Rosetta 3.4
Public Member Functions
protocols::anchored_design::AnchoredDesignMover Class Reference

#include <AnchorMovers.hh>

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List of all members.

Public Member Functions

 AnchoredDesignMover (protocols::anchored_design::AnchorMoversDataOP interface_in)
 constructor with arguments
 AnchoredDesignMover ()
 ctor with no arguments
 AnchoredDesignMover (AnchoredDesignMover const &rhs)
 copy ctor
AnchoredDesignMoveroperator= (AnchoredDesignMover const &rhs)
 assignment operator
virtual ~AnchoredDesignMover ()
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual bool reinitialize_for_new_input () const
virtual bool reinitialize_for_each_job () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.
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).
void set_fold_tree_and_cutpoints (core::pose::Pose &pose)
 creates the anchored design fold tree and applies it to the pose
void filter (core::pose::Pose &pose)
 runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed
void forget_initial_loops (core::pose::Pose &pose)
 implements the "extended" field of the loop file specification - sets extended phi/psi as needed
void calculate_rmsd (core::pose::Pose const &pose, core::pose::PoseCOP start_pose)
 calculate RMSD if desired; protected internally
void delete_interface_native_sidechains (core::pose::Pose &pose) const
 This function repacks the interface with use_input_sc forcibly off for benchmarking purposes.
void perturb_anchor (core::pose::Pose &pose) const
 handles perturbing the initial anchor placement
bool get_rmsd () const
 run RMSD calculations
std::string const & get_RMSD_only_this () const
 run only RMSD calculations against this input, don't do actual AnchoredDesign
bool get_delete_interface_native_sidechains () const
 delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
bool get_show_extended () const
 show_extended demonstrates that the code really forgets the input structure
bool get_vary_cutpoints () const
 pick a different cutpoint than the input; useful when you want to sample cutpoints
bool get_refine_only () const
 skip the perturbation step - useful when you already have a good structure
core::Real get_filter_score () const
 filter based on total complex score
core::Real get_filter_SASA () const
 filter based on complex SASA
bool get_filter_omega () const
 filter based on omega angles in the loops - filter out cis omegas
bool get_autoinitialize () const
 whether to automatically initialize from the options system; defaults to true
void set_rmsd (bool const rmsd)
 run RMSD calculations
void set_RMSD_only_this (std::string const &RMSD_only_this)
 run only RMSD calculations against this input, don't do actual AnchoredDesign
void set_delete_interface_native_sidechains (bool const delete_interface_native_sidechains)
 delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
void set_show_extended (bool const show_extended)
 show_extended demonstrates that the code really forsets the input structure
void set_vary_cutpoints (bool const vary_cutpoints)
 pick a different cutpoint than the input; useful when you want to sample cutpoints
void set_refine_only (bool const refine_only)
 skip the perturbation step - useful when you already have a good structure
void set_filter_score (core::Real const filter_score)
 filter based on total complex score
void set_filter_SASA (core::Real const filter_SASA)
 filter based on complex SASA
void set_filter_omega (bool const filter_omega)
 filter based on omega angles in the loops - filter out cis omegas
void set_autoinitialize (bool const autoinitialize)
 whether to automatically initialize from the options system; defaults to true
void read_options ()
 read in options from the options system

Constructor & Destructor Documentation

protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover ( protocols::anchored_design::AnchorMoversDataOP  interface_in)

constructor with arguments

References protocols::moves::Mover::type().

protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover ( )

ctor with no arguments

References protocols::moves::Mover::type().

Referenced by clone(), and fresh_instance().

protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover ( AnchoredDesignMover const &  rhs)

copy ctor

protocols::anchored_design::AnchoredDesignMover::~AnchoredDesignMover ( ) [virtual]

Member Function Documentation

void protocols::anchored_design::AnchoredDesignMover::apply ( core::pose::Pose pose) [virtual]
void protocols::anchored_design::AnchoredDesignMover::calculate_rmsd ( core::pose::Pose const &  pose,
core::pose::PoseCOP  start_pose 
)
protocols::moves::MoverOP protocols::anchored_design::AnchoredDesignMover::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 AnchoredDesignMover().

void protocols::anchored_design::AnchoredDesignMover::delete_interface_native_sidechains ( core::pose::Pose pose) const

This function repacks the interface with use_input_sc forcibly off for benchmarking purposes.

For benchmarking, it is a minor sin to allow native sidechains to leak through from the starting structure. AnchoredDesign runs best with use_input_sc because it does sidechain minimization, not because it needs starting sidechains. This function deletes the native sidechains by repacking the interface with use_input_sc forcibly off. DO NOT USE THIS FUNCTION for proper designs - it is meant for a specific benchmarking purpose.

References core::sequence::end, core::pack::task::EX_ONE_STDDEV, protocols::simple_moves::PackRotamersMover::task_factory(), and core::pose::Pose::total_residue().

