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protocols::seeded_abinitio::GrowPeptides Class Reference

#include <GrowPeptides.hh>

Inheritance diagram for protocols::seeded_abinitio::GrowPeptides:
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Public Member Functions

 GrowPeptides ()
 
virtual ~GrowPeptides ()
 
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...
 
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...
 
bool ddg ()
 
- 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 Member Functions

void append_residues_nterminally (core::Size seq_register, core::Size res_pos, core::Size stop, std::string &nat_seq, core::pose::Pose &target_seeds)
 functions More...
 
void append_residues_cterminally (core::Size seq_register, core::Size res_pos, core::Size stop, std::string &nat_seq, core::pose::Pose &target_seeds)
 
void grow_from_seeds (core::pose::Pose curr_pose, std::string sequence, protocols::loops::Loops &seeds, utility::vector1< Size > cutpoints)
 
void grow_from_verteces (core::pose::Pose &curr_pose, std::string sequence, protocols::loops::Loops &seeds, std::set< core::Size > vertex_set)
 
void setup_cached_observers (core::pose::Pose &pose)
 

Private Attributes

core::Size extend_nterm
 data More...
 
core::Size extend_cterm
 
std::string nsequence_
 
std::string csequence_
 
std::string seq_
 
bool all_ala_N
 
bool all_ala_C
 
bool ddg_
 
core::pose::PoseOP template_pdb_
 template pose to derrive a sequence from More...
 
bool template_presence
 
bool anchor_specified_
 
utility::vector1< core::Sizeanchors_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool output_centroid
 
utility::vector1< std::string > sequence_chunks_
 vector of sequence pieces More...
 
protocols::loops::Loops all_seeds_
 
bool fetch_foldtree
 
core::kinematics::FoldTreeOP seed_foldtree_
 foldtree after growing out peptide pieces More...
 
core::pose::PoseOP curr_pose_
 pointer for the current pose More...
 
std::set< core::Sizeverteces_
 

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::GrowPeptides::GrowPeptides ( )
protocols::seeded_abinitio::GrowPeptides::~GrowPeptides ( )
virtual

Member Function Documentation

void protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally ( core::Size  seq_register,
core::Size  res_pos,
core::Size  stop,
std::string &  nat_seq,
core::pose::Pose target_seeds 
)
private
void protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally ( core::Size  seq_register,
core::Size  res_pos,
core::Size  stop,
std::string &  nat_seq,
core::pose::Pose target_seeds 
)
private
void protocols::seeded_abinitio::GrowPeptides::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::seeded_abinitio::GrowPeptides::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.

bool protocols::seeded_abinitio::GrowPeptides::ddg ( )
protocols::moves::MoverOP protocols::seeded_abinitio::GrowPeptides::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.

std::string protocols::seeded_abinitio::GrowPeptides::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::seeded_abinitio::GrowPeptides::grow_from_seeds ( core::pose::Pose  curr_pose,
std::string  sequence,
protocols::loops::Loops seeds,
utility::vector1< Size cutpoints 
)
private
void protocols::seeded_abinitio::GrowPeptides::grow_from_verteces ( core::pose::Pose curr_pose,
std::string  sequence,
protocols::loops::Loops seeds,
std::set< core::Size vertex_set 
)
private
void protocols::seeded_abinitio::GrowPeptides::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::pose::parse_resnum(), core::import_pose::pose_from_pdb(), and core::TR().

void protocols::seeded_abinitio::GrowPeptides::setup_cached_observers ( core::pose::Pose pose)
private

Member Data Documentation

bool protocols::seeded_abinitio::GrowPeptides::all_ala_C
private
bool protocols::seeded_abinitio::GrowPeptides::all_ala_N
private
protocols::loops::Loops protocols::seeded_abinitio::GrowPeptides::all_seeds_
private
bool protocols::seeded_abinitio::GrowPeptides::anchor_specified_
private
utility::vector1< core::Size > protocols::seeded_abinitio::GrowPeptides::anchors_
private
std::string protocols::seeded_abinitio::GrowPeptides::csequence_
private
core::pose::PoseOP protocols::seeded_abinitio::GrowPeptides::curr_pose_
private

pointer for the current pose

bool protocols::seeded_abinitio::GrowPeptides::ddg_
private
core::Size protocols::seeded_abinitio::GrowPeptides::extend_cterm
private
core::Size protocols::seeded_abinitio::GrowPeptides::extend_nterm
private

data

bool protocols::seeded_abinitio::GrowPeptides::fetch_foldtree
private
std::string protocols::seeded_abinitio::GrowPeptides::nsequence_
private
bool protocols::seeded_abinitio::GrowPeptides::output_centroid
private
core::scoring::ScoreFunctionOP protocols::seeded_abinitio::GrowPeptides::scorefxn_
private
core::kinematics::FoldTreeOP protocols::seeded_abinitio::GrowPeptides::seed_foldtree_
private

foldtree after growing out peptide pieces

std::string protocols::seeded_abinitio::GrowPeptides::seq_
private
utility::vector1< std::string > protocols::seeded_abinitio::GrowPeptides::sequence_chunks_
private

vector of sequence pieces

core::pose::PoseOP protocols::seeded_abinitio::GrowPeptides::template_pdb_
private

template pose to derrive a sequence from

bool protocols::seeded_abinitio::GrowPeptides::template_presence
private
std::set< core::Size > protocols::seeded_abinitio::GrowPeptides::verteces_
private

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