Delete a chain from a Pose, or a set of chains. More...
#include <DeleteChainsMover.hh>
Public Member Functions | |
| DeleteChainsMover () | |
| Default Constructor. More... | |
| DeleteChainsMover (std::string const &chains) | |
| Constructor with chain. More... | |
| void | apply (core::pose::Pose &pose) override |
| Main Method. More... | |
| void | set_chains (std::string const &chains) |
| Set the chain Will figure out the chainIDs at apply time. More... | |
| std::string | chains () const |
| Get the chain. More... | |
| void | set_detect_bonds (bool detect_bonds) |
| Set the class to detect bonds after full deletion of chains? Default True. Override for speed and if you know there are no bonds between chains other than possible disulfides. More... | |
| bool | detect_bonds () const |
| void | set_detect_pseudobonds (bool detect_pseudobonds) |
| Set the class to detect psuedobonds after full deletion of chains? Default True. Override for speed and if you know there are no pseudobonds between chains other than possible disulfides. More... | |
| bool | detect_pseudobonds () const |
| moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_defaults () |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. 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 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... | |
| 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 |
| 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... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| 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... | |
Private Attributes | |
| std::string | chains_ |
| bool | detect_bonds_ |
| bool | detect_pseudobonds_ |
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 |
| 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
Delete a chain from a Pose, or a set of chains.
1) Deletes Each chain using conformation.delete_residue_range_slow 2) Calls detect bonds, pseudobonds, and disulfides 3) Makes sure PDBInfo is still intact 4) Sets a new reasonable FoldTree
Constructor & Destructor Documentation
◆ DeleteChainsMover() [1/2]
| protocols::simple_moves::DeleteChainsMover::DeleteChainsMover | ( | ) |
Default Constructor.
References set_defaults().
◆ DeleteChainsMover() [2/2]
| protocols::simple_moves::DeleteChainsMover::DeleteChainsMover | ( | std::string const & | chains | ) |
Constructor with chain.
References chains(), set_chains(), and set_defaults().
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chains_, core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), core::conformation::Conformation::detect_bonds(), detect_bonds_, core::conformation::Conformation::detect_disulfides(), core::conformation::Conformation::detect_pseudobonds(), detect_pseudobonds_, core::pose::get_chain_id_from_chain(), core::pose::Pose::is_fullatom(), core::pose::Pose::pdb_info(), and core::pose::set_reasonable_fold_tree().
Referenced by protocols::antibody::design::AntibodyDesignMover::apply().
◆ chains()
| std::string protocols::simple_moves::DeleteChainsMover::chains | ( | ) | const |
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
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.
◆ detect_bonds()
| bool protocols::simple_moves::DeleteChainsMover::detect_bonds | ( | ) | const |
References detect_bonds_.
Referenced by set_detect_bonds().
◆ detect_pseudobonds()
| bool protocols::simple_moves::DeleteChainsMover::detect_pseudobonds | ( | ) | const |
References detect_pseudobonds_.
Referenced by set_detect_pseudobonds().
◆ fresh_instance()
|
overridevirtual |
Generates a new Mover object freshly created with the default ctor.
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.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::simple_moves::DeleteChainsMoverCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References detect_bonds_, detect_pseudobonds_, set_chains(), set_defaults(), set_detect_bonds(), and set_detect_pseudobonds().
◆ provide_citation_info()
|
overridevirtual |
Provide the citation.
Reimplemented from protocols::moves::Mover.
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::simple_moves::DeleteChainsMoverCreator::provide_xml_schema().
◆ set_chains()
| void protocols::simple_moves::DeleteChainsMover::set_chains | ( | std::string const & | chains | ) |
Set the chain Will figure out the chainIDs at apply time.
References chains(), and chains_.
Referenced by protocols::antibody::design::AntibodyDesignMover::apply(), DeleteChainsMover(), and parse_my_tag().
◆ set_defaults()
| void protocols::simple_moves::DeleteChainsMover::set_defaults | ( | ) |
References set_detect_bonds(), and set_detect_pseudobonds().
Referenced by DeleteChainsMover(), and parse_my_tag().
◆ set_detect_bonds()
| void protocols::simple_moves::DeleteChainsMover::set_detect_bonds | ( | bool | detect_bonds | ) |
Set the class to detect bonds after full deletion of chains? Default True. Override for speed and if you know there are no bonds between chains other than possible disulfides.
References detect_bonds(), and detect_bonds_.
Referenced by parse_my_tag(), and set_defaults().
◆ set_detect_pseudobonds()
| void protocols::simple_moves::DeleteChainsMover::set_detect_pseudobonds | ( | bool | detect_pseudobonds | ) |
Set the class to detect psuedobonds after full deletion of chains? Default True. Override for speed and if you know there are no pseudobonds between chains other than possible disulfides.
References detect_pseudobonds(), and detect_pseudobonds_.
Referenced by parse_my_tag(), and set_defaults().
Member Data Documentation
◆ chains_
|
private |
Referenced by apply(), chains(), and set_chains().
◆ detect_bonds_
|
private |
Referenced by apply(), detect_bonds(), parse_my_tag(), and set_detect_bonds().
◆ detect_pseudobonds_
|
private |
Referenced by apply(), detect_pseudobonds(), parse_my_tag(), and set_detect_pseudobonds().
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/DeleteChainsMover.hh
- src/protocols/simple_moves/DeleteChainsMover.cc
