#include <HybridizeProtocol.hh>
Public Member Functions | |
| HybridizeProtocol () | |
| HybridizeProtocol (utility::vector1< core::pose::PoseOP > templates_in, utility::vector1< core::Real > template_weights_in, core::scoring::ScoreFunctionOP stage1_scorefxn_in, core::scoring::ScoreFunctionOP stage2_scorefxn_in, core::scoring::ScoreFunctionOP fa_scorefxn_in, std::string const &frag3_fn, std::string const &frag9_fn, std::string const &cen_cst_in, std::string const &fa_cst_in) | |
| void | init () |
| void | update_template (core::Size const template_idx) |
| void | add_template (std::string const &template_fn, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), bool const align_pdb_info=true) |
| void | add_null_template (core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1.) |
| void | add_template (core::pose::PoseOP template_pose, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), std::string const &filename="default", bool const align_pdb_info=true) |
| void | validate_template (std::string const &filename, std::string const &fasta, core::pose::PoseOP template_pose, bool &align_pdb_info) |
| core::Size | pick_starting_template () |
| void | do_intrastage_docking (core::pose::Pose &pose) |
| void | align_templates_by_domain (core::pose::PoseOP &ref_pose, utility::vector1< protocols::loops::Loops > domains=utility::vector1< protocols::loops::Loops >()) |
| void | align_by_domain (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< protocols::loops::Loops > domains) |
| void | domain_parse_templates (core::Size nres) |
| void | initialize_and_sample_loops (core::pose::Pose &pose, core::pose::PoseOP chosen_templ, protocols::loops::Loops template_contigs_icluster, core::scoring::ScoreFunctionOP scorefxn) |
| void | add_fragment_csts (core::pose::Pose &pose) |
| void | check_and_create_fragments (Pose &) |
| void | setup_templates_and_sampling_options (core::pose::Pose const &pose) |
| void | apply (Pose &) override |
| Main Method. More... | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | parse_my_tag (TagCOP, basic::datacache::DataMap &) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_batch_relax (core::Size newval) |
| void | add_big_fragments (core::fragment::FragSetOP newval) |
| void | add_small_fragments (core::fragment::FragSetOP newval) |
| void | set_stage1_scorefxn (core::scoring::ScoreFunctionOP newval) |
| void | set_stage2_scorefxn (core::scoring::ScoreFunctionOP newval) |
| void | set_stage2pack_scorefxn (core::scoring::ScoreFunctionOP newval) |
| void | set_stage2min_scorefxn (core::scoring::ScoreFunctionOP newval) |
| void | set_stage1_increase_cycles (core::Real newval) |
| void | set_stage2_increase_cycles (core::Real newval) |
| void | set_fullatom_scorefxn (core::scoring::ScoreFunctionOP newval) |
| void | set_add_hetatm (bool add_hetatm) |
| void | set_disulf_file (std::string const &dsf) |
| std::string const & | get_disulf_file () const |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Constructor & Destructor Documentation
◆ HybridizeProtocol() [1/2]
| protocols::hybridization::HybridizeProtocol::HybridizeProtocol | ( | ) |
References core::init::init().
◆ HybridizeProtocol() [2/2]
| protocols::hybridization::HybridizeProtocol::HybridizeProtocol | ( | utility::vector1< core::pose::PoseOP > | templates_in, |
| utility::vector1< core::Real > | template_weights_in, | ||
| core::scoring::ScoreFunctionOP | stage1_scorefxn_in, | ||
| core::scoring::ScoreFunctionOP | stage2_scorefxn_in, | ||
| core::scoring::ScoreFunctionOP | fa_scorefxn_in, | ||
| std::string const & | frag3_fn, | ||
| std::string const & | frag9_fn, | ||
| std::string const & | cen_cst_in, | ||
| std::string const & | fa_cst_in | ||
| ) |
References core::fragment::FragmentIO::read_data().
Member Function Documentation
◆ add_big_fragments()
|
inline |
References fragments_big_.
Referenced by protocols::hybridization::MRMover::apply().
