#include <NubInitioMover.hh>
Public Member Functions | |
| NubInitioMover () | |
| Empty Constructor. More... | |
| ~NubInitioMover () override | |
| Destructor. More... | |
| void | apply (core::pose::Pose &pose) override |
| Main application of the NubInitioMover. More... | |
| std::string | prefix () const |
| In rosettascripts, saves the user provided name. More... | |
| void | prefix (std::string const &prefix) |
| core::pose::Pose | template_pose () const |
| Store the unmodified pose as provided by apply. More... | |
| core::select::residue_selector::ResidueSelectorCOP | template_selector () const |
| void | template_selector (core::select::residue_selector::ResidueSelectorCOP const &selector) |
| core::scoring::ScoreFunctionOP | fullatom_scorefxn () const |
| score function to use on repacking after going back to full atom More... | |
| void | fullatom_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn) |
| utils::NubOP | nub () const |
| object that contains and processes the unfolded pose info More... | |
| void | nub (utils::NubOP nub) |
| bool | use_cst () const |
| when true, use constraint guided ab initio More... | |
| void | use_cst (bool pick) |
| bool | clear_motif_cst () const |
| when true, remove constraints transfered from the template into the inserted motif More... | |
| void | clear_motif_cst (bool pick) |
| core::Real | rmsd_threshold () const |
| limit of divergence allowed between the template structure and the ab initio output More... | |
| void | rmsd_threshold (core::Real threshold) |
| bool | rmsd_include_motif () const |
| when true, include the residues of the insertion in the RMSD evaluation (do only when insertion sizes are the same) More... | |
| void | rmsd_include_motif (bool pick) |
| bool | rmsd_include_unconstrained () const |
| when false, do not use residues without constraints in the RMSD evaluation More... | |
| void | rmsd_include_unconstrained (bool pick) |
| bool | repack_disulfides () const |
| when true, try to repack disulfides More... | |
| void | repack_disulfides (bool pick) |
| bool | disulfides_bb () const |
| when true, allow bb movements to try to repack the disulfides More... | |
| void | disulfides_bb (bool pick) |
| core::Size | disulfides_side () const |
| if disulfides_bb is true, how many residues around CYS are allowed to move? More... | |
| void | disulfides_side (core::Real value) |
| std::string | fragments_id () const |
| for rosettascripts, id of the fragmentsets in the datamap More... | |
| void | fragments_id (std::string const &name) |
| void | max_trials (core::Size choice) |
| how many times do we try to fold? More... | |
| core::Size | max_trials () const |
| void | binder_weight (core::Real value) |
| weight for binder related score terms, to provide to the ab initio process More... | |
| core::Real | binder_weight () const |
| void | angle_weight (core::Real value) |
| weight for angle constraints, to provide to the ab initio process More... | |
| core::Real | angle_weight () const |
| void | dihedral_weight (core::Real value) |
| weight for dihedral constraints, to provide to the ab initio process More... | |
| core::Real | dihedral_weight () const |
| void | correction_weights (core::Real value) |
| value automatically applied to weight to improve alpha/beta fold More... | |
| core::Real | correction_weights () const |
| bool | use_correction_weights () const |
| if true, apply the correction weights More... | |
| void | use_correction_weights (bool pick) |
| bool | dump_centroid () const |
| if true, generate silentfile with the centroid-level protein More... | |
| void | dump_centroid (bool pick) |
| bool | drop_unfolded_pose () const |
| if true, stop after generating the unfolded pose (for show and debug) More... | |
| void | drop_unfolded_pose (bool pick) |
| bool | design () const |
| if true, design the designable residues (TEMPLATE & COLDSPOT labels) More... | |
| void | design (bool pick) |
| std::string | residue_type () const |
| if given, design all designable residues to the provided one (TEMPLATE & COLDSPOT labels) More... | |
| void | residue_type (std::string pick) |
| std::string | sse () const |
| if given, allows to define the secondary structure of the template (in case it comes for PeptideStubMover) More... | |
| void | sse (std::string pick) |
| protocols::filters::FilterOP | filter () const |
| if given, define an alternative filter to RMSD More... | |
| void | filter (protocols::filters::FilterOP pick) |
| core::scoring::ScoreFunctionOP | filter_scorefxn () const |
| score function to use on provided filter More... | |
| void | filter_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn) |
| core::select::residue_selector::ResidueSelectorOP | design_chain_selector () const |
