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Rosetta 3.5
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Rosetta 3.5
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#include <StepWiseProteinPoseSetup.hh>
Public Member Functions | |
| StepWiseProteinPoseSetup (std::string const &desired_sequence, utility::vector1< std::string > const &start_tags, utility::vector1< std::string > const &silent_files_in) | |
| ~StepWiseProteinPoseSetup () | |
| virtual void | apply (core::pose::Pose &pose_to_visualize) |
| Apply the minimizer to one pose. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| utility::vector1< core::Size > const & | moving_residues () const |
| void | set_n_terminus (bool const setting) |
| void | set_c_terminus (bool const setting) |
| void | set_sample_junction (bool const setting) |
| void | set_add_peptide_plane (bool const &setting) |
 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 MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| 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... | |
| virtual 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 | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Member Functions | |
| void | match_specific_variants (core::pose::Pose const &pose, core::Size const &pose_res, core::pose::Pose &scratch_pose, core::Size const &scratch_pose_res, utility::vector1< core::chemical::VariantType > const &variant_types) const |
| void | match_end_variants (core::pose::Pose const &pose, core::pose::Pose &scratch_pose, core::Size const &start_res, core::Size const &end_res) const |
| void | add_end_variants (core::pose::Pose &pose) |
| Size | figure_out_nested_positions (std::string const &inside_sequence, std::string const &desired_sequence) const |
| void | initialize_from_scratch (core::pose::Pose &pose) |
| void | prepend_residues (core::pose::Pose &pose) |
| void | append_residues (core::pose::Pose &pose, core::pose::Pose const &start_pose) |
Private Attributes | |
| std::string const | desired_sequence_ |
| utility::vector1< std::string > const | start_tags_ |
| utility::vector1< std::string > const | silent_files_in_ |
| core::chemical::ResidueTypeSetCAP | rsd_set_ |
| Size const | nres_ |
| ObjexxFCL::FArray1D< bool > | input_residue_array_ |
| ObjexxFCL::FArray1D< bool > | junction_residue_array_ |
| ObjexxFCL::FArray1D< bool > | moving_residue_array_ |
| bool | sample_junction_ |
| utility::vector1< core::Size > | moving_residues_ |
| bool | n_terminus_ |
| bool | c_terminus_ |
| bool | add_peptide_plane_ |
| bool | verbose_ |
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 40 of file StepWiseProteinPoseSetup.hh.
| protocols::swa::protein::StepWiseProteinPoseSetup::StepWiseProteinPoseSetup | ( | std::string const & | desired_sequence, |
| utility::vector1< std::string > const & | start_tags, | ||
| utility::vector1< std::string > const & | silent_files_in | ||
| ) |
Definition at line 63 of file StepWiseProteinPoseSetup.cc.
| protocols::swa::protein::StepWiseProteinPoseSetup::~StepWiseProteinPoseSetup | ( | ) |
Definition at line 86 of file StepWiseProteinPoseSetup.cc.
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Definition at line 233 of file StepWiseProteinPoseSetup.cc.
References add_peptide_plane_, core::pose::add_variant_type_to_pose_residue(), c_terminus_, n_terminus_, and core::pose::Pose::total_residue().
Referenced by apply().
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Apply the minimizer to one pose.
Implements protocols::moves::Mover.
Definition at line 123 of file StepWiseProteinPoseSetup.cc.
References add_end_variants(), core::io::silent::SilentFileData::begin(), core::pose::copy_dofs(), desired_sequence_, core::pose::Pose::dump_pdb(), core::sequence::end, core::io::silent::SilentFileData::end(), figure_out_nested_positions(), protocols::swa::protein::fix_end_phi_psi(), input_residue_array_, core::conformation::Residue::is_protein(), junction_residue_array_, core::pose::make_pose_from_sequence(), match_end_variants(), moving_residue_array_, moving_residues_, nres_, core::import_pose::pose_from_pdb(), core::io::silent::SilentFileData::read_file(), core::pose::Pose::residue(), rsd_set_, sample_junction_, core::pose::Pose::sequence(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), silent_files_in_, start_tags_, core::pose::Pose::total_residue(), and verbose_.
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Definition at line 319 of file StepWiseProteinPoseSetup.cc.
References input_residue_array_.
Referenced by apply().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 91 of file StepWiseProteinPoseSetup.cc.
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Definition at line 298 of file StepWiseProteinPoseSetup.cc.
References match_specific_variants(), and core::pose::Pose::total_residue().
Referenced by apply().
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Definition at line 251 of file StepWiseProteinPoseSetup.cc.
References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_index(), core::conformation::Residue::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::set_xyz().
Referenced by match_end_variants().
| utility::vector1< core::Size > const & protocols::swa::protein::StepWiseProteinPoseSetup::moving_residues | ( | ) | const |
Definition at line 350 of file StepWiseProteinPoseSetup.cc.
References moving_residues_.
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| void protocols::swa::protein::StepWiseProteinPoseSetup::set_add_peptide_plane | ( | bool const & | setting) |
Definition at line 413 of file StepWiseProteinPoseSetup.cc.
References add_peptide_plane_.
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Definition at line 64 of file StepWiseProteinPoseSetup.hh.
References c_terminus_.
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Definition at line 61 of file StepWiseProteinPoseSetup.hh.
References n_terminus_.
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Definition at line 67 of file StepWiseProteinPoseSetup.hh.
References sample_junction_.
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Definition at line 123 of file StepWiseProteinPoseSetup.hh.
Referenced by add_end_variants(), and set_add_peptide_plane().
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Definition at line 121 of file StepWiseProteinPoseSetup.hh.
Referenced by add_end_variants(), and set_c_terminus().
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Definition at line 106 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 113 of file StepWiseProteinPoseSetup.hh.
Referenced by apply(), and figure_out_nested_positions().
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Definition at line 114 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 115 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 118 of file StepWiseProteinPoseSetup.hh.
Referenced by apply(), and moving_residues().
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Definition at line 120 of file StepWiseProteinPoseSetup.hh.
Referenced by add_end_variants(), and set_n_terminus().
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Definition at line 111 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 109 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 117 of file StepWiseProteinPoseSetup.hh.
Referenced by apply(), and set_sample_junction().
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Definition at line 108 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 107 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
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Definition at line 124 of file StepWiseProteinPoseSetup.hh.
Referenced by apply().
1.8.4