◆ add_fragment_csts()
| void protocols::hybridization::HybridizeProtocol::add_fragment_csts | ( | core::pose::Pose & | pose | ) |
◆ add_null_template()
| void protocols::hybridization::HybridizeProtocol::add_null_template | ( | core::pose::PoseOP | template_pose, |
| std::string | cst_fn, | ||
| std::string | symmdef_file = "NULL", |
||
| core::Real | weight = 1. |
||
| ) |
◆ add_small_fragments()
|
inline |
References fragments_small_.
Referenced by protocols::hybridization::MRMover::apply().
◆ add_template() [1/2]
| void protocols::hybridization::HybridizeProtocol::add_template | ( | core::pose::PoseOP | template_pose, |
| std::string const & | cst_fn, | ||
| std::string const & | symmdef_file = "NULL", |
||
| core::Real const | weight = 1., |
||
| utility::vector1< char > const & | rand_chains = utility::vector1<core::Size>(0), |
||
| std::string const & | filename = "default", |
||
| bool const | align_pdb_info = true |
||
| ) |
References protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), protocols::abinitio::filename(), core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::loops::Loops::num_loop(), protocols::loops::Loops::push_back(), and protocols::hybridization::TR().
◆ add_template() [2/2]
| void protocols::hybridization::HybridizeProtocol::add_template | ( | std::string const & | template_fn, |
| std::string const & | cst_fn, | ||
| std::string const & | symmdef_file = "NULL", |
||
| core::Real const | weight = 1., |
||
| utility::vector1< char > const & | rand_chains = utility::vector1<core::Size>(0), |
||
| bool const | align_pdb_info = true |
||
| ) |
References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::hybridization::TR().
Referenced by protocols::hybridization::MRMover::apply().
◆ align_by_domain()
| void protocols::hybridization::HybridizeProtocol::align_by_domain | ( | core::pose::Pose & | pose, |
| core::pose::Pose const & | ref_pose, | ||
| utility::vector1< protocols::loops::Loops > | domains | ||
| ) |
References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::element::F, core::pose::initialize_atomid_map(), core::chemical::ResidueTypeBase::is_protein(), protocols::constraint_generator::last_protein_residue(), protocols::hybridization::partial_align(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, protocols::hybridization::TMalign::TMscore(), protocols::hybridization::TR(), and core::conformation::Residue::xyz().
◆ align_templates_by_domain()
| void protocols::hybridization::HybridizeProtocol::align_templates_by_domain | ( | core::pose::PoseOP & | ref_pose, |
| utility::vector1< protocols::loops::Loops > | domains = utility::vector1 <protocols::loops::Loops>() |
||
| ) |
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::relax::FastRelax::apply(), protocols::symmetry::SetupForSymmetryMover::apply(), core::scoring::atom_pair_constraint, protocols::relax::FastRelax::batch_apply(), core::chemical::CENTROID, core::conformation::Residue::chain(), core::conformation::Conformation::chains_from_termini(), core::conformation::change_cys_state(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::kinematics::FoldTree::cutpoints(), core::pose::Pose::data(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::sequence::end, core::chemical::element::F, core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), protocols::hybridization::get_gdtmm(), core::chemical::element::I, core::pose::initialize_disulfide_bonds(), core::chemical::ResidueType::is_disulfide_bonded(), core::pose::Pose::is_fullatom(), core::pose::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), protocols::relax::RelaxProtocolBase::min_type(), core::conformation::Residue::natoms(), protocols::loops::Loops::num_loop(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::loops::Loops::push_back(), core::chemical::rings::q, protocols::geometry::random_reorientation_matrix(), core::scoring::constraints::remove_nonbb_constraints(), core::pose::Pose::residue(), core::scoring::rg, core::optimization::CartesianMinimizer::run(), core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear(), protocols::relax::FastRelax::set_force_nonideal(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), protocols::loops::Loop::set_start(), protocols::relax::RelaxProtocolBase::set_task_factory(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScore(), protocols::hybridization::setup_centroid_constraints(), protocols::hybridization::setup_constraints(), protocols::hybridization::setup_fullatom_constraints(), protocols::hybridization::setup_user_coordinate_constraints(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, protocols::hybridization::TR(), core::conformation::Residue::type(), core::scoring::vdw, and core::conformation::Residue::xyz().
Referenced by protocols::hybridization::MRMover::apply().
