|
Rosetta 3.5
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
|
Rosetta 3.5
|
#include <StarAbinitio.hh>
Public Member Functions | |
| StarAbinitio () | |
| void | apply (core::pose::Pose &pose) |
| protocols::moves::MoverOP | clone () const |
| Uses the copy constructor to create a new instance More... | |
| protocols::moves::MoverOP | fresh_instance () const |
| Uses the no-argument constructor to create a new instance More... | |
| std::string | get_name () const |
| Returns the name of this mover More... | |
 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) | |
| Mover & | operator= (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) |
| virtual void | parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| 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 Strings & | info () |
| 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 | setup_kinematics (const protocols::loops::Loops &aligned, const utility::vector1< unsigned > &interior_cuts, core::pose::Pose *pose) const |
| void | tear_down_kinematics (core::pose::Pose *pose) const |
| Removes virtual residue, cutpoint variants and restores simple kinematics More... | |
Private Attributes | |
| core::fragment::FragSetOP | fragments_lg_ |
| core::fragment::FragSetOP | fragments_sm_ |
| core::fragment::SecondaryStructureOP | pred_ss_ |
| protocols::simple_moves::SaneMinMoverOP | minimizer_ |
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... | |
Definition at line 36 of file StarAbinitio.hh.
| protocols::star::StarAbinitio::StarAbinitio | ( | ) |
Definition at line 330 of file StarAbinitio.cc.
References core::scoring::atom_pair_constraint, and core::scoring::ScoreFunctionFactory::create_score_function().
|
virtual |
Implements protocols::moves::Mover.
Definition at line 239 of file StarAbinitio.cc.
References protocols::simple_moves::rational_mc::RationalMonteCarlo::apply(), core::scoring::chainbreak, protocols::star::compute_per_residue_probabilities(), protocols::star::configure_rmc(), protocols::nonlocal::current_job(), protocols::star::emit_intermediate(), protocols::simple_moves::rational_mc::RationalMonteCarlo::enable_autotemp(), core::pose::Pose::fold_tree(), protocols::star::Extender::set_secondary_structure(), protocols::star::setup_constraints(), protocols::star::setup_score(), protocols::star::to_centroid(), core::pose::Pose::total_residue(), and protocols::star::TR().
|
virtual |
Uses the copy constructor to create a new instance
Reimplemented from protocols::moves::Mover.
Definition at line 372 of file StarAbinitio.cc.
|
virtual |
Uses the no-argument constructor to create a new instance
Reimplemented from protocols::moves::Mover.
Definition at line 376 of file StarAbinitio.cc.
|
virtual |
Returns the name of this mover
Implements protocols::moves::Mover.
Definition at line 368 of file StarAbinitio.cc.
|
private |
Sets up kinematics to keep the orientation of the aligned regions fixed with respect to one another. A virtual residue is placed at the aligned regions' center of mass. A jump from the virtual residue to the midpoint of each region is added. Interior cutpoints (i.e. those between consecutive aligned regions) are retrieved from the input parameter.
Definition at line 195 of file StarAbinitio.cc.
References core::util::add_cutpoint_variants(), core::pose::addVirtualResAsRoot(), protocols::loops::Loops::center_of_mass(), core::pose::Pose::fold_tree(), protocols::loops::Loops::num_loop(), core::pose::Pose::total_residue(), protocols::star::TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().
|
private |
Removes virtual residue, cutpoint variants and restores simple kinematics
Definition at line 324 of file StarAbinitio.cc.
References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::util::remove_cutpoint_variants(), protocols::star::simple_fold_tree(), and core::pose::Pose::total_residue().
|
private |
Definition at line 63 of file StarAbinitio.hh.
|
private |
Definition at line 64 of file StarAbinitio.hh.
|
private |
Definition at line 66 of file StarAbinitio.hh.
|
private |
Definition at line 65 of file StarAbinitio.hh.
1.8.4