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protocols::hybridization::HybridizeProtocol Class Reference

#include <HybridizeProtocol.hh>

Inheritance diagram for protocols::hybridization::HybridizeProtocol:
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Collaboration diagram for protocols::hybridization::HybridizeProtocol:
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Public Member Functions

 HybridizeProtocol ()
 
void init ()
 
void read_template_structures (utility::file::FileName template_list)
 Old way of parsing hybrid config files; RosettaScripts is now preferred. More...
 
void read_template_structures (utility::vector1< utility::file::FileName > const &template_filenames)
 
void add_template (std::string template_fn, std::string cst_fn, std::string symmdef_file, core::Real weight=1., core::Real domain_assembly_weight=0., core::Size cluster_id=1, utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0))
 
void pick_starting_template (core::Size &initial_template_index, core::Size &initial_template_index_icluster, utility::vector1< core::Size > &template_index_icluster, utility::vector1< core::pose::PoseOP > &templates_icluster, utility::vector1< core::Real > &weights_icluster, utility::vector1< protocols::loops::Loops > &template_chunks_icluster, utility::vector1< protocols::loops::Loops > &template_contigs_icluster)
 
utility::vector1< Loopsexpand_domains_to_full_length (utility::vector1< utility::vector1< Loops > > all_domains, Size ref_domains_index, Size n_residues)
 
void align_by_domain (utility::vector1< core::pose::PoseOP > &poses, utility::vector1< Loops > domains, core::pose::PoseOP &ref_pose)
 
void align_by_domain (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< Loops > domains)
 
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 check_and_create_fragments (Pose &)
 
virtual void apply (Pose &)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
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). More...
 
virtual void parse_my_tag (TagPtr const, DataMap &, Filters_map const &, Movers_map const &, Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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. More...
 
virtual bool reinitialize_for_new_input () const
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

utility::vector1< core::Sizestarting_templates_
 
core::Real stage1_probability_
 
core::Real stage1_increase_cycles_
 
core::Real stage2_increase_cycles_
 
core::Size stage1_1_cycles_
 
core::Size stage1_2_cycles_
 
core::Size stage1_3_cycles_
 
core::Size stage1_4_cycles_
 
core::Real frag_1mer_insertion_weight_
 
core::Real small_frag_insertion_weight_
 
core::Real big_frag_insertion_weight_
 
core::Real frag_weight_aligned_
 
bool auto_frag_insertion_weight_
 
core::Size max_registry_shift_
 
bool domain_assembly_
 
bool add_hetatm_
 
bool realign_domains_
 
bool realign_domains_stage2_
 
bool add_non_init_chunks_
 
bool no_global_frame_
 
bool linmin_only_
 
core::Real hetatm_cst_weight_
 
core::scoring::ScoreFunctionOP stage1_scorefxn_
 
core::scoring::ScoreFunctionOP stage2_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
std::string fa_cst_fn_
 
std::string disulf_file_
 
core::Size cartfrag_overlap_
 
core::Real pcut_
 
core::Real hcut_
 
core::Size length_
 
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::pose::PoseOP
templates_
 
utility::vector1< std::string > template_fn_
 
utility::vector1< std::string > template_cst_fn_
 
utility::vector1< std::string > symmdef_files_
 
utility::vector1< core::Realtemplate_weights_
 
utility::vector1< core::Realdomain_assembly_weights_
 
utility::vector1< core::Sizetemplate_clusterID_
 
utility::vector1
< protocols::loops::Loops
template_chunks_
 
utility::vector1
< protocols::loops::Loops
template_contigs_
 
utility::vector1
< utility::vector1< core::Size > > 
template_cst_reses_
 
core::Real template_weights_sum_
 
std::map< Size,
utility::vector1< Size > > 
clusterID_map_
 
utility::vector1
< protocols::loops::Loops
domains_
 
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_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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 init(), and read_template_structures().

