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protocols::hybridization::HybridizeProtocol Class Reference

#include <HybridizeProtocol.hh>

Inheritance diagram for protocols::hybridization::HybridizeProtocol:
Inheritance graph
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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 frag3_fn, std::string frag9_fn, std::string &cen_cst_in, std::string &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)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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...
 

Private Attributes

core::Real stage1_probability_
 
core::Real stage1_increase_cycles_
 
core::Real stage2_increase_cycles_
 
core::Real stage25_increase_cycles_
 
core::Size stage1_1_cycles_
 
core::Size stage1_2_cycles_
 
core::Size stage1_3_cycles_
 
core::Size stage1_4_cycles_
 
core::Real stage2_temperature_
 
core::Real frag_1mer_insertion_weight_
 
core::Real small_frag_insertion_weight_
 
core::Real big_frag_insertion_weight_
 
core::Real chunk_insertion_weight_
 
core::Real frag_weight_aligned_
 
bool auto_frag_insertion_weight_
 
core::Size max_registry_shift_
 
bool add_hetatm_
 
bool realign_domains_
 
bool realign_domains_stage2_
 
bool no_global_frame_
 
bool linmin_only_
 
core::Real add_non_init_chunks_
 
bool seqfrags_only_
 
bool skip_long_min_
 
core::Real hetatm_self_cst_weight_
 
core::Real hetatm_prot_cst_weight_
 
core::scoring::ScoreFunctionOP stage1_scorefxn_
 
core::scoring::ScoreFunctionOP stage2_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
core::scoring::ScoreFunctionOP stage2pack_scorefxn_
 
core::scoring::ScoreFunctionOP stage2min_scorefxn_
 
std::string fa_cst_fn_
 
std::string fa_cst_in_
 
std::string disulf_file_
 
core::Size cartfrag_overlap_
 
bool csts_from_frags_
 
int max_contig_insertion_
 
bool min_after_stage1_
 
core::Real fragprob_stage2_
 
core::Real randfragprob_stage2_
 
bool include_loop_ss_chunks_
 
bool cenrot_
 
core::Real pcut_
 
core::Real hcut_
 
core::Size length_
 
utility::vector1
< utility::vector1
< protocols::loops::Loops > > 
domains_all_templ_
 
core::Size batch_relax_
 
core::Size relax_repeats_
 
utility::vector1
< core::fragment::FragSetOP
fragments_big_
 
utility::vector1
< core::fragment::FragSetOP
fragments_small_
 
core::pose::PoseOP native_
 
core::sequence::SequenceAlignmentOP aln_
 
utility::vector1< core::Sizenon_null_template_indices_
 
utility::vector1
< core::pose::PoseOP
templates_
 
utility::vector1
< core::pose::PoseOP
templates_aln_
 
utility::vector1< std::string > template_fns_
 
utility::vector1< std::string > template_cst_fn_
 
utility::vector1< std::string > symmdef_files_
 
utility::vector1< core::Realtemplate_weights_
 
utility::vector1< boolshould_align_pdb_infos_
 
utility::vector1
< protocols::loops::Loops
template_chunks_
 
utility::vector1
< protocols::loops::Loops
template_contigs_
 
utility::vector1
< utility::vector1< char > > 
randomize_chains_
 
utility::vector1
< detailedControlsTagSetting
detailed_controls_settings_
 
std::string cen_cst_in_
 
std::string pairings_file_
 
utility::vector1< core::Sizesheets_
 
utility::vector1< core::Sizerandom_sheets_
 
bool filter_templates_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
strand_pairs_
 
utility::vector1< boolresidue_sample_template_
 
utility::vector1< boolresidue_sample_abinitio_
 
utility::vector1< core::Sizeresidue_max_registry_shift_
 
bool jump_move_
 
core::Size jump_move_repeat_
 
bool keep_pose_constraint_
 
std::string coord_cst_res_
 
utility::vector1< core::Sizeuser_csts_
 

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

protocols::hybridization::HybridizeProtocol::HybridizeProtocol ( )

References core::init::init().

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  frag3_fn,
std::string  frag9_fn,
std::string &  cen_cst_in,
std::string &  fa_cst_in 
)

Member Function Documentation

void protocols::hybridization::HybridizeProtocol::add_big_fragments ( core::fragment::FragSetOP  newval)
inline
void protocols::hybridization::HybridizeProtocol::add_fragment_csts ( core::pose::Pose pose)
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. 
)
void protocols::hybridization::HybridizeProtocol::add_small_fragments ( core::fragment::FragSetOP  newval)
inline
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 
)
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 
)
void protocols::hybridization::HybridizeProtocol::align_by_domain ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
utility::vector1< protocols::loops::Loops domains 
)
void protocols::hybridization::HybridizeProtocol::align_templates_by_domain ( core::pose::PoseOP ref_pose,
utility::vector1< protocols::loops::Loops domains = utility::vector1 <protocols::loops::Loops>() 
)
void protocols::hybridization::HybridizeProtocol::apply ( Pose )
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::symmetry::SetupForSymmetryMover::apply(), protocols::relax::FastRelax::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::pose::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(), 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().