◆ check_and_create_fragments()
| void protocols::hybridization::HybridizeProtocol::check_and_create_fragments | ( | Pose & | pose | ) |
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::fragment::chop_fragments(), core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), protocols::stepwise::modeler::is_protein(), core::pose::symmetry::is_symmetric(), protocols::mean_field::min(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), core::pose::read_psipred_ss2_file(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and core::pose::Pose::size().
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
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.
◆ do_intrastage_docking()
| void protocols::hybridization::HybridizeProtocol::do_intrastage_docking | ( | core::pose::Pose & | pose | ) |
◆ domain_parse_templates()
| void protocols::hybridization::HybridizeProtocol::domain_parse_templates | ( | core::Size | nres | ) |
◆ fresh_instance()
|
overridevirtual |
Generates a new Mover object freshly created with the default ctor.
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.
◆ get_disulf_file()
|
inline |
References disulf_file_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ init()
| void protocols::hybridization::HybridizeProtocol::init | ( | void | ) |
References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::get_score_function(), core::fragment::FragmentIO::read_data(), protocols::antibody::design::relax, core::scoring::rg, and protocols::hybridization::TR().
◆ initialize_and_sample_loops()
| void protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops | ( | core::pose::Pose & | pose, |
| core::pose::PoseOP | chosen_templ, | ||
| protocols::loops::Loops | template_contigs_icluster, | ||
| core::scoring::ScoreFunctionOP | scorefxn | ||
| ) |
References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::loops::add_cutpoint_variants(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::scoring::rg, protocols::loops::set_extended_torsions(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and protocols::hybridization::TR().
◆ mover_name()
|
static |
◆ parse_my_tag()
|
overridevirtual |
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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References core::scoring::coordinate_constraint, protocols::hybridization::off, protocols::hybridization::on, core::pack::task::parse_task_operations(), core::fragment::FragmentIO::read_data(), protocols::hybridization::TR(), and protocols::hybridization::unset.
◆ pick_starting_template()
| core::Size protocols::hybridization::HybridizeProtocol::pick_starting_template | ( | ) |
References core::scoring::rg.
◆ provide_citation_info()
|
overridevirtual |
Provide the citation.
Reimplemented from protocols::moves::Mover.
◆ provide_xml_schema()
|
static |
References core::pose::attributes_for_get_resnum_selector(), core::pack::task::attributes_for_parse_task_operations(), protocols::hybridization::hybridize_subelement_ct_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().
Referenced by protocols::hybridization::HybridizeProtocolCreator::provide_xml_schema().
◆ set_add_hetatm()
|
inline |
References add_hetatm_.
◆ set_batch_relax()
|
inline |
References batch_relax_.
Referenced by protocols::hybridization::MRMover::apply().
◆ set_disulf_file()
|
inline |
References disulf_file_.
◆ set_fullatom_scorefxn()
|
inline |
References fa_scorefxn_.
◆ set_stage1_increase_cycles()
|
inline |
References stage1_increase_cycles_.
Referenced by protocols::hybridization::MRMover::apply().
◆ set_stage1_scorefxn()
|
inline |
References stage1_scorefxn_.
Referenced by protocols::hybridization::MRMover::apply().
◆ set_stage2_increase_cycles()
|
inline |
References stage2_increase_cycles_.
Referenced by protocols::hybridization::MRMover::apply().
◆ set_stage2_scorefxn()
|
inline |
References stage2_scorefxn_.
Referenced by protocols::hybridization::MRMover::apply().
◆ set_stage2min_scorefxn()
|
inline |
References stage2min_scorefxn_.
◆ set_stage2pack_scorefxn()
|
inline |
References stage2pack_scorefxn_.
◆ setup_templates_and_sampling_options()
| void protocols::hybridization::HybridizeProtocol::setup_templates_and_sampling_options | ( | core::pose::Pose const & | pose | ) |
◆ update_template()
| void protocols::hybridization::HybridizeProtocol::update_template | ( | core::Size const | template_idx | ) |
◆ validate_template()
| void protocols::hybridization::HybridizeProtocol::validate_template | ( | std::string const & | filename, |
| std::string const & | fasta, | ||
| core::pose::PoseOP | template_pose, | ||
| bool & | align_pdb_info | ||
| ) |
References core::sequence::SWAligner::align(), core::pose::symmetry::extract_asymmetric_unit(), protocols::abinitio::filename(), protocols::magnesium::is_ligand(), core::id::SequenceMapping::reverse(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), and protocols::hybridization::TR().
