner2=false, bool const repack_non_ala=true)
 DesignMinimizeHbonds (ScoreFunctionOP scorefxn_repack, ScoreFunctionOP scorefxn_minimize, core::Size const target_residue, bool const donors, bool const acceptors, bool const bb_hbond, bool const sc_hbond, core::Real const hbond_energy_threshold, core::Real interface_distance_cutoff=8.0, bool const repack_partner1=true, bool const repack_partner2=false, bool const repack_non_ala=true)
virtual ~DesignMinimizeHbonds ()
void apply (Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
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).
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, 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.

Detailed Description

used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined.


Member Typedef Documentation

Reimplemented from protocols::moves::Mover.


Constructor & Destructor Documentation

protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds ( )
protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds ( ScoreFunctionCOP  scorefxn_repack,
ScoreFunctionCOP  scorefxn_minimize,
utility::vector1< core::Size > const  target_residues,
bool const  donors,
bool const  acceptors,
bool const  bb_hbond,
bool const  sc_hbond,
core::Real const  hbond_energy_threshold,
core::Real  interface_distance_cutoff = 8.0,
bool const  repack_partner1 = true,
bool const  repack_partner2 = false,
bool const  repack_non_ala = true 
)
protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds ( ScoreFunctionOP  scorefxn_repack,
ScoreFunctionOP  scorefxn_minimize,
core::Size const  target_residue,
bool const  donors,
bool const  acceptors,
bool const  bb_hbond,
bool const  sc_hbond,
core::Real const  hbond_energy_threshold,
core::Real  interface_distance_cutoff = 8.0,
bool const  repack_partner1 = true,
bool const  repack_partner2 = false,
bool const  repack_non_ala = true 
)
protocols::protein_interface_design::movers::DesignMinimizeHbonds::~DesignMinimizeHbonds ( ) [virtual]

Member Function Documentation

void protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply ( pose::Pose pose) [virtual]

Residues within a 10.0 Ang sphere around the set of target residues are designed with acceptors or donors (or both) and the design is minimized. All residues that were changed but are not hbonded to the target residues are reverted. If only backbone hbonding is desired all residues except PRO, CYS, and GLY are used in design.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, protocols::simple_moves::DesignRepackMover::allowed_aas_, protocols::simple_moves::DesignRepackMover::automatic_repacking_definition_, protocols::scoring::Interface::calculate(), protocols::simple_moves::DesignRepackMover::curr_min_bb_, protocols::simple_moves::DesignRepackMover::curr_min_rb_, protocols::simple_moves::DesignRepackMover::curr_min_sc_, core::kinematics::distance(), protocols::scoring::Interface::distance(), core::pose::Pose::fold_tree(), hbonded(), protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), MinimizeInterface(), core::chemical::ResidueType::name(), core::chemical::num_canonical_aas, protocols::simple_moves::DesignRepackMover::optimize_foldtree_, core::pack::pack_rotamers(), core::kinematics::FoldTree::partition_by_jump(), protocols::simple_moves::DesignRepackMover::repack_non_ala_, protocols::simple_moves::DesignRepackMover::repack_partner1_, protocols::simple_moves::DesignRepackMover::repack_partner2_, core::pose::Pose::residue(), protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack_, protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::DesignRepackMover::target_residues_, protocols::simple_moves::DesignRepackMover::task_, core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR(), core::conformation::Residue::type(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::DesignMinimizeHbonds::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.

Implements protocols::simple_moves::DesignRepackMover.

References DesignMinimizeHbonds().

protocols::moves::MoverOP protocols::protein_interface_design::movers::DesignMinimizeHbonds::fresh_instance ( ) const [inline, 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.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::DesignMinimizeHbonds::get_name ( ) const [virtual]

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator::mover_name().

void protocols::protein_interface_design::movers::DesignMinimizeHbonds::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::simple_moves::DesignRepackMover.

References core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack_, protocols::simple_moves::DesignRepackMover::target_residues_, and protocols::protein_interface_design::movers::TR().


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