Grafts only one CDR onto a framework. More...
#include <GraftOneCDRLoop.hh>
Public Member Functions | |
| GraftOneCDRLoop () | |
| GraftOneCDRLoop (CDRNameEnum const &cdr_name, AntibodyInfoOP antibody_info, Ab_TemplateInfoOP ab_t_info) | |
| ~GraftOneCDRLoop () override | |
| void | apply (core::pose::Pose &pose_in) override |
| Main Method. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | enable_benchmark_mode (bool setting) |
| enable benchmark mode More... | |
| void | set_scorefxn (core::scoring::ScoreFunctionOP scorefxn) |
| users can pass their own scorefunction for packing after grafting More... | |
| void | set_no_stem_copy (bool const &setting) |
| R2 just graft R2 by copying some stem residues, and remove H3 to do H3 loop modeling later. But the terminal has been changed by this grafting. Therefore, in R3, an option for not copying h3 stem is provided. More... | |
| void | set_flank_size (core::Size setting) |
| GraftOneCDRLoop (GraftOneCDRLoop const &rhs) | |
| copy ctor More... | |
| GraftOneCDRLoop & | operator= (GraftOneCDRLoop const &rhs) |
| assignment operator 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 MoverOP | clone () const |
| Return a clone of the Mover object. 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... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. 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 |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| 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 Strings & | info () |
| 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... | |
Private Member Functions | |
| void | set_default () |
| void | init () |
| void | finalize_setup () |
| void | initForEqualOperatorAndCopyConstructor (GraftOneCDRLoop &lhs, GraftOneCDRLoop const &rhs) |
Private Attributes | |
| core::Size | flank_size_ |
| core::Size | stem_copy_size_ |
| CDRNameEnum | cdr_name_ |
| AntibodyInfoOP | ab_info_ |
| Ab_TemplateInfoOP | ab_t_info_ |
| bool | benchmark_ |
| bool | stem_not_graft_ |
| core::scoring::ScoreFunctionCOP | scorefxn_ |
| std::string | preprocessing_script_version_ |
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 |
| 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... | |
| 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... | |
Detailed Description
Grafts only one CDR onto a framework.
Constructor & Destructor Documentation
◆ GraftOneCDRLoop() [1/3]
|
default |
◆ GraftOneCDRLoop() [2/3]
| protocols::antibody::GraftOneCDRLoop::GraftOneCDRLoop | ( | CDRNameEnum const & | cdr_name, |
| AntibodyInfoOP | antibody_info, | ||
| Ab_TemplateInfoOP | ab_t_info | ||
| ) |
References ab_info_, ab_t_info_, cdr_name_, init(), and set_default().
◆ ~GraftOneCDRLoop()
|
overridedefault |
◆ GraftOneCDRLoop() [3/3]
| protocols::antibody::GraftOneCDRLoop::GraftOneCDRLoop | ( | GraftOneCDRLoop const & | rhs | ) |
copy ctor
References initForEqualOperatorAndCopyConstructor().
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References ab_info_, ab_t_info_, core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_name(), cdr_name_, core::pose::Pose::conformation(), core::conformation::Conformation::fill_missing_atoms(), finalize_setup(), flank_size_, core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), preprocessing_script_version_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_secstruct(), core::pose::Pose::set_xyz(), stem_copy_size_, core::scoring::superimpose_pose(), TRG(), and core::conformation::Residue::xyz().
◆ enable_benchmark_mode()
|
inline |
enable benchmark mode
References benchmark_.
◆ finalize_setup()
|
private |
References core::scoring::get_score_function(), scorefxn_, stem_copy_size_, and stem_not_graft_.
Referenced by apply().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ init()
|
private |
References protocols::idealize::IdealizeMover::fast().
Referenced by GraftOneCDRLoop().
◆ initForEqualOperatorAndCopyConstructor()
|
private |
References ab_info_, ab_t_info_, benchmark_, cdr_name_, flank_size_, stem_copy_size_, and stem_not_graft_.
Referenced by GraftOneCDRLoop(), and operator=().
◆ operator=()
| GraftOneCDRLoop & protocols::antibody::GraftOneCDRLoop::operator= | ( | GraftOneCDRLoop const & | rhs | ) |
assignment operator
References initForEqualOperatorAndCopyConstructor().
◆ set_default()
|
private |
References ab_info_, ab_t_info_, benchmark_, flank_size_, preprocessing_script_version_, stem_copy_size_, and stem_not_graft_.
Referenced by GraftOneCDRLoop().
◆ set_flank_size()
|
inline |
References flank_size_.
◆ set_no_stem_copy()
|
inline |
R2 just graft R2 by copying some stem residues, and remove H3 to do H3 loop modeling later. But the terminal has been changed by this grafting. Therefore, in R3, an option for not copying h3 stem is provided.
References stem_not_graft_.
◆ set_scorefxn()
|
inline |
users can pass their own scorefunction for packing after grafting
References scorefxn_.
Member Data Documentation
◆ ab_info_
|
private |
Referenced by apply(), GraftOneCDRLoop(), initForEqualOperatorAndCopyConstructor(), and set_default().
◆ ab_t_info_
|
private |
Referenced by apply(), GraftOneCDRLoop(), initForEqualOperatorAndCopyConstructor(), and set_default().
◆ benchmark_
|
private |
Referenced by enable_benchmark_mode(), initForEqualOperatorAndCopyConstructor(), and set_default().
◆ cdr_name_
|
private |
Referenced by apply(), GraftOneCDRLoop(), and initForEqualOperatorAndCopyConstructor().
◆ flank_size_
|
private |
Referenced by apply(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_flank_size().
◆ preprocessing_script_version_
|
private |
Referenced by apply(), and set_default().
◆ scorefxn_
|
private |
Referenced by finalize_setup(), and set_scorefxn().
◆ stem_copy_size_
|
private |
Referenced by apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), and set_default().
◆ stem_not_graft_
|
private |
Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_no_stem_copy().
The documentation for this class was generated from the following files:
- src/protocols/antibody/GraftOneCDRLoop.hh
- src/protocols/antibody/GraftOneCDRLoop.cc
