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Rosetta
2021.16
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Rosetta
2021.16
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#include <WorkUnit_Loop.hh>
Public Member Functions | |
| WorkUnit_PartialAbinitio (core::Size const nsteps=0, bool const reconstruct=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_res1 (core::Size const setting) |
| void | set_res2 (core::Size const setting) |
| void | set_reconstruct (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::SilentStructStore & | decoys () const |
| Accessor for decoy store. More... | |
| protocols::wum::SilentStructStore & | decoys () |
| 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_res1 () const |
| core::Size | get_res2 () const |
| core::Size | get_reconstruct () 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 Member Functions | |
| core::scoring::ScoreFunctionOP | setup_score (std::string sfxn_name) const |
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... | |
| protocols::mpi_refinement::WorkUnit_PartialAbinitio::WorkUnit_PartialAbinitio | ( | core::Size const | nsteps = 0, |
| bool const | reconstruct = false |
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Reimplemented from protocols::wum::WorkUnitBase.
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Run the workunit - overloaded by children of this class.
Implements protocols::mpi_refinement::WorkUnit_Sampler.
References protocols::moves::accept_reject, core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::moves::RepeatMover::apply(), core::scoring::cart_bonded, core::chemical::CENTROID, protocols::wum::SilentStructStore::clear(), protocols::mpi_refinement::constrain_residue(), protocols::mpi_refinement::copy_pose_crd(), protocols::wum::WorkUnit_SilentStructStore::decoys(), core::pose::Pose::energies(), core::chemical::FA_STANDARD, protocols::mpi_refinement::WorkUnit_Sampler::get_energy(), protocols::wum::SilentStructStore::get_pose(), protocols::wum::SilentStructStore::get_struct(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::scoring::linear_chainbreak, protocols::mpi_refinement::loopstring_to_loopregions(), protocols::mpi_refinement::loopstring_to_loopvector(), core::scoring::overlap_chainbreak, protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), core::fragment::FragmentIO::read_data(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::abinitio::abscript::setup_score(), protocols::wum::SilentStructStore::size(), core::pose::Pose::size(), protocols::mpi_refinement::WorkUnit_Sampler::store_to_decoys(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), core::scoring::Energies::total_energies(), and protocols::mpi_refinement::TR().
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References core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::env, core::scoring::hs_pair, core::scoring::linear_chainbreak, core::scoring::pair, core::scoring::rama, core::scoring::rsigma, core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights(), core::scoring::sheet, core::scoring::ss_pair, and core::scoring::vdw.
1.8.7