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protocols::fold_from_loops::NubInitioMover Class Reference

#include <NubInitioMover.hh>

Inheritance diagram for protocols::fold_from_loops::NubInitioMover:
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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 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 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...
 

Static Private Member Functions

static std::string default_prefix ()
 
static
core::select::residue_selector::ResidueSelectorCOP 
default_template_selector ()
 
static
core::scoring::ScoreFunctionOP 
default_fullatom_scorefxn ()
 
static bool default_use_cst ()
 
static bool default_clear_motif_cst ()
 
static core::Real default_rmsd_threshold ()
 
static bool default_rmsd_include_motif ()
 
static bool default_rmsd_include_unconstrained ()
 
static bool default_repack_disulfides ()
 
static bool default_disulfides_bb ()
 
static core::Size default_disulfides_side ()
 
static core::Size default_max_trials ()
 
static core::Real default_mc_binder_weight ()
 
static core::Real default_mc_angle_weight ()
 
static core::Real default_mc_dihedral_weight ()
 
static core::Real default_mc_correction_weights ()
 
static bool default_use_correction_weights ()
 
static bool default_dump_centroid ()
 
static bool default_drop_unfolded_pose ()
 
static bool default_design ()
 
static std::string default_residue_type ()
 
static std::string default_sse ()
 
static std::string default_filter_name ()
 
static
core::scoring::ScoreFunctionOP 
default_filter_scorefxn ()
 

Private Attributes

std::string prefix_
 
core::pose::Pose template_pose_
 
core::select::residue_selector::ResidueSelectorCOP template_selector_
 
core::scoring::ScoreFunctionOP fullatom_scorefxn_
 
core::scoring::ScoreFunctionOP abinitio_score_
 
utils::NubOP nub_
 
std::string sse_
 
bool use_cst_
 
bool clear_motif_cst_
 
core::Real rmsd_threshold_
 
bool rmsd_include_motif_
 
bool rmsd_include_unconstrained_
 
bool repack_disulfides_
 
bool disulfides_bb_
 
core::Size disulfides_side_
 
std::string fragments_id_
 
core::Real trials_
 
core::Real max_trials_
 
core::Real mc_binder_weight_
 
core::Real mc_angle_weight_
 
core::Real mc_dihedral_weight_
 
core::Real mc_correction_weights_
 
bool use_correction_weights_
 
bool has_betas_
 
bool has_alphas_
 
bool dump_centroid_
 
bool drop_unfolded_pose_
 
bool design_
 
std::string residue_type_
 
core::io::silent::SilentFileDataOP silent_score_file_
 
protocols::filters::FilterOP filter_
 
bool filter_defined_
 
core::scoring::ScoreFunctionOP filter_scorefxn_
 
std::string pose_name_
 

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::fold_from_loops::NubInitioMover::NubInitioMover ( )

Empty Constructor.

protocols::fold_from_loops::NubInitioMover::~NubInitioMover ( )
override

Destructor.

Member Function Documentation

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_.

core::Real protocols::fold_from_loops::NubInitioMover::angle_weight ( ) const

References mc_binder_weight_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::NubInitioMover::apply ( core::pose::Pose pose)
overridevirtual
core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::apply_abinitio ( core::pose::Pose pose)
private
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().

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_.

core::Real protocols::fold_from_loops::NubInitioMover::binder_weight ( ) const

References mc_binder_weight_.

Referenced by parse_my_tag().

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().

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().

void protocols::fold_from_loops::NubInitioMover::clear_motif_cst ( bool  pick)

References clear_motif_cst_.

protocols::moves::MoverOP protocols::fold_from_loops::NubInitioMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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().

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_.

core::Real protocols::fold_from_loops::NubInitioMover::correction_weights ( ) const
core::Size protocols::fold_from_loops::NubInitioMover::count_contacts ( core::pose::Pose pose) const
private
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().

bool protocols::fold_from_loops::NubInitioMover::default_clear_motif_cst ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_design ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_disulfides_bb ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::Size protocols::fold_from_loops::NubInitioMover::default_disulfides_side ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_drop_unfolded_pose ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_dump_centroid ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

std::string protocols::fold_from_loops::NubInitioMover::default_filter_name ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::default_filter_scorefxn ( )
staticprivate
core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::default_fullatom_scorefxn ( )
staticprivate
core::Size protocols::fold_from_loops::NubInitioMover::default_max_trials ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::Real protocols::fold_from_loops::NubInitioMover::default_mc_angle_weight ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::Real protocols::fold_from_loops::NubInitioMover::default_mc_binder_weight ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::Real protocols::fold_from_loops::NubInitioMover::default_mc_correction_weights ( )
staticprivate
core::Real protocols::fold_from_loops::NubInitioMover::default_mc_dihedral_weight ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

std::string protocols::fold_from_loops::NubInitioMover::default_prefix ( )
staticprivate

Referenced by parse_my_tag().

bool protocols::fold_from_loops::NubInitioMover::default_repack_disulfides ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

std::string protocols::fold_from_loops::NubInitioMover::default_residue_type ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_rmsd_include_motif ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_rmsd_include_unconstrained ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::Real protocols::fold_from_loops::NubInitioMover::default_rmsd_threshold ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

std::string protocols::fold_from_loops::NubInitioMover::default_sse ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::NubInitioMover::default_template_selector ( )
staticprivate
bool protocols::fold_from_loops::NubInitioMover::default_use_correction_weights ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::NubInitioMover::default_use_cst ( )
staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

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().

void protocols::fold_from_loops::NubInitioMover::design ( bool  pick)

References design_.