void protocols::hybridization::HybridizeProtocol::check_and_create_fragments ( Pose pose)
protocols::moves::MoverOP protocols::hybridization::HybridizeProtocol::clone ( ) const
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.

void protocols::hybridization::HybridizeProtocol::do_intrastage_docking ( core::pose::Pose pose)
void protocols::hybridization::HybridizeProtocol::domain_parse_templates ( core::Size  nres)
protocols::moves::MoverOP protocols::hybridization::HybridizeProtocol::fresh_instance ( ) const
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.

std::string protocols::hybridization::HybridizeProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::HybridizeProtocol::init ( void  )
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 
)
std::string protocols::hybridization::HybridizeProtocol::mover_name ( )
static
void protocols::hybridization::HybridizeProtocol::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
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.

core::Size protocols::hybridization::HybridizeProtocol::pick_starting_template ( )

References core::scoring::rg.

void protocols::hybridization::HybridizeProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::hybridization::HybridizeProtocol::set_add_hetatm ( bool  add_hetatm)
inline

References add_hetatm_.

void protocols::hybridization::HybridizeProtocol::set_batch_relax ( core::Size  newval)
inline
void protocols::hybridization::HybridizeProtocol::set_fullatom_scorefxn ( core::scoring::ScoreFunctionOP  newval)
inline

References fa_scorefxn_.

void protocols::hybridization::HybridizeProtocol::set_stage1_increase_cycles ( core::Real  newval)
inline
void protocols::hybridization::HybridizeProtocol::set_stage1_scorefxn ( core::scoring::ScoreFunctionOP  newval)
inline
void protocols::hybridization::HybridizeProtocol::set_stage2_increase_cycles ( core::Real  newval)
inline
void protocols::hybridization::HybridizeProtocol::set_stage2_scorefxn ( core::scoring::ScoreFunctionOP  newval)
inline
void protocols::hybridization::HybridizeProtocol::set_stage2min_scorefxn ( core::scoring::ScoreFunctionOP  newval)
inline

References stage2min_scorefxn_.

void protocols::hybridization::HybridizeProtocol::set_stage2pack_scorefxn ( core::scoring::ScoreFunctionOP  newval)
inline

References stage2pack_scorefxn_.

void protocols::hybridization::HybridizeProtocol::setup_templates_and_sampling_options ( core::pose::Pose const &  pose)
void protocols::hybridization::HybridizeProtocol::update_template ( core::Size const  template_idx)
void protocols::hybridization::HybridizeProtocol::validate_template ( std::string const &  filename,
std::string const &  fasta,
core::pose::PoseOP  template_pose,
bool align_pdb_info 
)

Member Data Documentation

bool protocols::hybridization::HybridizeProtocol::add_hetatm_
private

Referenced by set_add_hetatm().

core::Real protocols::hybridization::HybridizeProtocol::add_non_init_chunks_
private
core::sequence::SequenceAlignmentOP protocols::hybridization::HybridizeProtocol::aln_
private
bool protocols::hybridization::HybridizeProtocol::auto_frag_insertion_weight_
private
core::Size protocols::hybridization::HybridizeProtocol::batch_relax_
private

Referenced by set_batch_relax().

core::Real protocols::hybridization::HybridizeProtocol::big_frag_insertion_weight_
private
core::Size protocols::hybridization::HybridizeProtocol::cartfrag_overlap_
private
std::string protocols::hybridization::HybridizeProtocol::cen_cst_in_
private
bool protocols::hybridization::HybridizeProtocol::cenrot_
private
core::Real protocols::hybridization::HybridizeProtocol::chunk_insertion_weight_
private
std::string protocols::hybridization::HybridizeProtocol::coord_cst_res_
private
bool protocols::hybridization::HybridizeProtocol::csts_from_frags_
private
utility::vector1< detailedControlsTagSetting > protocols::hybridization::HybridizeProtocol::detailed_controls_settings_
private
std::string protocols::hybridization::HybridizeProtocol::disulf_file_
private
utility::vector1< utility::vector1< protocols::loops::Loops > > protocols::hybridization::HybridizeProtocol::domains_all_templ_
private
std::string protocols::hybridization::HybridizeProtocol::fa_cst_fn_
private
std::string protocols::hybridization::HybridizeProtocol::fa_cst_in_
private
core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::fa_scorefxn_
private

Referenced by set_fullatom_scorefxn().