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::hybridization::HybridizeProtocol::add_template ( std::string  template_fn,
std::string  cst_fn,
std::string  symmdef_file,
core::Real  weight = 1.,
core::Real  domain_assembly_weight = 0.,
core::Size  cluster_id = 1,
utility::vector1< core::Size cst_reses = utility::vector1<core::Size>(0) 
)
void protocols::hybridization::HybridizeProtocol::align_by_domain ( utility::vector1< core::pose::PoseOP > &  poses,
utility::vector1< Loops domains,
core::pose::PoseOP ref_pose 
)

Referenced by apply().

void protocols::hybridization::HybridizeProtocol::align_by_domain ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
utility::vector1< Loops domains 
)
void protocols::hybridization::HybridizeProtocol::apply ( Pose pose)
virtual

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), add_hetatm_, add_non_init_chunks_, protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), core::pose::addVirtualResAsRoot(), align_by_domain(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::relax::FastRelax::apply(), core::conformation::Residue::atom_index(), auto_frag_insertion_weight_, protocols::relax::FastRelax::batch_apply(), batch_relax_, big_frag_insertion_weight_, core::scoring::cart_bonded, cartfrag_overlap_, core::chemical::CENTROID, check_and_create_fragments(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::pose::Pose::data(), disulf_file_, domain_assembly_, domain_assembly_weights_, domains_, expand_domains_to_full_length(), protocols::loops::extract_continuous_chunks(), protocols::loops::extract_secondary_structure_chunks(), fa_cst_fn_, fa_scorefxn_, core::chemical::FA_STANDARD, filter_templates_, core::pose::Pose::fold_tree(), frag_1mer_insertion_weight_, frag_weight_aligned_, fragments_big_, fragments_small_, protocols::hybridization::get_gdtmm(), core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), hcut_, hetatm_cst_weight_, initialize_and_sample_loops(), core::pose::initialize_disulfide_bonds(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), length_, linmin_only_, core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), max_registry_shift_, native_, no_global_frame_, pairings_file_, pcut_, pick_starting_template(), random_sheets_, realign_domains_, realign_domains_stage2_, relax_repeats_, core::pose::Pose::residue(), protocols::hybridization::RG(), core::kinematics::FoldTree::root(), core::optimization::CartesianMinimizer::run(), protocols::hybridization::DomainAssembly::run(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::relax::FastRelax::set_force_nonideal(), core::kinematics::MoveMap::set_jump(), protocols::relax::RelaxProtocolBase::set_min_type(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), protocols::relax::RelaxProtocolBase::set_task_factory(), core::pose::setPoseExtraScores(), protocols::hybridization::setup_centroid_constraints(), protocols::hybridization::setup_fullatom_constraints(), sheets_, small_frag_insertion_weight_, protocols::hybridization::DDomainParse::split(), stage1_1_cycles_, stage1_2_cycles_, stage1_3_cycles_, stage1_4_cycles_, stage1_increase_cycles_, stage1_probability_, stage1_scorefxn_, stage2_increase_cycles_, stage2_scorefxn_, protocols::loops::start, protocols::loops::stop, strand_pairs_, symmdef_files_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), template_chunks_, template_clusterID_, template_contigs_, template_cst_fn_, template_cst_reses_, template_fn_, template_weights_, templates_, core::pose::Pose::total_residue(), protocols::hybridization::TR(), and core::pose::Pose::xyz().

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

utility::vector1< Loops > protocols::hybridization::HybridizeProtocol::expand_domains_to_full_length ( utility::vector1< utility::vector1< Loops > >  all_domains,
Size  ref_domains_index,
Size  n_residues 
)
protocols::moves::MoverOP protocols::hybridization::HybridizeProtocol::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 HybridizeProtocol().

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

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 
)
void protocols::hybridization::HybridizeProtocol::parse_my_tag ( TagPtr const  tag,
moves::DataMap data,
filters::Filters_map const &  filters,
moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual
void protocols::hybridization::HybridizeProtocol::pick_starting_template ( core::Size initial_template_index,
core::Size initial_template_index_icluster,
utility::vector1< core::Size > &  template_index_icluster,
utility::vector1< core::pose::PoseOP > &  templates_icluster,
utility::vector1< core::Real > &  weights_icluster,
utility::vector1< protocols::loops::Loops > &  template_chunks_icluster,
utility::vector1< protocols::loops::Loops > &  template_contigs_icluster 
)
void protocols::hybridization::HybridizeProtocol::read_template_structures ( utility::file::FileName  template_list)

Old way of parsing hybrid config files; RosettaScripts is now preferred.