Referenced by apply(), read_options(), and set_delete_interface_native_sidechains().

void protocols::anchored_design::AnchoredDesignMover::filter ( core::pose::Pose pose)
void protocols::anchored_design::AnchoredDesignMover::forget_initial_loops ( core::pose::Pose pose)

implements the "extended" field of the loop file specification - sets extended phi/psi as needed

implements the is_extended boolean for the Loop class. If the boolean is on, this function resets phi/psi for those regions to be extended (-150phi, 150psi). This function does not affect omega, or residues outside of defined loops, or the anchor.

References protocols::nonlocal::current_job(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

protocols::moves::MoverOP protocols::anchored_design::AnchoredDesignMover::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 AnchoredDesignMover().

bool protocols::anchored_design::AnchoredDesignMover::get_autoinitialize ( ) const

whether to automatically initialize from the options system; defaults to true

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_delete_interface_native_sidechains ( ) const

delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_filter_omega ( ) const

filter based on omega angles in the loops - filter out cis omegas

Referenced by operator=().

core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_SASA ( ) const

filter based on complex SASA

Referenced by operator=().

core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_score ( ) const

filter based on total complex score

Referenced by operator=().

std::string protocols::anchored_design::AnchoredDesignMover::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

bool protocols::anchored_design::AnchoredDesignMover::get_refine_only ( ) const

skip the perturbation step - useful when you already have a good structure

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_rmsd ( ) const

run RMSD calculations

Referenced by operator=().

std::string const & protocols::anchored_design::AnchoredDesignMover::get_RMSD_only_this ( ) const

run only RMSD calculations against this input, don't do actual AnchoredDesign

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_show_extended ( ) const

show_extended demonstrates that the code really forgets the input structure

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_vary_cutpoints ( ) const

pick a different cutpoint than the input; useful when you want to sample cutpoints

Referenced by operator=().

AnchoredDesignMover & protocols::anchored_design::AnchoredDesignMover::operator= ( AnchoredDesignMover const &  rhs)
void protocols::anchored_design::AnchoredDesignMover::perturb_anchor ( core::pose::Pose pose) const

handles perturbing the initial anchor placement

when using anchor_noise_constraints_mode, this function perturbs the initial anchor a bit. Requested test by a reviewer.

References protocols::anchored_design::ANCHOR_TARGET(), protocols::frag_picker::CA, core::pose::Pose::conformation(), core::conformation::Conformation::downstream_jump_stub(), core::pose::Pose::residue_type(), protocols::RG(), core::pose::Pose::set_jump(), T_design(), core::conformation::Conformation::upstream_jump_stub(), and core::pose::Pose::xyz().

Referenced by apply().

void protocols::anchored_design::AnchoredDesignMover::read_options ( )
bool protocols::anchored_design::AnchoredDesignMover::reinitialize_for_each_job ( ) const [virtual]

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

bool protocols::anchored_design::AnchoredDesignMover::reinitialize_for_new_input ( ) const [virtual]

generally returns true; will return false for RMSD_only_this mode

Reimplemented from protocols::moves::Mover.

References protocols::anchored_design::EMPTY_STRING().

void protocols::anchored_design::AnchoredDesignMover::set_autoinitialize ( bool const  autoinitialize)

whether to automatically initialize from the options system; defaults to true

void protocols::anchored_design::AnchoredDesignMover::set_delete_interface_native_sidechains ( bool const  delete_interface_native_sidechains)

delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

References delete_interface_native_sidechains().

void protocols::anchored_design::AnchoredDesignMover::set_filter_omega ( bool const  filter_omega)

filter based on omega angles in the loops - filter out cis omegas

void protocols::anchored_design::AnchoredDesignMover::set_filter_SASA ( core::Real const  filter_SASA)

filter based on complex SASA

void protocols::anchored_design::AnchoredDesignMover::set_filter_score ( core::Real const  filter_score)

filter based on total complex score

void protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints ( core::pose::Pose pose)
void protocols::anchored_design::AnchoredDesignMover::set_refine_only ( bool const  refine_only)

skip the perturbation step - useful when you already have a good structure

void protocols::anchored_design::AnchoredDesignMover::set_rmsd ( bool const  rmsd)

run RMSD calculations

void protocols::anchored_design::AnchoredDesignMover::set_RMSD_only_this ( std::string const &  RMSD_only_this)

run only RMSD calculations against this input, don't do actual AnchoredDesign

void protocols::anchored_design::AnchoredDesignMover::set_show_extended ( bool const  show_extended)

show_extended demonstrates that the code really forsets the input structure

void protocols::anchored_design::AnchoredDesignMover::set_vary_cutpoints ( bool const  vary_cutpoints)

pick a different cutpoint than the input; useful when you want to sample cutpoints

pick a different cutpoint than the input { _ = ;} useful when you want to sample cutpoints


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