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().

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_.

core::Real protocols::fold_from_loops::NubInitioMover::dihedral_weight ( ) const

References mc_dihedral_weight_.

Referenced by parse_my_tag().

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().

void protocols::fold_from_loops::NubInitioMover::disulfides_bb ( bool  pick)

References disulfides_bb_.

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().

void protocols::fold_from_loops::NubInitioMover::disulfides_side ( core::Real  value)

References disulfides_side_.

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().

void protocols::fold_from_loops::NubInitioMover::drop_unfolded_pose ( bool  pick)

References drop_unfolded_pose_.

void protocols::fold_from_loops::NubInitioMover::dump_centroid ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionOP  scorefxn 
)
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::jd2::current_output_filename(), protocols::jd2::current_output_name(), dump_centroid_, core::pose::Pose::fold_tree(), protocols::jd2::jd2_used(), silent_score_file_, and protocols::fold_from_loops::TR().

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().

void protocols::fold_from_loops::NubInitioMover::dump_centroid ( bool  pick)

References dump_centroid_.

protocols::filters::FilterOP protocols::fold_from_loops::NubInitioMover::filter ( ) const

if given, define an alternative filter to RMSD

References filter_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::NubInitioMover::filter ( protocols::filters::FilterOP  pick)

References filter_.

core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::filter_scorefxn ( ) const

score function to use on provided filter

References filter_scorefxn_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::NubInitioMover::filter_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References filter_scorefxn_.

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().

void protocols::fold_from_loops::NubInitioMover::fragments_id ( std::string const &  name)
protocols::moves::MoverOP protocols::fold_from_loops::NubInitioMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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().

void protocols::fold_from_loops::NubInitioMover::fullatom_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References fullatom_scorefxn_.

std::string protocols::fold_from_loops::NubInitioMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::NubInitioMover::get_template_pieces ( core::pose::Pose const &  pose) const
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().

core::select::residue_selector::ResidueRangesOP protocols::fold_from_loops::NubInitioMover::make_template_ranges ( core::select::residue_selector::ResidueRanges  original) const
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(), core::select::residue_selector::ResidueRange::start(), core::select::residue_selector::ResidueRange::stop(), and template_pose_.

Referenced by get_template_pieces().

void protocols::fold_from_loops::NubInitioMover::make_unfolded_pose ( core::pose::Pose 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 protocols::moves::DsspMover::apply(), 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().

void protocols::fold_from_loops::NubInitioMover::manage_constraints ( core::pose::Pose pose)
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().

void protocols::fold_from_loops::NubInitioMover::max_trials ( core::Size  choice)

how many times do we try to fold?

References max_trials_.

core::Size protocols::fold_from_loops::NubInitioMover::max_trials ( ) const

References max_trials_.

Referenced by parse_my_tag().

std::string protocols::fold_from_loops::NubInitioMover::mover_name ( )
static
utils::NubOP protocols::fold_from_loops::NubInitioMover::nub ( ) const

object that contains and processes the unfolded pose info

References nub_.

Referenced by nub().

void protocols::fold_from_loops::NubInitioMover::nub ( utils::NubOP  nub)

References nub(), and nub_.

void protocols::fold_from_loops::NubInitioMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::fold_from_loops::NubInitioMover::post_process ( core::pose::Pose pose)
private
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().

void protocols::fold_from_loops::NubInitioMover::prefix ( std::string const &  prefix)

References prefix(), and prefix_.

void protocols::fold_from_loops::NubInitioMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::fold_from_loops::NubInitioMover::refold_pose ( core::pose::Pose 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(), apply_abinitio(), core::chemical::CENTROID, core::pose::Pose::detached_copy(), drop_unfolded_pose_, filter_, filter_defined_, max_trials_, 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().

void protocols::fold_from_loops::NubInitioMover::repack ( core::pose::Pose pose)
private
bool protocols::fold_from_loops::NubInitioMover::repack_disulfides ( ) const

when true, try to repack disulfides

References repack_disulfides_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::NubInitioMover::repack_disulfides ( bool  pick)

References repack_disulfides_.

void protocols::fold_from_loops::NubInitioMover::repack_minimize_disulfides ( core::pose::Pose pose)
private
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().

void protocols::fold_from_loops::NubInitioMover::residue_type ( std::string  pick)

References residue_type_.

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().

void protocols::fold_from_loops::NubInitioMover::rmsd_include_motif ( bool  pick)

References rmsd_include_motif_.