| Selects the chain considered as DESIGN by the NubInitioMover instance. More... | |
| core::select::residue_selector::ResidueSelectorOP | context_chain_selector () const |
| Selects ALL the chains NOT considered as DESIGN by the NubInitioMover instance. More... | |
| core::select::residue_selector::ResidueSelectorOP | used_template_selector () const |
| INVERTS the INSERTION selector in the REFERENCE TEMPLATE POSE. More... | |
| core::select::residue_selector::ResidueSelectorOP | work_motif_selector () const |
| Selects the residues that are MOTIF from the DESIGN CHAIN. More... | |
| core::select::residue_selector::ResidueSelectorOP | work_template_selector () const |
| Selects the residues that are TEMPLATE from the DESIGN CHAIN. More... | |
| core::select::residue_selector::ResidueSelectorOP | bb_movable_selector () const |
| Selects the residues that are TEMPLATE or FLEXIBLE from the DESIGN CHAIN. More... | |
| core::select::residue_selector::ResidueSelectorOP | chi_movable_selector () const |
| Selects the residues that are TEMPLATE or COLDSPOT from the DESIGN CHAIN. More... | |
| core::select::residue_selector::ResidueSelectorOP | cys_design_selector () const |
| Selects residues that are DISULFIDIZE from the DESIGN CHAIN. More... | |
| core::select::residue_selector::ResidueRanges | template_insertion_ranges () const |
| Range of residues representing the INSERTION regions (checks that there is one) More... | |
| core::select::residue_selector::ResidueRanges | used_template_ranges (bool terminals=false) const |
| Range of residues kept from the TEMPLATE (checks that there is one) If terminals, adds N and C-terminal empty ranges (0, 0) if there is a N or C-terminal insertion. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| parse XML tag (to use this Mover in Rosetta Scripts) More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| required in the context of the parser/scripting scheme More... | |
| protocols::moves::MoverOP | clone () const override |
| required in the context of the parser/scripting scheme More... | |
| 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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 Member Functions | |
| void | make_unfolded_pose (core::pose::Pose &pose) |
| Prepare the unfolded pose previous to folding. More... | |
| core::Size | refold_pose (core::pose::Pose &pose) |
| Refold the unfolded pose. More... | |
| void | post_process (core::pose::Pose &pose) |
| Finishup the folded structure. More... | |
| void | sanity_check (core::pose::Pose const &pose) |
| Checks that input make sense for the particular run. More... | |
| utility::vector1< core::pose::PoseOP > | get_template_pieces (core::pose::Pose const &pose) const |
| List of Poses from the template that will become the UNFOLDED REGIONS. More... | |
| core::select::residue_selector::ResidueRangesOP | make_template_ranges (core::select::residue_selector::ResidueRanges original) const |
| Splits the template selected regions if needed. More... | |
| void | manage_constraints (core::pose::Pose &pose) |
| core::scoring::ScoreFunctionOP | apply_abinitio (core::pose::Pose &pose) |
| core::Real | template_rmsd (core::pose::Pose &pose) |
| evaluate rmsd with template More... | |
| core::Size | count_contacts (core::pose::Pose &pose) const |
| Counts how many residues in the pose DESIGN CHAIN are in contact with the inserted motif and labels them as CONTACT. More... | |
| void | dump_centroid (core::pose::Pose const &pose, core::scoring::ScoreFunctionOP scorefxn) |
| Dumps the pose at centroid level in a silent file with the same file name and pose TAG but ending with "_CENTROID". Uses the provided score to evaluate it. More... | |
| void | repack_minimize_disulfides (core::pose::Pose &pose) |
| fix the pose after refitting the sidechains More... | |
| void | repack (core::pose::Pose &pose) |
| Repack sidechains without alter bb. 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
◆ NubInitioMover()
| protocols::fold_from_loops::NubInitioMover::NubInitioMover | ( | ) |
Empty Constructor.
◆ ~NubInitioMover()
|
override |
Destructor.
Member Function Documentation
◆ angle_weight() [1/2]
| core::Real protocols::fold_from_loops::NubInitioMover::angle_weight | ( | ) | const |
References mc_binder_weight_.
Referenced by parse_my_tag().
◆ angle_weight() [2/2]
| void protocols::fold_from_loops::NubInitioMover::angle_weight | ( | core::Real | value | ) |
weight for angle constraints, to provide to the ab initio process
References mc_angle_weight_.
◆ apply()
|
overridevirtual |
Main application of the NubInitioMover.
Implements protocols::moves::Mover.
References protocols::moves::FAIL_DO_NOT_RETRY, make_unfolded_pose(), protocols::moves::MS_SUCCESS, post_process(), refold_pose(), and protocols::moves::Mover::set_last_move_status().
