Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::mpi_refinement::WorkUnit_FragInsert Class Reference

#include <WorkUnit_Loop.hh>

Inheritance diagram for protocols::mpi_refinement::WorkUnit_FragInsert:
Inheritance graph

Public Member Functions

 WorkUnit_FragInsert (core::Size const nsteps=0, core::Size const scoretype=0, core::Size const res1=0, core::Size const res2=0, bool const fullatom=false)
protocols::wum::WorkUnitBaseOP clone () const override
void run () override
 Run the workunit - overloaded by children of this class. More...
void set_nsteps (core::Size const setting)
void set_scoretype (core::Size const setting)
void set_res1 (core::Size const setting)
void set_res2 (core::Size const setting)
- Public Member Functions inherited from protocols::mpi_refinement::WorkUnit_Sampler
 WorkUnit_Sampler ()
virtual void init_from_cmd (const core::Size mpi_rank)
- Public Member Functions inherited from protocols::wum::WorkUnit_SilentStructStore
 WorkUnit_SilentStructStore ()
 ~WorkUnit_SilentStructStore () override=default
protocols::wum::WorkUnitBaseOP clone () const override
void run () override
 This Work unit doesnt do anything - its just keeps the structures. More...
void serialize () override
 write decoys into serial data store overwritinge whatever was there before. It basically syncs the silent struct store with the derial data More...
void deserialize () override
 Make ready for working. More...
const protocols::wum::SilentStructStoredecoys () const
 Accessor for decoy store. More...
protocols::wum::SilentStructStoredecoys ()
 Accessor for decoy store. More...
- Public Member Functions inherited from protocols::wum::WorkUnitBase
 WorkUnitBase ()
 ~WorkUnitBase () override=default
virtual void clear_serial_data ()
 Remove all data, make sure that the memory is also cleared, hence the cals to reserve. More...
void print (std::ostream &out, bool verbose=false) const
 Print header information to the stream, single line by default or verbose if verbose is set to true. More...
core::Size id ()
 Accessor to the ID of the WorkUnit. More...
core::Size extra_data_1 ()
 Accessor to the extra_data_1 and 3 field of the header. More...
core::Size extra_data_2 ()
core::Size extra_data_3 ()
void set_extra_data_1 (core::Size const value)
void set_extra_data_2 (core::Size const value)
void set_extra_data_3 (core::Size const value)
void add_blacklist (int mpi_rank)
 Adds to the blacklist. More...
void clear_blacklist ()
 Erases the blacklist. More...
bool in_blacklist (int mpi_rank)
 Finds in blacklist, true if is, false if it isn't. More...
void set_options (const std::string &text)
 Accesor to the "options" text field. More...
core::Size get_run_time ()
 Returns the differrence between unix start and stop times. More...
std::string get_wu_type () const
 Accessor to header structure, return the WorkUnit Type. More...
void set_wu_type (const std::string &text)
 Accessor to header structure, sets the WorkUnit Type. More...
std::string get_options () const
 Optain the options string from the header. More...
virtual core::Size mem_footprint () const
 Return the memory usage of this WorkUnit. More...
core::Size last_received_from ()

Protected Member Functions

core::Size get_nsteps () const
core::Size get_scoretype () const
core::Size get_res1 () const
core::Size get_res2 () const
void set_defaults ()
- Protected Member Functions inherited from protocols::mpi_refinement::WorkUnit_Sampler
core::kinematics::MoveMapOP get_movemap (core::pose::Pose const &pose, std::string const &mode, bool const nonideal) const
void store_to_decoys (core::io::silent::SilentStructCOP start_struct, core::pose::Pose const &pose, std::string const &additional_tag="")
void store_to_decoys (core::io::silent::SilentStructCOP start_struct, core::io::silent::SilentStructOP ss, std::string const &additional_tag="")
void repack (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn)
void ramp_minpack_loop2 (core::pose::Pose &pose, utility::vector1< core::Size > const &loopres, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal=true, bool const ramp=true, bool const efficient=false, core::Real dist_cut=0.0)
void superimpose_to_ref (core::pose::Pose const &pose_ref, core::pose::Pose &pose_work, utility::vector1< core::Size > exclude_res=utility::vector1< core::Size >(0)) const
core::scoring::ScoreFunctionOP get_energy (std::string const &sfxn_name, bool const softpack=false, core::Real const weight_coord_cst=0.0) const
void revert_facts_params () const
- Protected Member Functions inherited from protocols::wum::WorkUnitBase
void create_unique_id ()
 Make a unique number out of Processor Number and unix timestamp ? More...
std::string & serial_data ()
 Accessor to the serial data field. More...
const std::string & serial_data () const
 Accessor to the serial data field. More...
void set_run_start ()
 Set the unixtime of the start of the execution of this WorkUnit. More...
void set_run_stop ()
 Set the unixtime of the stop of the execution of this WorkUnit. More...

