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protocols::denovo_design::movers::FoldArchitectMover Class Reference

Mover that builds and folds a structure via fragment insertion. More...

#include <FoldArchitectMover.hh>

Inheritance diagram for protocols::denovo_design::movers::FoldArchitectMover:
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Public Types

typedef core::Real FoldScore
 
typedef utility::vector1
< connection::ConnectionArchitectCOP
ConnectionArchitectCOPs
 
typedef utility::vector1
< protocols::moves::MoverOP
MoverOPs
 
typedef utility::vector1
< protocols::filters::FilterCOP
FilterCOPs
 
typedef
core::select::residue_selector::ResidueVector 
ResidueVector
 
typedef
protocols::constraint_generator::ConstraintGeneratorOP 
ConstraintGeneratorOP
 
typedef
protocols::constraint_generator::ConstraintGeneratorCOP 
ConstraintGeneratorCOP
 
typedef
protocols::constraint_generator::ConstraintGeneratorCOPs 
ConstraintGeneratorCOPs
 
typedef components::RegisterShift RegisterShift
 
typedef
components::StrandOrientation 
StrandOrientation
 
- 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
 

Public Member Functions

 FoldArchitectMover ()
 
 ~FoldArchitectMover () override
 
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...
 
void apply (core::pose::Pose &pose) override
 Main Method. 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...
 
std::string const & id () const
 
void set_id (std::string const &id_value)
 Sets the ID of this mover. More...
 
void set_architect (architects::DeNovoArchitect const &architect)
 Sets the architect that will be used to build blueprints dynamically. More...
 
void set_folder (components::PoseFolder const &folder)
 Sets the pose folder that will be used to sample conformations. More...
 
void set_folder (components::PoseFolderOP folder)
 Sets the pose folder that will be used to sample conformations. More...
 
void set_builder (components::PoseBuilder const &builder)
 Sets the pose builder that will be used to create the extended-chain pose. More...
 
void set_builder (components::PoseBuilderOP builder)
 Sets the pose builder that will be used to create the extended-chain pose. More...
 
void set_perturber (components::StructureDataPerturber const &perturber)
 Sets the perturber that will be used to change the plans of the architects. More...
 
void set_perturber (components::StructureDataPerturberOP perturber)
 Sets the perturber that will be used to change the plans of the architects. More...
 
void set_start_segments (std::string const &segments_csv)
 sets names of segments to be included in the starting build phase More...
 
void set_start_segments (SegmentNameSet const &segments)
 sets names of segments to be included in the starting build phase More...
 
void set_stop_segments (std::string const &segments_csv)
 sets names of segments to be included in the final build phase More...
 
void set_stop_segments (SegmentNameSet const &segments)
 sets names of segments to be included in the final build phase More...
 
void set_build_overlap (core::Size const overlap_val)
 Sets the number of residues of overlap to use between build phases. More...
 
void set_score_filter (protocols::filters::Filter const &filter)
 Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false. More...
 
void setup_from_xml_file (std::string const &xml_file, basic::datacache::DataMap &data)
 Reads/parses an XML file and uses it to set up the mover. More...
 
void setup_from_xml_string (std::string const &xml_string, basic::datacache::DataMap &data)
 Reads/parses an XML string and uses it to set up the mover. More...
 
void setup_from_xml_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 Reads/parses a Tag object and uses it to set up the mover. More...
 
void clear_prefold_movers ()
 Clears the list of prefold movers. More...
 
void add_prefold_mover (protocols::moves::Mover const &mover)
 Adds a mover to the list of prefold movers. More...
 
void clear_postfold_movers ()
 Clears the list of postfold movers. More...
 
void add_postfold_mover (protocols::moves::Mover const &mover)
 Adds a mover to the list of postfold movers. More...
 
void add_filter (protocols::filters::Filter const &filter)
 Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt. More...
 
void clear_filters ()
 Clears the list of filters used to indicate whether a given folding attempt is successful. More...
 
void set_dump_pdbs (bool const dump)
 If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted. More...
 
void set_debug (bool const debug)
 The debug value of the poseBuilder will be set based on this. More...
 
void set_iterations_per_phase (core::Size const niter)
 Sets the number of folding attempts for each build phase. 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 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 void provide_xml_schema_with_name (utility::tag::XMLSchemaDefinition &xsd, std::string const &mover_name)
 
- 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

FoldScore folding_score (core::pose::Pose const &pose) const
 
void fold (core::pose::Pose &pose) const
 
void check_pose (core::pose::Pose const &pose) const
 runs user-provided filters on the pose More...
 