◆ apply_abinitio()
|
private |
Sets up the extra weights that seem appropiate for each case and runs the ab initio simulation.
References core::scoring::angle_constraint, core::scoring::dihedral_constraint, core::scoring::dslfc_ang, core::scoring::dslfc_bb_dih, core::scoring::dslfc_cb_dih, core::scoring::dslfc_cb_dst, core::scoring::dslfc_cen_dst, has_alphas_, has_betas_, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::hs_pair, core::scoring::interchain_contact, core::scoring::interchain_env, core::scoring::interchain_pair, core::scoring::interchain_vdw, mc_angle_weight_, mc_binder_weight_, mc_correction_weights_, mc_dihedral_weight_, nub_, repack_disulfides_, core::scoring::rsigma, core::pose::Pose::secstruct(), core::scoring::sheet, core::scoring::ss_pair, protocols::fold_from_loops::TR(), use_correction_weights_, and use_cst_.
Referenced by refold_pose().
◆ bb_movable_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::bb_movable_selector | ( | ) | const |
Selects the residues that are TEMPLATE or FLEXIBLE from the DESIGN CHAIN.
References design_chain_selector(), and nub_.
Referenced by repack_minimize_disulfides().
◆ binder_weight() [1/2]
| core::Real protocols::fold_from_loops::NubInitioMover::binder_weight | ( | ) | const |
References mc_binder_weight_.
Referenced by parse_my_tag().
◆ binder_weight() [2/2]
| void protocols::fold_from_loops::NubInitioMover::binder_weight | ( | core::Real | value | ) |
weight for binder related score terms, to provide to the ab initio process
References mc_binder_weight_.
◆ chi_movable_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::chi_movable_selector | ( | ) | const |
Selects the residues that are TEMPLATE or COLDSPOT from the DESIGN CHAIN.
References design_chain_selector(), and nub_.
Referenced by repack(), and repack_minimize_disulfides().
◆ clear_motif_cst() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::clear_motif_cst | ( | ) | const |
when true, remove constraints transfered from the template into the inserted motif
References clear_motif_cst_.
Referenced by parse_my_tag().
◆ clear_motif_cst() [2/2]
| void protocols::fold_from_loops::NubInitioMover::clear_motif_cst | ( | bool | pick | ) |
References clear_motif_cst_.
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ context_chain_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::context_chain_selector | ( | ) | const |
Selects ALL the chains NOT considered as DESIGN by the NubInitioMover instance.
References design_chain_selector().
Referenced by count_contacts().
◆ correction_weights() [1/2]
| core::Real protocols::fold_from_loops::NubInitioMover::correction_weights | ( | ) | const |
References mc_correction_weights_.
◆ correction_weights() [2/2]
| void protocols::fold_from_loops::NubInitioMover::correction_weights | ( | core::Real | value | ) |
value automatically applied to weight to improve alpha/beta fold
References mc_correction_weights_.
◆ count_contacts()
|
private |
Counts how many residues in the pose DESIGN CHAIN are in contact with the inserted motif and labels them as CONTACT.
References protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply(), context_chain_selector(), core::select::residue_selector::count_selected(), nub_, core::select::residue_selector::represent_residue_selector(), protocols::fold_from_loops::TR(), and work_motif_selector().
Referenced by post_process().
◆ cys_design_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::cys_design_selector | ( | ) | const |
Selects residues that are DISULFIDIZE from the DESIGN CHAIN.
References design_chain_selector(), and nub_.
Referenced by repack_minimize_disulfides().
◆ default_clear_motif_cst()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_design()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_disulfides_bb()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_disulfides_side()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_drop_unfolded_pose()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_dump_centroid()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_filter_name()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_filter_scorefxn()
|
staticprivate |
References core::scoring::get_score_function().
◆ default_fullatom_scorefxn()
|
staticprivate |
References core::scoring::get_score_function().
◆ default_max_trials()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_mc_angle_weight()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_mc_binder_weight()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_mc_correction_weights()
|
staticprivate |
◆ default_mc_dihedral_weight()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_prefix()
|
staticprivate |
Referenced by parse_my_tag().
◆ default_repack_disulfides()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_residue_type()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_rmsd_include_motif()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_rmsd_include_unconstrained()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_rmsd_threshold()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_sse()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_template_selector()
|
staticprivate |
◆ default_use_correction_weights()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_use_cst()
|
staticprivate |
Referenced by parse_my_tag(), and provide_xml_schema().
◆ design() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::design | ( | ) | const |
if true, design the designable residues (TEMPLATE & COLDSPOT labels)
References design_.