Member Data Documentation
◆ add_hetatm_
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private |
Referenced by set_add_hetatm().
◆ add_non_init_chunks_
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private |
◆ aln_
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private |
◆ auto_frag_insertion_weight_
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private |
◆ batch_relax_
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private |
Referenced by set_batch_relax().
◆ big_frag_insertion_weight_
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private |
◆ cartfrag_overlap_
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private |
◆ cen_cst_in_
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private |
◆ cenrot_
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private |
◆ chunk_insertion_weight_
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private |
◆ coord_cst_res_
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private |
◆ csts_from_frags_
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private |
◆ detailed_controls_settings_
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private |
◆ disulf_file_
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private |
Referenced by get_disulf_file(), and set_disulf_file().
◆ domains_all_templ_
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private |
◆ fa_cst_fn_
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private |
◆ fa_cst_in_
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private |
◆ fa_scorefxn_
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private |
Referenced by set_fullatom_scorefxn().
◆ filter_templates_
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private |
◆ frag_1mer_insertion_weight_
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private |
◆ frag_weight_aligned_
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private |
◆ fragments_big_
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private |
Referenced by add_big_fragments().
◆ fragments_small_
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private |
Referenced by add_small_fragments().
◆ fragprob_stage2_
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private |
◆ hcut_
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private |
◆ hetatm_prot_cst_weight_
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private |
◆ hetatm_self_cst_weight_
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private |
◆ include_loop_ss_chunks_
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private |
◆ jump_move_
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private |
◆ jump_move_repeat_
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private |
◆ keep_pose_constraint_
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private |
◆ length_
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private |
◆ linmin_only_
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private |
◆ max_contig_insertion_
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private |
◆ max_registry_shift_
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private |
◆ min_after_stage1_
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private |
◆ native_
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private |
◆ native_needs_load_
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private |
Do we need to load the native state from disk?
Done once, lazily.
◆ native_needs_load_from_align_rmsd_target_
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private |
Do we need to load the native state from disk using the align_rmsd_target option?
◆ no_global_frame_
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private |
◆ non_null_template_indices_
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private |
◆ pairings_file_
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private |
◆ pcut_
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private |
◆ randfragprob_stage2_
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private |
◆ random_sheets_
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private |
◆ randomize_chains_
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private |
◆ realign_domains_
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private |
◆ realign_domains_stage2_
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private |
◆ relax_repeats_
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private |
◆ residue_max_registry_shift_
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private |
◆ residue_sample_abinitio_
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private |
◆ residue_sample_template_
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private |
◆ seqfrags_only_
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private |
◆ sheets_
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private |
◆ should_align_pdb_infos_
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private |
◆ skip_long_min_
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private |
◆ small_frag_insertion_weight_
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private |
◆ stage1_1_cycles_
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private |
◆ stage1_2_cycles_
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private |
◆ stage1_3_cycles_
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private |
◆ stage1_4_cycles_
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private |
◆ stage1_increase_cycles_
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private |
Referenced by set_stage1_increase_cycles().
◆ stage1_probability_
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private |
◆ stage1_scorefxn_
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private |
Referenced by set_stage1_scorefxn().
◆ stage25_increase_cycles_
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private |
◆ stage2_increase_cycles_
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private |
Referenced by set_stage2_increase_cycles().
◆ stage2_scorefxn_
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private |
Referenced by set_stage2_scorefxn().
◆ stage2_temperature_
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private |
◆ stage2min_scorefxn_
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private |
Referenced by set_stage2min_scorefxn().
◆ stage2pack_scorefxn_
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private |
Referenced by set_stage2pack_scorefxn().
◆ strand_pairs_
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private |
◆ symmdef_files_
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private |
◆ template_chunks_
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private |
◆ template_contigs_
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private |
◆ template_cst_fn_
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private |
◆ template_fns_
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private |
◆ template_weights_
|
private |
◆ templates_
|
private |
◆ templates_aln_
|
private |
◆ user_csts_
|
private |
The documentation for this class was generated from the following files:
- src/protocols/hybridization/HybridizeProtocol.hh
- src/protocols/hybridization/HybridizeProtocol.cc
