Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::seeded_abinitio::SeedFoldTree Class Reference

#include <SeedFoldTree.hh>

Inheritance diagram for protocols::seeded_abinitio::SeedFoldTree:
Inheritance graph

Public Member Functions

 SeedFoldTree ()
 SeedFoldTree (core::kinematics::FoldTreeOP ft)
 ~SeedFoldTree () override
void fold_tree (core::kinematics::FoldTreeOP ft)
core::kinematics::FoldTreeOP fold_tree () const
void apply (core::pose::Pose &pose) override
 Main Method. More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
core::scoring::ScoreFunctionOP scorefxn () const
void scorefxn (core::scoring::ScoreFunctionOP scorefxn)
utility::vector1< core::Sizeget_cutpoints ()
core::Size best_by_ala_scan (core::Size start, core::Size end, core::pose::PoseOP &ts_pose)
std::set< core::Sizeget_folding_vertices ()
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
core::kinematics::FoldTreeOP set_foldtree (core::pose::PoseOP &seed_target_chain, std::string secstr, protocols::loops::Loops &loops, bool protein_not_folded_yet)
bool ddg_based ()
void ddg_based (bool ddgb)
void set_anchor_res (utility::vector1< core::Size > anchor)
void anchor_specified (bool anchor_specified)
bool anchor_specified ()
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 Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
static void register_options ()
 Overload this static method if you access options within the mover. More...

Private Attributes

core::kinematics::FoldTreeOP fold_tree_
 newly generated foldtree OP More...
bool pdb_contains_target_
 check whether there is a second target chain loaded More...
bool twochains_
 is the input pose submitted with the target More...
utility::vector1< core::Sizecut_points_
 vector containing all cutpoints More...
protocols::loops::Loops all_seeds_
 seed info More...
bool set_jumps_manually
 for manual set up More...
utility::vector1< core::Sizeanchors_
 anchor residues More...
bool anchor_specified_
bool ddg_based_
 should the jump atoms be computed based on ddG More...
core::scoring::ScoreFunctionOP scorefxn_
 scorefunction for ala scan More...
utility::vector1< std::pair< core::Size, core::Size > > manual_jump_pairs_
core::pose::PoseOP template_pdb_
core::pose::PoseOP target_chain_
core::pose::PoseOP seeds_only_
core::pose::PoseOP only_seeds_chain_
std::set< core::Sizefolding_vertices_

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

◆ SeedFoldTree() [1/2]

protocols::seeded_abinitio::SeedFoldTree::SeedFoldTree ( )

◆ SeedFoldTree() [2/2]

protocols::seeded_abinitio::SeedFoldTree::SeedFoldTree ( core::kinematics::FoldTreeOP  ft)

◆ ~SeedFoldTree()

protocols::seeded_abinitio::SeedFoldTree::~SeedFoldTree ( )

Member Function Documentation

◆ anchor_specified() [1/2]

bool protocols::seeded_abinitio::SeedFoldTree::anchor_specified ( )

References anchor_specified_.

Referenced by anchor_specified().

◆ anchor_specified() [2/2]

void protocols::seeded_abinitio::SeedFoldTree::anchor_specified ( bool  anchor_specified)

◆ apply()

void protocols::seeded_abinitio::SeedFoldTree::apply ( core::pose::Pose )

◆ best_by_ala_scan()

core::Size protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan ( core::Size  start,
core::Size  end,
core::pose::PoseOP ts_pose 

◆ clone()

protocols::moves::MoverOP protocols::seeded_abinitio::SeedFoldTree::clone ( ) const

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ ddg_based() [1/2]

bool protocols::seeded_abinitio::SeedFoldTree::ddg_based ( )

References ddg_based_.

◆ ddg_based() [2/2]

void protocols::seeded_abinitio::SeedFoldTree::ddg_based ( bool  ddgb)

References ddg_based_.

◆ fold_tree() [1/2]

core::kinematics::FoldTreeOP protocols::seeded_abinitio::SeedFoldTree::fold_tree ( ) const

References fold_tree_.