Referenced by design_chain_selector(), parse_my_tag(), work_motif_selector(), and work_template_selector().
◆ design() [2/2]
| void protocols::fold_from_loops::NubInitioMover::design | ( | bool | pick | ) |
References design_.
◆ design_chain_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::design_chain_selector | ( | ) | const |
Selects the chain considered as DESIGN by the NubInitioMover instance.
References design(), and nub_.
Referenced by bb_movable_selector(), chi_movable_selector(), context_chain_selector(), cys_design_selector(), and template_rmsd().
◆ dihedral_weight() [1/2]
| core::Real protocols::fold_from_loops::NubInitioMover::dihedral_weight | ( | ) | const |
References mc_dihedral_weight_.
Referenced by parse_my_tag().
◆ dihedral_weight() [2/2]
| void protocols::fold_from_loops::NubInitioMover::dihedral_weight | ( | core::Real | value | ) |
weight for dihedral constraints, to provide to the ab initio process
References mc_dihedral_weight_.
◆ disulfides_bb() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::disulfides_bb | ( | ) | const |
when true, allow bb movements to try to repack the disulfides
References disulfides_bb_.
Referenced by parse_my_tag().
◆ disulfides_bb() [2/2]
| void protocols::fold_from_loops::NubInitioMover::disulfides_bb | ( | bool | pick | ) |
References disulfides_bb_.
◆ disulfides_side() [1/2]
| core::Size protocols::fold_from_loops::NubInitioMover::disulfides_side | ( | ) | const |
if disulfides_bb is true, how many residues around CYS are allowed to move?
References disulfides_side_.
Referenced by parse_my_tag().
◆ disulfides_side() [2/2]
| void protocols::fold_from_loops::NubInitioMover::disulfides_side | ( | core::Real | value | ) |
References disulfides_side_.
◆ drop_unfolded_pose() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::drop_unfolded_pose | ( | ) | const |
if true, stop after generating the unfolded pose (for show and debug)
References drop_unfolded_pose_.
Referenced by parse_my_tag().
◆ drop_unfolded_pose() [2/2]
| void protocols::fold_from_loops::NubInitioMover::drop_unfolded_pose | ( | bool | pick | ) |
References drop_unfolded_pose_.
◆ dump_centroid() [1/3]
| bool protocols::fold_from_loops::NubInitioMover::dump_centroid | ( | ) | const |
if true, generate silentfile with the centroid-level protein
References dump_centroid_.
Referenced by parse_my_tag(), and post_process().
◆ dump_centroid() [2/3]
| void protocols::fold_from_loops::NubInitioMover::dump_centroid | ( | bool | pick | ) |
References dump_centroid_.
◆ dump_centroid() [3/3]
|
private |
Dumps the pose at centroid level in a silent file with the same file name and pose TAG but ending with "_CENTROID". Uses the provided score to evaluate it.
References core::pose::add_comment(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::jd2::current_output_filename(), protocols::jd2::current_output_name(), dump_centroid_, core::pose::Pose::fold_tree(), protocols::jd2::jd2_used(), silent_score_file_, protocols::fold_from_loops::TR(), and protocols::fold_from_loops::movers::DisplayPoseLabelsMover::write().
◆ filter() [1/2]
| protocols::filters::FilterOP protocols::fold_from_loops::NubInitioMover::filter | ( | ) | const |
◆ filter() [2/2]
| void protocols::fold_from_loops::NubInitioMover::filter | ( | protocols::filters::FilterOP | pick | ) |
References filter_.
◆ filter_scorefxn() [1/2]
| core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::filter_scorefxn | ( | ) | const |
◆ filter_scorefxn() [2/2]
| void protocols::fold_from_loops::NubInitioMover::filter_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn | ) |
References filter_scorefxn_.
◆ fragments_id() [1/2]
| std::string protocols::fold_from_loops::NubInitioMover::fragments_id | ( | ) | const |
for rosettascripts, id of the fragmentsets in the datamap
References fragments_id_.
Referenced by parse_my_tag().
◆ fragments_id() [2/2]
| void protocols::fold_from_loops::NubInitioMover::fragments_id | ( | std::string const & | name | ) |
References fragments_id_, and protocols::moves::Mover::name().
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ fullatom_scorefxn() [1/2]
| core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::fullatom_scorefxn | ( | ) | const |
score function to use on repacking after going back to full atom
References fullatom_scorefxn_.
Referenced by parse_my_tag().
◆ fullatom_scorefxn() [2/2]
| void protocols::fold_from_loops::NubInitioMover::fullatom_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn | ) |
References fullatom_scorefxn_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_template_pieces()
|
private |
List of Poses from the template that will become the UNFOLDED REGIONS.