void check_and_accept (core::pose::Pose const &orig, core::pose::Pose &pose, FoldScore &bestscore) const
 
protocols::loops::Loops create_loops (core::pose::Pose const &pose, ResidueVector &overlap_residues, SegmentNames &movable_segments) const
 
core::select::residue_selector::ResidueSubset select_movable_residues (core::pose::Pose const &pose, SegmentNames const &movable_segments, ResidueVector const &overlap_residues) const
 
SegmentNames segments_to_fold (components::StructureData const &sd) const
 
MoverOPs prefold_movers (core::pose::Pose const &pose, protocols::loops::Loops const &loops, ConstraintGeneratorCOPs const &generators) const
 
MoverOPs postfold_movers (core::pose::Pose const &pose, protocols::loops::Loops const &loops, ConstraintGeneratorCOPs const &generators) const
 
void apply_movers (MoverOPs const &movers, core::pose::Pose &pose) const
 
SegmentNames find_roots (core::pose::Pose const &pose, protocols::loops::Loops const &loops) const
 
ConstraintGeneratorCOPs create_constraint_generators (ResidueVector const &residues) const
 
ConstraintGeneratorOP create_overlap_constraint_generator (ResidueVector const &residues) const
 builds a constraint generator for residues that overlap between phases More...
 
void remove_cutpoints (components::StructureData &sd, protocols::loops::Loops const &loops) const
 
void parse_architect (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
void parse_folder (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
void parse_perturber (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
void parse_filters (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
void parse_prefold_movers (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
void parse_postfold_movers (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
MoverOPs parse_movers (utility::tag::TagCOP tag, basic::datacache::DataMap &data) const
 
core::pose::PoseOP build_in_phases (components::StructureData const &full_sd, components::BuildPhases const &phases, SegmentNameSet const &finished, core::Size const phase_num) const
 builds/folds pose in phases using recursive algorithm More...
 
void fold_attempt (core::pose::Pose &pose) const
 

Static Private Member Functions

static protocols::filters::FilterOP default_score_filter ()
 
static std::string build_denovo_backbone_ct_naming_func (std::string)
 
static std::string prefold_ct_naming_func (std::string)
 
static std::string postfold_ct_naming_func (std::string)
 
static std::string filters_ct_naming_func (std::string)
 
static std::string connections_ct_naming_func (std::string)
 
static std::string folder_ct_namer (std::string)
 
static std::string perturber_ct_namer (std::string)
 
static void define_folder_group (utility::tag::XMLSchemaDefinition &)
 
static void define_perturber_group (utility::tag::XMLSchemaDefinition &)
 
static void define_filters_ct (utility::tag::XMLSchemaDefinition &)
 
static void define_prefold_movers_ct (utility::tag::XMLSchemaDefinition &)
 
static void define_postfold_movers_ct (utility::tag::XMLSchemaDefinition &)
 
static std::string perturber_group_name ()
 
static std::string folder_group_name ()
 

Private Attributes

architects::DeNovoArchitectCOP architect_
 
components::PoseBuilderOP builder_
 
components::PoseFolderOP folder_
 
components::StructureDataPerturberOP perturber_
 
MoverOPs prefold_movers_
 
MoverOPs postfold_movers_
 
FilterCOPs filters_
 
protocols::filters::FilterCOP score_filter_
 
std::string id_
 
bool dry_run_
 
bool dump_pdbs_
 
bool debug_
 
core::Size build_overlap_
 
core::Size iterations_per_phase_
 
SegmentNameSet start_segments_
 
SegmentNameSet stop_segments_
 

Additional Inherited Members

- 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...
 

Detailed Description

Mover that builds and folds a structure via fragment insertion.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::denovo_design::movers::FoldArchitectMover::FoldArchitectMover ( )

References debug_, and set_debug().

protocols::denovo_design::movers::FoldArchitectMover::~FoldArchitectMover ( )
overridedefault

Member Function Documentation

void protocols::denovo_design::movers::FoldArchitectMover::add_filter ( protocols::filters::Filter const &  filter)

Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt.

References protocols::filters::Filter::clone(), and filters_.

Referenced by parse_filters().

void protocols::denovo_design::movers::FoldArchitectMover::add_postfold_mover ( protocols::moves::Mover const &  mover)

Adds a mover to the list of postfold movers.

References protocols::moves::Mover::clone(), and postfold_movers_.

Referenced by parse_postfold_movers().

void protocols::denovo_design::movers::FoldArchitectMover::add_prefold_mover ( protocols::moves::Mover const &  mover)

Adds a mover to the list of prefold movers.

