Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::simple_moves::DeleteChainsMover Class Reference

Delete a chain from a Pose, or a set of chains. More...

#include <DeleteChainsMover.hh>

Inheritance diagram for protocols::simple_moves::DeleteChainsMover:
Inheritance graph
[legend]

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...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

protocols::simple_moves::DeleteChainsMover::DeleteChainsMover ( )

Default Constructor.

References set_defaults().

protocols::simple_moves::DeleteChainsMover::DeleteChainsMover ( std::string const &  chains)

Constructor with chain.

References set_chains(), and set_defaults().

Member Function Documentation

void protocols::simple_moves::DeleteChainsMover::apply ( core::pose::Pose )
overridevirtual
std::string protocols::simple_moves::DeleteChainsMover::chains ( ) const

Get the chain.

References chains_.

Referenced by set_chains().

moves::MoverOP protocols::simple_moves::DeleteChainsMover::clone ( ) const
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.

bool protocols::simple_moves::DeleteChainsMover::detect_bonds ( ) const

References detect_bonds_.

Referenced by set_detect_bonds().

bool protocols::simple_moves::DeleteChainsMover::detect_pseudobonds ( ) const

References detect_pseudobonds_.

Referenced by set_detect_pseudobonds().

moves::MoverOP protocols::simple_moves::DeleteChainsMover::fresh_instance ( ) const
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.

std::string protocols::simple_moves::DeleteChainsMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::simple_moves::DeleteChainsMover::mover_name ( )
static
bool protocols::simple_moves::DeleteChainsMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

void protocols::simple_moves::DeleteChainsMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::simple_moves::DeleteChainsMover::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

void protocols::simple_moves::DeleteChainsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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().

void protocols::simple_moves::DeleteChainsMover::set_defaults ( )
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().

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

std::string protocols::simple_moves::DeleteChainsMover::chains_
private

Referenced by apply(), chains(), and set_chains().

bool protocols::simple_moves::DeleteChainsMover::detect_bonds_
private
bool protocols::simple_moves::DeleteChainsMover::detect_pseudobonds_
private

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