This provides the pieces of the template that will be kept and attached to the functional motif as the unfolded segments. As a rule, the number of these pieces has to be twice the number of functional motifs; thus, if N-terminal or C-terminal motif insertions exist, empty Poses can be provided here in order to make this work properly.
References protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply_without_merge(), make_template_ranges(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_ranges(), and used_template_ranges().
Referenced by make_unfolded_pose().
◆ make_template_ranges()
|
private |
Splits the template selected regions if needed.
This calculates if the original ranges in the template provided by the user are enough or not. If needs be, it will split ranges between to insertion motifs to allow for cutpoinst or it will add empty ranges to keep the 2 to 1 proportion between the insertion motifs and the unfolded template segments.
References protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure(), protocols::sic_dock::range(), core::pose::Pose::secstruct(), and template_pose_.
Referenced by get_template_pieces().
◆ make_unfolded_pose()
|
private |
Prepare the unfolded pose previous to folding.
STEP1 of NubInitioMover This checks that all inputs are as expected and that the starting pose (unfolded) is properly generated. This function is only runned once, regardless of how many structures are requested; thus, the NubInitioMover in a given run can only be runned for the same funtional motif - template pair.
References core::pose::Pose::conformation(), core::conformation::disulfide_bonds(), protocols::simple_filters::dssp(), get_template_pieces(), manage_constraints(), nub_, sanity_check(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), sse_, template_selector_, and protocols::fold_from_loops::TR().
Referenced by apply().
◆ manage_constraints()
|
private |
Here the constraint options are set. Also, the score terms that inform in the context in which the constraints are used is added.
- Remarks
- This function can change the ConstraintSet of the Pose by: (1) removing them from the nub (static) segments and (2) bt remaping them to the new legnth of the unfolded pose if needed.
References core::pose::add_score_line_string(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::apply(), clear_motif_cst_, core::pose::Pose::constraint_set(), nub_, core::pose::setPoseExtraScore(), template_selector_, and use_cst_.
Referenced by make_unfolded_pose().
◆ max_trials() [1/2]
| core::Size protocols::fold_from_loops::NubInitioMover::max_trials | ( | ) | const |
References max_trials_.
Referenced by parse_my_tag().
◆ max_trials() [2/2]
| void protocols::fold_from_loops::NubInitioMover::max_trials | ( | core::Size | choice | ) |
how many times do we try to fold?
References max_trials_.
◆ mover_name()
|
static |
Referenced by get_name(), protocols::fold_from_loops::NubInitioMoverCreator::keyname(), and provide_xml_schema().
◆ nub() [1/2]
| utils::NubOP protocols::fold_from_loops::NubInitioMover::nub | ( | ) | const |
◆ nub() [2/2]
| void protocols::fold_from_loops::NubInitioMover::nub | ( | utils::NubOP | nub | ) |
◆ parse_my_tag()
|
overridevirtual |
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
References angle_weight(), binder_weight(), clear_motif_cst(), default_clear_motif_cst(), default_design(), default_disulfides_bb(), default_disulfides_side(), default_drop_unfolded_pose(), default_dump_centroid(), default_filter_name(), default_max_trials(), default_mc_angle_weight(), default_mc_binder_weight(), default_mc_dihedral_weight(), default_prefix(), default_repack_disulfides(), default_residue_type(), default_rmsd_include_motif(), default_rmsd_include_unconstrained(), default_rmsd_threshold(), default_sse(), default_use_correction_weights(), default_use_cst(), design(), dihedral_weight(), disulfides_bb(), disulfides_side(), drop_unfolded_pose(), dump_centroid(), filter(), filter_defined_, filter_scorefxn(), fragments_id(), fragments_id_, fullatom_scorefxn(), max_trials(), nub_, protocols::rosetta_scripts::parse_filter_or_null(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), prefix(), repack_disulfides(), residue_type(), rmsd_include_motif(), rmsd_include_unconstrained(), rmsd_threshold(), sse(), template_selector(), protocols::fold_from_loops::TR(), use_correction_weights(), and use_cst().
◆ post_process()
|
private |
Finishup the folded structure.
STEP3 of the NubInitioMover Close loops, score, recover full atoms, pack and/or design
References abinitio_score_, core::pose::add_comment(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side_ramp(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid(), core::pose::correctly_add_cutpoint_variants(), count_contacts(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::simple_filters::dssp(), dump_centroid(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::label(), nub_, core::pose::Pose::pdb_info(), pose_name_, core::pose::remove_variant_type_from_pose_residue(), repack(), repack_minimize_disulfides(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::setPoseExtraScore(), core::pose::Pose::size(), protocols::fold_from_loops::TR(), core::pose::Pose::update_residue_neighbors(), core::chemical::UPPER_TERMINUS_VARIANT, and protocols::fold_from_loops::movers::DisplayPoseLabelsMover::write().