References add_template(), and protocols::hybridization::TR().

Referenced by HybridizeProtocol(), and parse_my_tag().

void protocols::hybridization::HybridizeProtocol::read_template_structures ( utility::vector1< utility::file::FileName > const &  template_filenames)

Member Data Documentation

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

Referenced by apply(), init(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::add_non_init_chunks_
private

Referenced by apply(), init(), and parse_my_tag().

core::sequence::SequenceAlignmentOP protocols::hybridization::HybridizeProtocol::aln_
private
bool protocols::hybridization::HybridizeProtocol::auto_frag_insertion_weight_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::batch_relax_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::big_frag_insertion_weight_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::cartfrag_overlap_
private

Referenced by apply(), init(), and parse_my_tag().

std::map< Size, utility::vector1 < Size > > protocols::hybridization::HybridizeProtocol::clusterID_map_
private
std::string protocols::hybridization::HybridizeProtocol::disulf_file_
private

Referenced by apply(), init(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::domain_assembly_
private

Referenced by apply(), init(), and parse_my_tag().

utility::vector1< core::Real > protocols::hybridization::HybridizeProtocol::domain_assembly_weights_
private

Referenced by add_template(), and apply().

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeProtocol::domains_
private

Referenced by apply().

std::string protocols::hybridization::HybridizeProtocol::fa_cst_fn_
private

Referenced by apply(), init(), and parse_my_tag().

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

Referenced by apply(), init(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::filter_templates_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::frag_1mer_insertion_weight_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::frag_weight_aligned_
private

Referenced by apply(), init(), and parse_my_tag().

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

Referenced by apply(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::hetatm_cst_weight_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::length_
private

Referenced by apply(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::linmin_only_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::max_registry_shift_
private

Referenced by apply(), init(), and parse_my_tag().

core::pose::PoseOP protocols::hybridization::HybridizeProtocol::native_
private

Referenced by apply(), and init().

bool protocols::hybridization::HybridizeProtocol::no_global_frame_
private

Referenced by apply(), init(), and parse_my_tag().

std::string protocols::hybridization::HybridizeProtocol::pairings_file_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::pcut_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::hybridization::HybridizeProtocol::random_sheets_
private

Referenced by apply(), init(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::realign_domains_
private

Referenced by apply(), init(), and parse_my_tag().

bool protocols::hybridization::HybridizeProtocol::realign_domains_stage2_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::relax_repeats_
private

Referenced by apply(), init(), and parse_my_tag().

utility::vector1<core::Size> protocols::hybridization::HybridizeProtocol::sheets_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::small_frag_insertion_weight_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::stage1_1_cycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::stage1_2_cycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::stage1_3_cycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::HybridizeProtocol::stage1_4_cycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::stage1_increase_cycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::stage1_probability_
private

Referenced by apply(), init(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage1_scorefxn_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::HybridizeProtocol::stage2_increase_cycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::HybridizeProtocol::stage2_scorefxn_
private

Referenced by apply(), init(), and parse_my_tag().

utility::vector1< core::Size > protocols::hybridization::HybridizeProtocol::starting_templates_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::HybridizeProtocol::strand_pairs_
private

Referenced by apply().

utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::symmdef_files_
private

Referenced by add_template(), and apply().

utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeProtocol::template_chunks_
private
utility::vector1< core::Size > protocols::hybridization::HybridizeProtocol::template_clusterID_
private
utility::vector1< protocols::loops::Loops > protocols::hybridization::HybridizeProtocol::template_contigs_
private
utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::template_cst_fn_
private

Referenced by add_template(), and apply().

utility::vector1< utility::vector1<core::Size> > protocols::hybridization::HybridizeProtocol::template_cst_reses_
private

Referenced by add_template(), and apply().

utility::vector1< std::string > protocols::hybridization::HybridizeProtocol::template_fn_
private

Referenced by add_template(), and apply().

utility::vector1< core::Real > protocols::hybridization::HybridizeProtocol::template_weights_
private
core::Real protocols::hybridization::HybridizeProtocol::template_weights_sum_
private
utility::vector1< core::pose::PoseOP > protocols::hybridization::HybridizeProtocol::templates_
private

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