References protocols::moves::Mover::clone(), and prefold_movers_.

Referenced by parse_prefold_movers().

void protocols::denovo_design::movers::FoldArchitectMover::apply ( core::pose::Pose )
overridevirtual
void protocols::denovo_design::movers::FoldArchitectMover::apply_movers ( MoverOPs const &  movers,
core::pose::Pose pose 
) const
private

References protocols::TR().

Referenced by fold_attempt().

std::string protocols::denovo_design::movers::FoldArchitectMover::build_denovo_backbone_ct_naming_func ( std::string  subelement_name)
staticprivate
core::pose::PoseOP protocols::denovo_design::movers::FoldArchitectMover::build_in_phases ( components::StructureData const &  full_sd,
components::BuildPhases const &  phases,
SegmentNameSet const &  finished,
core::Size const  phase_num 
) const
private
void protocols::denovo_design::movers::FoldArchitectMover::check_and_accept ( core::pose::Pose const &  orig,
core::pose::Pose pose,
FoldScore bestscore 
) const
private
void protocols::denovo_design::movers::FoldArchitectMover::check_pose ( core::pose::Pose const &  pose) const
private

runs user-provided filters on the pose

checks the pose for whether it folded correctly, according to user's filters

Filters are called for each build phase, and for every folding attempt, in order. If a filter fails, an exception is thrown and no later filters are run.

Exceptions
EXCN_FilterFailedif any filter fails

References filters_.

Referenced by fold_attempt().

void protocols::denovo_design::movers::FoldArchitectMover::clear_filters ( )

Clears the list of filters used to indicate whether a given folding attempt is successful.

References filters_.

Referenced by parse_filters(), and setup_from_xml_tag().

void protocols::denovo_design::movers::FoldArchitectMover::clear_postfold_movers ( )

Clears the list of postfold movers.

References postfold_movers_.

Referenced by setup_from_xml_tag().

void protocols::denovo_design::movers::FoldArchitectMover::clear_prefold_movers ( )

Clears the list of prefold movers.

References prefold_movers_.

Referenced by setup_from_xml_tag().

protocols::moves::MoverOP protocols::denovo_design::movers::FoldArchitectMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

static std::string protocols::denovo_design::movers::FoldArchitectMover::connections_ct_naming_func ( std::string  )
staticprivate
FoldArchitectMover::ConstraintGeneratorCOPs protocols::denovo_design::movers::FoldArchitectMover::create_constraint_generators ( ResidueVector const &  residues) const
private
protocols::loops::Loops protocols::denovo_design::movers::FoldArchitectMover::create_loops ( core::pose::Pose const &  pose,
ResidueVector overlap_residues,
SegmentNames movable_segments 
) const
private
FoldArchitectMover::ConstraintGeneratorOP protocols::denovo_design::movers::FoldArchitectMover::create_overlap_constraint_generator ( ResidueVector const &  residues) const
private

builds a constraint generator for residues that overlap between phases

Parameters
[in]residuesVector of resids corresponding to the overlap residues

References protocols::TR().

Referenced by create_constraint_generators().

protocols::filters::FilterOP protocols::denovo_design::movers::FoldArchitectMover::default_score_filter ( )
staticprivate
void protocols::denovo_design::movers::FoldArchitectMover::define_filters_ct ( utility::tag::XMLSchemaDefinition &  xsd)
staticprivate
void protocols::denovo_design::movers::FoldArchitectMover::define_folder_group ( utility::tag::XMLSchemaDefinition &  xsd)
staticprivate
void protocols::denovo_design::movers::FoldArchitectMover::define_perturber_group ( utility::tag::XMLSchemaDefinition &  xsd)
staticprivate
void protocols::denovo_design::movers::FoldArchitectMover::define_postfold_movers_ct ( utility::tag::XMLSchemaDefinition &  xsd)
staticprivate
void protocols::denovo_design::movers::FoldArchitectMover::define_prefold_movers_ct ( utility::tag::XMLSchemaDefinition &  xsd)
staticprivate
std::string protocols::denovo_design::movers::FoldArchitectMover::filters_ct_naming_func ( std::string  subelement_name)
staticprivate
SegmentNames protocols::denovo_design::movers::FoldArchitectMover::find_roots ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  loops 
) const
private
void protocols::denovo_design::movers::FoldArchitectMover::fold ( core::pose::Pose pose) const
private
void protocols::denovo_design::movers::FoldArchitectMover::fold_attempt ( core::pose::Pose pose) const
private
std::string protocols::denovo_design::movers::FoldArchitectMover::folder_ct_namer ( std::string  folder_name)
staticprivate

Referenced by define_folder_group().

std::string protocols::denovo_design::movers::FoldArchitectMover::folder_group_name ( )
staticprivate
FoldArchitectMover::FoldScore protocols::denovo_design::movers::FoldArchitectMover::folding_score ( core::pose::Pose const &  pose) const
private
protocols::moves::MoverOP protocols::denovo_design::movers::FoldArchitectMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::denovo_design::movers::FoldArchitectMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::denovo_design::movers::BuildDeNovoBackboneMover.