Referenced by apply().
◆ prefix() [1/2]
| std::string protocols::fold_from_loops::NubInitioMover::prefix | ( | ) | const |
In rosettascripts, saves the user provided name.
References prefix_.
Referenced by parse_my_tag(), and prefix().
◆ prefix() [2/2]
| void protocols::fold_from_loops::NubInitioMover::prefix | ( | std::string const & | prefix | ) |
◆ provide_xml_schema()
|
static |
References core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), core::scoring::attributes_for_parse_score_function_w_description(), protocols::moves::complex_type_name_for_mover(), default_clear_motif_cst(), default_design(), default_disulfides_bb(), default_disulfides_side(), default_drop_unfolded_pose(), default_dump_centroid(), default_filter_name(), default_max_trials(), default_mc_angle_weight(), default_mc_binder_weight(), default_mc_dihedral_weight(), default_repack_disulfides(), default_residue_type(), default_rmsd_include_motif(), default_rmsd_include_unconstrained(), default_rmsd_threshold(), default_sse(), default_use_correction_weights(), default_use_cst(), mover_name(), protocols::fold_from_loops::utils::Nub::provide_xml_definition(), and core::id::to_string().
Referenced by protocols::fold_from_loops::NubInitioMoverCreator::provide_xml_schema().
◆ refold_pose()
|
private |
Refold the unfolded pose.
STEP2 of NubInitioMover This is the main job of the mover. It will execute the ab initio and it will evaluate the result. 0: success; 1: undolded pose (debug & showcase); 2: fail
References abinitio_score_, protocols::moves::AddPyMOLObserver(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), apply_abinitio(), core::chemical::CENTROID, core::pose::Pose::detached_copy(), drop_unfolded_pose_, filter_, filter_defined_, max_trials_, protocols::fold_from_loops::movers::DisplayPoseLabelsMover::movemap_factory(), nub_, core::pose::Pose::pdb_info(), pose_name_, rmsd_threshold_, core::pose::setPoseExtraScore(), template_pose_, template_rmsd(), protocols::fold_from_loops::TR(), and trials_.
Referenced by apply().
◆ repack()
|
private |
Repack sidechains without alter bb.
Repacking is necessary to obtain a accetable scored protein. Here it also takes care of designing of changing all residues to x if requested.
References core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::apply(), protocols::minimization_packing::PackRotamersMover::apply(), chi_movable_selector(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::clone(), core::pack::task::operation::DisallowIfNonnativeRLT::clone(), design_, core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), fullatom_scorefxn_, protocols::fold_from_loops::movers::AlignByResidueSelectorMover::query_selector(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::reference_pose(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::reference_selector(), residue_type_, protocols::fold_from_loops::TR(), and work_motif_selector().
Referenced by post_process().
◆ repack_disulfides() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::repack_disulfides | ( | ) | const |
◆ repack_disulfides() [2/2]
| void protocols::fold_from_loops::NubInitioMover::repack_disulfides | ( | bool | pick | ) |
References repack_disulfides_.
◆ repack_minimize_disulfides()
|
private |
fix the pose after refitting the sidechains
If there are disulfides in the scaffold or the motif, it tries to fix them as well as possible.
References bb_movable_selector(), chi_movable_selector(), core::pose::Pose::conformation(), cys_design_selector(), disulfides_bb_, disulfides_side_, core::scoring::dslf_fa13, core::scoring::fa_dun, core::conformation::Conformation::fix_disulfides(), fullatom_scorefxn_, core::select::movemap::mm_enable, nub_, core::util::rebuild_disulfide(), repack_disulfides_, core::pose::setPoseExtraScore(), and protocols::fold_from_loops::TR().
Referenced by post_process().
◆ residue_type() [1/2]
| std::string protocols::fold_from_loops::NubInitioMover::residue_type | ( | ) | const |
if given, design all designable residues to the provided one (TEMPLATE & COLDSPOT labels)
References residue_type_.
Referenced by parse_my_tag().
◆ residue_type() [2/2]
| void protocols::fold_from_loops::NubInitioMover::residue_type | ( | std::string | pick | ) |
References residue_type_.
◆ rmsd_include_motif() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::rmsd_include_motif | ( | ) | const |
when true, include the residues of the insertion in the RMSD evaluation (do only when insertion sizes are the same)
References rmsd_include_motif_.
