Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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
[legend]
Collaboration diagram for protocols::seeded_abinitio::SeedFoldTree:
Collaboration graph
[legend]

Public Member Functions

 SeedFoldTree ()
 
 SeedFoldTree (core::kinematics::FoldTreeOP ft)
 
virtual ~SeedFoldTree ()
 
void fold_tree (core::kinematics::FoldTreeOP ft)
 
core::kinematics::FoldTreeOP fold_tree () const
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
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_verteces ()
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 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 ()
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
void set_current_tag (std::string const &new_tag)
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

core::kinematics::FoldTreeOP fold_tree_
 newly generated foldtree OP More...
 
bool add_target_
 is there a second target chain to add 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< 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
< Size, 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_verteces_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Constructor & Destructor Documentation

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

Referenced by clone().

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

Member Function Documentation

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

References anchor_specified_.

Referenced by anchor_specified().

void protocols::seeded_abinitio::SeedFoldTree::apply ( core::pose::Pose pose)
virtual
core::Size protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan ( core::Size  start,
core::Size  end,
core::pose::PoseOP ts_pose 
)
protocols::moves::MoverOP protocols::seeded_abinitio::SeedFoldTree::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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

Reimplemented from protocols::moves::Mover.

References SeedFoldTree().

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

References ddg_based_.

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

References ddg_based_.

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

References fold_tree_.

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

References fold_tree_.

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

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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

Reimplemented from protocols::moves::Mover.

utility::vector1< core::Size > protocols::seeded_abinitio::SeedFoldTree::get_cutpoints ( )
std::set< core::Size > protocols::seeded_abinitio::SeedFoldTree::get_folding_verteces ( )
std::string protocols::seeded_abinitio::SeedFoldTree::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::seeded_abinitio::SeedFoldTreeCreator::mover_name().

void protocols::seeded_abinitio::SeedFoldTree::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References core::sequence::end, protocols::moves::DataMap::get(), core::import_pose::pose_from_pdb(), and protocols::seeded_abinitio::TR().

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

References scorefxn_.

Referenced by scorefxn().

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

References scorefxn(), and scorefxn_.

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

References anchors_.

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

bool protocols::seeded_abinitio::SeedFoldTree::add_target_
private

is there a second target chain to add

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

seed info

Referenced by SeedFoldTree().

bool protocols::seeded_abinitio::SeedFoldTree::anchor_specified_
private

Referenced by anchor_specified(), and SeedFoldTree().

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

anchor residues

Referenced by SeedFoldTree(), and set_anchor_res().

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

vector containing all cutpoints

Referenced by SeedFoldTree().

bool protocols::seeded_abinitio::SeedFoldTree::ddg_based_
private

should the jump atoms be computed based on ddG

Referenced by ddg_based(), and SeedFoldTree().

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

newly generated foldtree OP

Referenced by fold_tree(), and SeedFoldTree().

std::set< core::Size > protocols::seeded_abinitio::SeedFoldTree::folding_verteces_
private

Referenced by SeedFoldTree().

utility::vector1< std::pair< Size, Size > > protocols::seeded_abinitio::SeedFoldTree::manual_jump_pairs_
private
core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::only_seeds_chain_
private
bool protocols::seeded_abinitio::SeedFoldTree::pdb_contains_target_
private

check whether there is a second target chain loaded

Referenced by SeedFoldTree().

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

scorefunction for ala scan

Referenced by scorefxn().

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::seeds_only_
private
bool protocols::seeded_abinitio::SeedFoldTree::set_jumps_manually
private

for manual set up

Referenced by SeedFoldTree().

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::target_chain_
private
core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::template_pdb_
private
bool protocols::seeded_abinitio::SeedFoldTree::twochains_
private

is the input pose submitted with the target

Referenced by SeedFoldTree().


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