◆ fold_tree() [2/2]

void protocols::seeded_abinitio::SeedFoldTree::fold_tree ( core::kinematics::FoldTreeOP  ft)

References fold_tree_.

◆ fresh_instance()

protocols::moves::MoverOP protocols::seeded_abinitio::SeedFoldTree::fresh_instance ( ) const

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_cutpoints()

utility::vector1< core::Size > protocols::seeded_abinitio::SeedFoldTree::get_cutpoints ( )

◆ get_folding_vertices()

std::set< core::Size > protocols::seeded_abinitio::SeedFoldTree::get_folding_vertices ( )

◆ get_name()

std::string protocols::seeded_abinitio::SeedFoldTree::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ mover_name()

std::string protocols::seeded_abinitio::SeedFoldTree::mover_name ( )

◆ parse_my_tag()

void protocols::seeded_abinitio::SeedFoldTree::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::sequence::end, core::scoring::parse_score_function(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::seeded_abinitio::TR().

◆ provide_xml_schema()

void protocols::seeded_abinitio::SeedFoldTree::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedFoldTree::scorefxn ( ) const

References scorefxn_.

Referenced by scorefxn().

◆ scorefxn() [2/2]

void protocols::seeded_abinitio::SeedFoldTree::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

References scorefxn(), and scorefxn_.

◆ set_anchor_res()

void protocols::seeded_abinitio::SeedFoldTree::set_anchor_res ( utility::vector1< core::Size anchor)

References anchors_.

◆ set_foldtree()

core::kinematics::FoldTreeOP protocols::seeded_abinitio::SeedFoldTree::set_foldtree ( core::pose::PoseOP seed_target_chain,
std::string  secstr,
protocols::loops::Loops loops,
bool  protein_not_folded_yet 

Member Data Documentation

◆ all_seeds_

protocols::loops::Loops protocols::seeded_abinitio::SeedFoldTree::all_seeds_

seed info

Referenced by SeedFoldTree().

◆ anchor_specified_

bool protocols::seeded_abinitio::SeedFoldTree::anchor_specified_

Referenced by anchor_specified(), and SeedFoldTree().

◆ anchors_

utility::vector1< core::Size > protocols::seeded_abinitio::SeedFoldTree::anchors_

anchor residues

Referenced by SeedFoldTree(), and set_anchor_res().

◆ cut_points_

utility::vector1<core::Size> protocols::seeded_abinitio::SeedFoldTree::cut_points_

vector containing all cutpoints

Referenced by SeedFoldTree().

◆ ddg_based_

bool protocols::seeded_abinitio::SeedFoldTree::ddg_based_

should the jump atoms be computed based on ddG

Referenced by ddg_based(), and SeedFoldTree().

◆ fold_tree_

core::kinematics::FoldTreeOP protocols::seeded_abinitio::SeedFoldTree::fold_tree_

newly generated foldtree OP

Referenced by fold_tree(), and SeedFoldTree().

◆ folding_vertices_

std::set< core::Size > protocols::seeded_abinitio::SeedFoldTree::folding_vertices_

Referenced by SeedFoldTree().

◆ manual_jump_pairs_

utility::vector1< std::pair< core::Size, core::Size > > protocols::seeded_abinitio::SeedFoldTree::manual_jump_pairs_

◆ only_seeds_chain_

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::only_seeds_chain_

◆ pdb_contains_target_

bool protocols::seeded_abinitio::SeedFoldTree::pdb_contains_target_

check whether there is a second target chain loaded

Referenced by SeedFoldTree().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedFoldTree::scorefxn_

scorefunction for ala scan

Referenced by scorefxn().

◆ seeds_only_

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::seeds_only_

◆ set_jumps_manually

bool protocols::seeded_abinitio::SeedFoldTree::set_jumps_manually

for manual set up

Referenced by SeedFoldTree().

◆ target_chain_

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::target_chain_

◆ template_pdb_

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::template_pdb_

◆ twochains_

bool protocols::seeded_abinitio::SeedFoldTree::twochains_

is the input pose submitted with the target

Referenced by SeedFoldTree().

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