bool protocols::hybridization::HybridizeProtocol::filter_templates_
private
core::Real protocols::hybridization::HybridizeProtocol::frag_1mer_insertion_weight_
private
core::Real protocols::hybridization::HybridizeProtocol::frag_weight_aligned_
private
utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeProtocol::fragments_big_
private

Referenced by add_big_fragments().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::HybridizeProtocol::fragments_small_
private

Referenced by add_small_fragments().

core::Real protocols::hybridization::HybridizeProtocol::fragprob_stage2_
private
core::Real protocols::hybridization::HybridizeProtocol::hcut_
private
core::Real protocols::hybridization::HybridizeProtocol::hetatm_prot_cst_weight_
private
core::Real protocols::hybridization::HybridizeProtocol::hetatm_self_cst_weight_
private
bool protocols::hybridization::HybridizeProtocol::include_loop_ss_chunks_
private
bool protocols::hybridization::HybridizeProtocol::jump_move_
private
core::Size protocols::hybridization::HybridizeProtocol::jump_move_repeat_
private
bool protocols::hybridization::HybridizeProtocol::keep_pose_constraint_
private
core::Size protocols::hybridization::HybridizeProtocol::length_
private
bool protocols::hybridization::HybridizeProtocol::linmin_only_
private
int protocols::hybridization::HybridizeProtocol::max_contig_insertion_
private
core::Size protocols::hybridization::HybridizeProtocol::max_registry_shift_
private
bool protocols::hybridization::HybridizeProtocol::min_after_stage1_
private
core::pose::PoseOP protocols::hybridization::HybridizeProtocol::native_
private
bool protocols::hybridization::HybridizeProtocol::no_global_frame_
private
utility::vector1< core::Size > protocols::hybridization::HybridizeProtocol::non_null_template_indices_
private
std::string protocols::hybridization::HybridizeProtocol::pairings_file_
private
core::Real protocols::hybridization::HybridizeProtocol::pcut_
private
core::Real protocols::hybridization::HybridizeProtocol::randfragprob_stage2_
private
utility::vector1<core::Size> protocols::hybridization::HybridizeProtocol::random_sheets_
private
utility::vector1< utility::vector1<char> > protocols::hybridization::HybridizeProtocol::randomize_chains_
private
bool protocols::hybridization::HybridizeProtocol::realign_domains_
private
bool protocols::hybridization::HybridizeProtocol::realign_domains_stage2_
private
core::Size protocols::hybridization::HybridizeProtocol::relax_repeats_
private
utility::vector1<core::Size> protocols::hybridization::HybridizeProtocol::residue_max_registry_shift_
private
utility::vector1<bool> protocols::hybridization::HybridizeProtocol::residue_sample_abinitio_
private
utility::vector1<bool> protocols::hybridization::HybridizeProtocol::residue_sample_template_
private
bool protocols::hybridization::HybridizeProtocol::seqfrags_only_
private
utility::vector1<core::Size> protocols::hybridization::HybridizeProtocol::sheets_
private
utility::vector1< bool > protocols::hybridization::HybridizeProtocol::should_align_pdb_infos_
private
bool protocols::hybridization::HybridizeProtocol::skip_long_min_
private
core::Real protocols::hybridization::HybridizeProtocol::small_frag_insertion_weight_
private
core::Size protocols::hybridization::HybridizeProtocol::stage1_1_cycles_
private
core::Size protocols::hybridization::HybridizeProtocol::stage1_2_cycles_
private
core::Size protocols::hybridization::HybridizeProtocol::stage1_3_cycles_
private
core::Size protocols::hybridization::HybridizeProtocol::stage1_4_cycles_
private
core::Real protocols::hybridization::HybridizeProtocol::stage1_increase_cycles_
private
core::Real protocols::hybridization::HybridizeProtocol::stage1_probability_
private
core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage1_scorefxn_
private

Referenced by set_stage1_scorefxn().

core::Real protocols::hybridization::HybridizeProtocol::stage25_increase_cycles_
private
core::Real protocols::hybridization::HybridizeProtocol::stage2_increase_cycles_
private
core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2_scorefxn_
private

Referenced by set_stage2_scorefxn().

core::Real protocols::hybridization::HybridizeProtocol::stage2_temperature_
private
core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2min_scorefxn_
private

Referenced by set_stage2min_scorefxn().

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2pack_scorefxn_
private

Referenced by set_stage2pack_scorefxn().

utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::HybridizeProtocol::strand_pairs_
private
utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::symmdef_files_
private
utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeProtocol::template_chunks_
private
utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeProtocol::template_contigs_
private
utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::template_cst_fn_
private
utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::template_fns_
private
utility::vector1< core::Real > protocols::hybridization::HybridizeProtocol::template_weights_
private
utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeProtocol::templates_
private
utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeProtocol::templates_aln_
private
utility::vector1< core::Size > protocols::hybridization::HybridizeProtocol::user_csts_
private

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