References mover_name().

Referenced by apply(), and setup_from_xml_tag().

std::string const & protocols::denovo_design::movers::FoldArchitectMover::id ( ) const

References id_.

Referenced by find_roots().

std::string protocols::denovo_design::movers::FoldArchitectMover::mover_name ( )
static
void protocols::denovo_design::movers::FoldArchitectMover::parse_architect ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
private

References set_architect().

Referenced by setup_from_xml_tag().

void protocols::denovo_design::movers::FoldArchitectMover::parse_filters ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
private
void protocols::denovo_design::movers::FoldArchitectMover::parse_folder ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
private
FoldArchitectMover::MoverOPs protocols::denovo_design::movers::FoldArchitectMover::parse_movers ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
) const
private
void protocols::denovo_design::movers::FoldArchitectMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::denovo_design::movers::FoldArchitectMover::parse_perturber ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
private
void protocols::denovo_design::movers::FoldArchitectMover::parse_postfold_movers ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
private

References add_postfold_mover(), and parse_movers().

Referenced by setup_from_xml_tag().

void protocols::denovo_design::movers::FoldArchitectMover::parse_prefold_movers ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
private

References add_prefold_mover(), and parse_movers().

Referenced by setup_from_xml_tag().

std::string protocols::denovo_design::movers::FoldArchitectMover::perturber_ct_namer ( std::string  perturber_name)
staticprivate

Referenced by define_perturber_group().

std::string protocols::denovo_design::movers::FoldArchitectMover::perturber_group_name ( )
staticprivate
std::string protocols::denovo_design::movers::FoldArchitectMover::postfold_ct_naming_func ( std::string  subelement_name)
staticprivate
FoldArchitectMover::MoverOPs protocols::denovo_design::movers::FoldArchitectMover::postfold_movers ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  loops,
ConstraintGeneratorCOPs const &  generators 
) const
private

References postfold_movers_, and core::pose::Pose::size().

Referenced by fold_attempt().

std::string protocols::denovo_design::movers::FoldArchitectMover::prefold_ct_naming_func ( std::string  subelement_name)
staticprivate
FoldArchitectMover::MoverOPs protocols::denovo_design::movers::FoldArchitectMover::prefold_movers ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  loops,
ConstraintGeneratorCOPs const &  generators 
) const
private
void protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema_with_name ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  mover_name 
)
static
void protocols::denovo_design::movers::FoldArchitectMover::remove_cutpoints ( components::StructureData sd,
protocols::loops::Loops const &  loops 
) const
private
SegmentNames protocols::denovo_design::movers::FoldArchitectMover::segments_to_fold ( components::StructureData const &  sd) const
private
core::select::residue_selector::ResidueSubset protocols::denovo_design::movers::FoldArchitectMover::select_movable_residues ( core::pose::Pose const &  pose,
SegmentNames const &  movable_segments,
ResidueVector const &  overlap_residues 
) const
private
void protocols::denovo_design::movers::FoldArchitectMover::set_architect ( architects::DeNovoArchitect const &  architect)
void protocols::denovo_design::movers::FoldArchitectMover::set_build_overlap ( core::Size const  overlap_val)

Sets the number of residues of overlap to use between build phases.

References build_overlap_.

Referenced by protocols::denovo_design::movers::ExtendChainMover::apply(), protocols::denovo_design::movers::BridgeChainsMover::apply(), and parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_builder ( components::PoseBuilder const &  builder)

Sets the pose builder that will be used to create the extended-chain pose.

Clones the provided PoseBuilder

References protocols::denovo_design::components::PoseBuilder::clone().

void protocols::denovo_design::movers::FoldArchitectMover::set_builder ( components::PoseBuilderOP  builder)

Sets the pose builder that will be used to create the extended-chain pose.

Uses/stores the provided PoseBuilder pointer directly

References builder_.

void protocols::denovo_design::movers::FoldArchitectMover::set_debug ( bool const  debug)

The debug value of the poseBuilder will be set based on this.