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().

void protocols::fold_from_loops::NubInitioMover::rmsd_include_unconstrained ( bool  pick)
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().

void protocols::fold_from_loops::NubInitioMover::rmsd_threshold ( core::Real  threshold)

References rmsd_threshold_.

void protocols::fold_from_loops::NubInitioMover::sanity_check ( core::pose::Pose const &  pose)
private
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().

void protocols::fold_from_loops::NubInitioMover::sse ( std::string  pick)

References sse_.

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().

core::pose::Pose protocols::fold_from_loops::NubInitioMover::template_pose ( ) const

Store the unmodified pose as provided by apply.

References template_pose_.

core::Real protocols::fold_from_loops::NubInitioMover::template_rmsd ( core::pose::Pose pose)
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().

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::NubInitioMover::template_selector ( ) const

References template_selector_.

Referenced by parse_my_tag(), and sanity_check().

void protocols::fold_from_loops::NubInitioMover::template_selector ( core::select::residue_selector::ResidueSelectorCOP const &  selector)

References template_selector_.

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().

void protocols::fold_from_loops::NubInitioMover::use_correction_weights ( bool  pick)
bool protocols::fold_from_loops::NubInitioMover::use_cst ( ) const

when true, use constraint guided ab initio

References use_cst_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::NubInitioMover::use_cst ( bool  pick)

References use_cst_.

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().

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().

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().

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

core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::abinitio_score_
private

Referenced by post_process(), and refold_pose().

bool protocols::fold_from_loops::NubInitioMover::clear_motif_cst_
private
bool protocols::fold_from_loops::NubInitioMover::design_
private

Referenced by design(), and repack().

bool protocols::fold_from_loops::NubInitioMover::disulfides_bb_
private
core::Size protocols::fold_from_loops::NubInitioMover::disulfides_side_
private
bool protocols::fold_from_loops::NubInitioMover::drop_unfolded_pose_
private

Referenced by drop_unfolded_pose(), and refold_pose().

bool protocols::fold_from_loops::NubInitioMover::dump_centroid_
private

Referenced by dump_centroid().

protocols::filters::FilterOP protocols::fold_from_loops::NubInitioMover::filter_
private

Referenced by filter(), and refold_pose().

bool protocols::fold_from_loops::NubInitioMover::filter_defined_
private

Referenced by parse_my_tag(), and refold_pose().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::filter_scorefxn_
private

Referenced by filter_scorefxn().

std::string protocols::fold_from_loops::NubInitioMover::fragments_id_
private

Referenced by fragments_id(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::NubInitioMover::fullatom_scorefxn_
private
bool protocols::fold_from_loops::NubInitioMover::has_alphas_
private

Referenced by apply_abinitio(), and sanity_check().

bool protocols::fold_from_loops::NubInitioMover::has_betas_
private

Referenced by apply_abinitio(), and sanity_check().

core::Real protocols::fold_from_loops::NubInitioMover::max_trials_
private

Referenced by max_trials(), and refold_pose().

core::Real protocols::fold_from_loops::NubInitioMover::mc_angle_weight_
private

Referenced by angle_weight(), and apply_abinitio().

core::Real protocols::fold_from_loops::NubInitioMover::mc_binder_weight_
private
core::Real protocols::fold_from_loops::NubInitioMover::mc_correction_weights_
private
core::Real protocols::fold_from_loops::NubInitioMover::mc_dihedral_weight_
private

Referenced by apply_abinitio(), and dihedral_weight().

utils::NubOP protocols::fold_from_loops::NubInitioMover::nub_
private
std::string protocols::fold_from_loops::NubInitioMover::pose_name_
private

Referenced by post_process(), and refold_pose().

std::string protocols::fold_from_loops::NubInitioMover::prefix_
private

Referenced by prefix().

bool protocols::fold_from_loops::NubInitioMover::repack_disulfides_
private
std::string protocols::fold_from_loops::NubInitioMover::residue_type_
private

Referenced by repack(), and residue_type().

bool protocols::fold_from_loops::NubInitioMover::rmsd_include_motif_
private

Referenced by rmsd_include_motif().

bool protocols::fold_from_loops::NubInitioMover::rmsd_include_unconstrained_
private
core::Real protocols::fold_from_loops::NubInitioMover::rmsd_threshold_
private
core::io::silent::SilentFileDataOP protocols::fold_from_loops::NubInitioMover::silent_score_file_
private

Referenced by dump_centroid().

std::string protocols::fold_from_loops::NubInitioMover::sse_
private

Referenced by make_unfolded_pose(), and sse().

core::pose::Pose protocols::fold_from_loops::NubInitioMover::template_pose_
private
core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::NubInitioMover::template_selector_
private
core::Real protocols::fold_from_loops::NubInitioMover::trials_
private

Referenced by refold_pose().

bool protocols::fold_from_loops::NubInitioMover::use_correction_weights_
private
bool protocols::fold_from_loops::NubInitioMover::use_cst_
private

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