Referenced by parse_my_tag(), and template_rmsd().
◆ rmsd_include_motif() [2/2]
| void protocols::fold_from_loops::NubInitioMover::rmsd_include_motif | ( | bool | pick | ) |
References rmsd_include_motif_.
◆ rmsd_include_unconstrained() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::rmsd_include_unconstrained | ( | ) | const |
when false, do not use residues without constraints in the RMSD evaluation
References rmsd_include_unconstrained_.
Referenced by parse_my_tag(), and template_rmsd().
◆ rmsd_include_unconstrained() [2/2]
| void protocols::fold_from_loops::NubInitioMover::rmsd_include_unconstrained | ( | bool | pick | ) |
References rmsd_include_unconstrained_.
◆ rmsd_threshold() [1/2]
| core::Real protocols::fold_from_loops::NubInitioMover::rmsd_threshold | ( | ) | const |
limit of divergence allowed between the template structure and the ab initio output
References rmsd_threshold_.
Referenced by parse_my_tag().
◆ rmsd_threshold() [2/2]
| void protocols::fold_from_loops::NubInitioMover::rmsd_threshold | ( | core::Real | threshold | ) |
References rmsd_threshold_.
◆ sanity_check()
|
private |
Checks that input make sense for the particular run.
References core::pose::Pose::constraint_set(), core::select::residue_selector::count_selected(), core::pose::Pose::detached_copy(), has_alphas_, has_betas_, nub_, core::pose::Pose::num_chains(), core::pose::Pose::pdb_info(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), template_pose_, template_selector(), protocols::fold_from_loops::TR(), core::pose::Pose::transfer_constraint_set(), use_cst_, and used_template_selector().
Referenced by make_unfolded_pose().
◆ sse() [1/2]
| std::string protocols::fold_from_loops::NubInitioMover::sse | ( | ) | const |
if given, allows to define the secondary structure of the template (in case it comes for PeptideStubMover)
References sse_.
Referenced by parse_my_tag().
◆ sse() [2/2]
| void protocols::fold_from_loops::NubInitioMover::sse | ( | std::string | pick | ) |
References sse_.
◆ template_insertion_ranges()
| core::select::residue_selector::ResidueRanges protocols::fold_from_loops::NubInitioMover::template_insertion_ranges | ( | ) | const |
Range of residues representing the INSERTION regions (checks that there is one)
References core::select::residue_selector::count_selected(), template_pose_, and template_selector_.
Referenced by used_template_ranges().
◆ template_pose()
| core::pose::Pose protocols::fold_from_loops::NubInitioMover::template_pose | ( | ) | const |
Store the unmodified pose as provided by apply.
References template_pose_.
◆ template_rmsd()
|
private |
evaluate rmsd with template
Compare the new folded pose with the template. The function compares according to whatever options the user has picked and sets the appropiate score terms to log those decisions.
References core::pose::add_score_line_string(), design_chain_selector(), nub_, rmsd_include_motif(), rmsd_include_unconstrained(), rmsd_threshold_, core::pose::setPoseExtraScore(), template_pose_, protocols::fold_from_loops::TR(), used_template_selector(), and work_template_selector().
Referenced by refold_pose().
◆ template_selector() [1/2]
| core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::NubInitioMover::template_selector | ( | ) | const |
References template_selector_.
Referenced by parse_my_tag(), and sanity_check().
◆ template_selector() [2/2]
| void protocols::fold_from_loops::NubInitioMover::template_selector | ( | core::select::residue_selector::ResidueSelectorCOP const & | selector | ) |
References template_selector_.
◆ use_correction_weights() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::use_correction_weights | ( | ) | const |
if true, apply the correction weights
References use_correction_weights_.
Referenced by parse_my_tag().
◆ use_correction_weights() [2/2]
| void protocols::fold_from_loops::NubInitioMover::use_correction_weights | ( | bool | pick | ) |
References use_correction_weights_.
◆ use_cst() [1/2]
| bool protocols::fold_from_loops::NubInitioMover::use_cst | ( | ) | const |
◆ use_cst() [2/2]
| void protocols::fold_from_loops::NubInitioMover::use_cst | ( | bool | pick | ) |
References use_cst_.
◆ used_template_ranges()
| core::select::residue_selector::ResidueRanges protocols::fold_from_loops::NubInitioMover::used_template_ranges | ( | bool | terminals = false | ) | const |
Range of residues kept from the TEMPLATE (checks that there is one) If terminals, adds N and C-terminal empty ranges (0, 0) if there is a N or C-terminal insertion.