References builder_, core::pack::interaction_graph::debug, and debug_.

Referenced by FoldArchitectMover(), and parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_dump_pdbs ( bool const  dump)
inline

If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted.

References dump_pdbs_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_folder ( components::PoseFolder const &  folder)
void protocols::denovo_design::movers::FoldArchitectMover::set_folder ( components::PoseFolderOP  folder)

Sets the pose folder that will be used to sample conformations.

Uses the provided PoseFolder pointer directly

References folder_.

void protocols::denovo_design::movers::FoldArchitectMover::set_id ( std::string const &  id_value)

Sets the ID of this mover.

References id_.

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_iterations_per_phase ( core::Size const  niter)

Sets the number of folding attempts for each build phase.

References iterations_per_phase_.

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), and parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_perturber ( components::StructureDataPerturber const &  perturber)

Sets the perturber that will be used to change the plans of the architects.

Clones the provided Perturber

References protocols::denovo_design::components::StructureDataPerturber::clone().

Referenced by parse_perturber().

void protocols::denovo_design::movers::FoldArchitectMover::set_perturber ( components::StructureDataPerturberOP  perturber)

Sets the perturber that will be used to change the plans of the architects.

Uses/stores the provided Perturber pointer directly

References perturber_.

void protocols::denovo_design::movers::FoldArchitectMover::set_score_filter ( protocols::filters::Filter const &  filter)

Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false.

References protocols::filters::Filter::clone(), and score_filter_.

void protocols::denovo_design::movers::FoldArchitectMover::set_start_segments ( std::string const &  segments_csv)

sets names of segments to be included in the starting build phase

Parameters
[in]segments_csvComma-separated string containing segment names

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_start_segments ( SegmentNameSet const &  segments)

sets names of segments to be included in the starting build phase

Parameters
[in]segmentsSet of segment names

References start_segments_.

void protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments ( std::string const &  segments_csv)

sets names of segments to be included in the final build phase

Parameters
[in]segments_csvComma-separated string containing segment names

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments ( SegmentNameSet const &  segments)

sets names of segments to be included in the final build phase

Parameters
[in]segmentsSet of segment names

References stop_segments_.

void protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_file ( std::string const &  xml_file,
basic::datacache::DataMap &  data 
)

Reads/parses an XML file and uses it to set up the mover.

References setup_from_xml_tag().

Referenced by parse_my_tag().

void protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_string ( std::string const &  xml_string,
basic::datacache::DataMap &  data 
)

Reads/parses an XML string and uses it to set up the mover.

References setup_from_xml_tag().

void protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)

Member Data Documentation

architects::DeNovoArchitectCOP protocols::denovo_design::movers::FoldArchitectMover::architect_
private

Referenced by apply(), and set_architect().

core::Size protocols::denovo_design::movers::FoldArchitectMover::build_overlap_
private
components::PoseBuilderOP protocols::denovo_design::movers::FoldArchitectMover::builder_
private
bool protocols::denovo_design::movers::FoldArchitectMover::debug_
private
bool protocols::denovo_design::movers::FoldArchitectMover::dry_run_
private
bool protocols::denovo_design::movers::FoldArchitectMover::dump_pdbs_
private
FilterCOPs protocols::denovo_design::movers::FoldArchitectMover::filters_
private
components::PoseFolderOP protocols::denovo_design::movers::FoldArchitectMover::folder_
private

Referenced by fold_attempt(), and set_folder().

std::string protocols::denovo_design::movers::FoldArchitectMover::id_
private

Referenced by id(), and set_id().

core::Size protocols::denovo_design::movers::FoldArchitectMover::iterations_per_phase_
private
components::StructureDataPerturberOP protocols::denovo_design::movers::FoldArchitectMover::perturber_
private

Referenced by build_in_phases(), and set_perturber().

MoverOPs protocols::denovo_design::movers::FoldArchitectMover::postfold_movers_
private
MoverOPs protocols::denovo_design::movers::FoldArchitectMover::prefold_movers_
private
protocols::filters::FilterCOP protocols::denovo_design::movers::FoldArchitectMover::score_filter_
private

Referenced by folding_score(), and set_score_filter().

SegmentNameSet protocols::denovo_design::movers::FoldArchitectMover::start_segments_
private

Referenced by apply(), and set_start_segments().

SegmentNameSet protocols::denovo_design::movers::FoldArchitectMover::stop_segments_
private

Referenced by apply(), and set_stop_segments().


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