Private Attributes

bool fullatom_

Additional Inherited Members

- Protected Attributes inherited from protocols::wum::WorkUnitBase
WU_Header header
 The header data. More...
core::Size last_received_from_
 Contains the serial number of whatever Rank/Node this WU was last receeived from. More...
std::vector< int > blacklist_
 Contains blacklist of nodes. This data is NOT sent, and is only used on the sending side to determine where not to send a workunit. More...

Constructor & Destructor Documentation

◆ WorkUnit_FragInsert()

protocols::mpi_refinement::WorkUnit_FragInsert::WorkUnit_FragInsert ( core::Size const  nsteps = 0,
core::Size const  scoretype = 0,
core::Size const  res1 = 0,
core::Size const  res2 = 0,
bool const  fullatom = false 

Member Function Documentation

◆ clone()

protocols::wum::WorkUnitBaseOP protocols::mpi_refinement::WorkUnit_FragInsert::clone ( ) const

Reimplemented from protocols::wum::WorkUnitBase.

◆ get_nsteps()

core::Size protocols::mpi_refinement::WorkUnit_FragInsert::get_nsteps ( ) const

◆ get_res1()

core::Size protocols::mpi_refinement::WorkUnit_FragInsert::get_res1 ( ) const

◆ get_res2()

core::Size protocols::mpi_refinement::WorkUnit_FragInsert::get_res2 ( ) const

◆ get_scoretype()

core::Size protocols::mpi_refinement::WorkUnit_FragInsert::get_scoretype ( ) const

◆ run()

void protocols::mpi_refinement::WorkUnit_FragInsert::run ( )

Run the workunit - overloaded by children of this class.

Implements protocols::mpi_refinement::WorkUnit_Sampler.

References protocols::hybridization::CartesianSampler::apply(), protocols::wum::SilentStructStore::clear(), protocols::wum::WorkUnit_SilentStructStore::decoys(), core::chemical::FA_STANDARD, protocols::mpi_refinement::WorkUnit_Sampler::get_energy(), protocols::wum::SilentStructStore::get_pose(), protocols::wum::SilentStructStore::get_struct(), core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), core::pose::Pose::residue_type(), protocols::hybridization::CartesianSampler::set_bbmove(), protocols::hybridization::CartesianSampler::set_fa_scorefunction(), protocols::hybridization::CartesianSampler::set_frag_sizes(), protocols::hybridization::CartesianSampler::set_fullatom(), protocols::hybridization::CartesianSampler::set_mc_scorefunction(), protocols::hybridization::CartesianSampler::set_ncycles(), protocols::hybridization::CartesianSampler::set_nfrags(), protocols::hybridization::CartesianSampler::set_nminsteps(), protocols::hybridization::CartesianSampler::set_restore_csts(), protocols::hybridization::CartesianSampler::set_rms_cutoff(), protocols::hybridization::CartesianSampler::set_scorefunction(), protocols::hybridization::CartesianSampler::set_strategy(), protocols::hybridization::CartesianSampler::set_temp(), protocols::hybridization::CartesianSampler::set_userpos(), core::pose::Pose::set_xyz(), protocols::wum::SilentStructStore::size(), core::pose::Pose::size(), protocols::mpi_refinement::WorkUnit_Sampler::store_to_decoys(), protocols::mpi_refinement::TR(), and core::pose::Pose::xyz().

◆ set_defaults()

void protocols::mpi_refinement::WorkUnit_FragInsert::set_defaults ( )

◆ set_nsteps()

void protocols::mpi_refinement::WorkUnit_FragInsert::set_nsteps ( core::Size const  setting)

◆ set_res1()

void protocols::mpi_refinement::WorkUnit_FragInsert::set_res1 ( core::Size const  setting)

◆ set_res2()

void protocols::mpi_refinement::WorkUnit_FragInsert::set_res2 ( core::Size const  setting)

◆ set_scoretype()

void protocols::mpi_refinement::WorkUnit_FragInsert::set_scoretype ( core::Size const  setting)

Member Data Documentation

◆ fullatom_

bool protocols::mpi_refinement::WorkUnit_FragInsert::fullatom_

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