References core::select::residue_selector::count_selected(), core::select::residue_selector::represent_residue_selector(), core::pose::Pose::size(), protocols::loops::start, template_insertion_ranges(), template_pose_, template_selector_, protocols::fold_from_loops::TR(), and used_template_selector().
Referenced by get_template_pieces().
◆ used_template_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::used_template_selector | ( | ) | const |
INVERTS the INSERTION selector in the REFERENCE TEMPLATE POSE.
References template_selector_.
Referenced by sanity_check(), template_rmsd(), and used_template_ranges().
◆ work_motif_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::work_motif_selector | ( | ) | const |
Selects the residues that are MOTIF from the DESIGN CHAIN.
References design(), and nub_.
Referenced by count_contacts(), and repack().
◆ work_template_selector()
| core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::NubInitioMover::work_template_selector | ( | ) | const |
Selects the residues that are TEMPLATE from the DESIGN CHAIN.
References design(), and nub_.
Referenced by template_rmsd().
Member Data Documentation
◆ abinitio_score_
|
private |
Referenced by post_process(), and refold_pose().
◆ clear_motif_cst_
|
private |
Referenced by clear_motif_cst(), and manage_constraints().
◆ design_
|
private |
◆ disulfides_bb_
|
private |
Referenced by disulfides_bb(), and repack_minimize_disulfides().
◆ disulfides_side_
|
private |
Referenced by disulfides_side(), and repack_minimize_disulfides().
◆ drop_unfolded_pose_
|
private |
Referenced by drop_unfolded_pose(), and refold_pose().
◆ dump_centroid_
|
private |
Referenced by dump_centroid().
◆ filter_
|
private |
Referenced by filter(), and refold_pose().
◆ filter_defined_
|
private |
Referenced by parse_my_tag(), and refold_pose().
◆ filter_scorefxn_
|
private |
Referenced by filter_scorefxn().
◆ fragments_id_
|
private |
Referenced by fragments_id(), and parse_my_tag().
◆ fullatom_scorefxn_
|
private |
Referenced by fullatom_scorefxn(), repack(), and repack_minimize_disulfides().
◆ has_alphas_
|
private |
Referenced by apply_abinitio(), and sanity_check().
◆ has_betas_
|
private |
Referenced by apply_abinitio(), and sanity_check().
◆ max_trials_
|
private |
Referenced by max_trials(), and refold_pose().
◆ mc_angle_weight_
|
private |
Referenced by angle_weight(), and apply_abinitio().
◆ mc_binder_weight_
|
private |
Referenced by angle_weight(), apply_abinitio(), and binder_weight().
◆ mc_correction_weights_
|
private |
Referenced by apply_abinitio(), and correction_weights().
◆ mc_dihedral_weight_
|
private |
Referenced by apply_abinitio(), and dihedral_weight().
◆ nub_
|
private |
Referenced by apply_abinitio(), bb_movable_selector(), chi_movable_selector(), count_contacts(), cys_design_selector(), design_chain_selector(), make_unfolded_pose(), manage_constraints(), nub(), parse_my_tag(), post_process(), refold_pose(), repack_minimize_disulfides(), sanity_check(), template_rmsd(), work_motif_selector(), and work_template_selector().
◆ pose_name_
|
private |
Referenced by post_process(), and refold_pose().
◆ prefix_
|
private |
Referenced by prefix().
◆ repack_disulfides_
|
private |
Referenced by apply_abinitio(), repack_disulfides(), and repack_minimize_disulfides().
◆ residue_type_
|
private |
Referenced by repack(), and residue_type().
◆ rmsd_include_motif_
|
private |
Referenced by rmsd_include_motif().
◆ rmsd_include_unconstrained_
|
private |
Referenced by rmsd_include_unconstrained().
◆ rmsd_threshold_
|
private |
Referenced by refold_pose(), rmsd_threshold(), and template_rmsd().
◆ silent_score_file_
|
private |
Referenced by dump_centroid().
◆ sse_
|
private |
Referenced by make_unfolded_pose(), and sse().
◆ template_pose_
|
private |
◆ template_selector_
|
private |
◆ trials_
|
private |
Referenced by refold_pose().
◆ use_correction_weights_
|
private |
Referenced by apply_abinitio(), and use_correction_weights().
◆ use_cst_
|
private |
Referenced by apply_abinitio(), manage_constraints(), sanity_check(), and use_cst().
The documentation for this class was generated from the following files:
- src/protocols/fold_from_loops/NubInitioMover.hh
- src/protocols/fold_from_loops/NubInitioMover.cc
