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Rosetta
3.8
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Add Membrane protein ligand mover. More...
#include <AddMPLigandMover.hh>
Public Member Functions | |
AddMPLigandMover () | |
Constructors ///. More... | |
AddMPLigandMover (core::Size closest_rsd, core::Size ligand_seqpos) | |
Add Membrane protein ligand mover (custom) More... | |
AddMPLigandMover (AddMPLigandMover const &src) | |
Copy Constructor. More... | |
~AddMPLigandMover () override | |
Destructor. More... | |
protocols::moves::MoverOP | clone () const override |
Rosetta Scripts Methods ///. More... | |
protocols::moves::MoverOP | fresh_instance () const override |
Create a Fresh Instance of this Mover. More... | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override |
Pase Rosetta Scripts Options for this Mover. More... | |
void | apply (core::pose::Pose &pose) override |
Mover Methods ///. More... | |
std::string | get_name () const override |
Show the name of this mvoer. More... | |
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Mover () | |
~Mover () override | |
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 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 |
void | set_type (std::string const &setting) |
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 | 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) |
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 |
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... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
Static Public Member Functions | |
static std::string | mover_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Private Attributes | |
core::Size | closest_rsd_ |
core::Size | ligand_seqpos_ |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef protocols::filters::Filters_map | Filters_map |
typedef std::list< std::string > | Strings |
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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... | |
Add Membrane protein ligand mover.
Accommodate membrane protein ligand in the membrane foldtree
protocols::membrane::AddMPLigandMover::AddMPLigandMover | ( | ) |
Constructors ///.
Add membrane protein ligand mover
Attach ligand downstream in the foldtree for refinement at the last residue as a default. DO NOT USE
Referenced by clone(), and fresh_instance().
protocols::membrane::AddMPLigandMover::AddMPLigandMover | ( | core::Size | closest_rsd, |
core::Size | ligand_seqpos | ||
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Add Membrane protein ligand mover (custom)
Attach ligand downstream in the foldtree of the closest residue to the binding pocket. Also specify sequence position of the ligand
Attach ligand downstream in the foldtree of the closest residue to the binding pocket
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default |
Copy Constructor.
Mkae a deep copy of this mover
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overridedefault |
Destructor.
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overridevirtual |
Mover Methods ///.
Create a new copy of this mover.
Mover Apply Method
Return the Name of this mover (as seen by Rscripts) Mover name for Rosetta Scripts Mover Methods /// Mover Apply Method
Implements protocols::moves::Mover.
References core::pose::Pose::chain(), core::pose::chain_end_res(), closest_rsd_, core::pose::Pose::conformation(), protocols::membrane::create_specific_membrane_foldtree(), core::pose::Pose::fold_tree(), protocols::membrane::get_anchor_points_for_tmcom(), core::conformation::Conformation::is_membrane(), ligand_seqpos_, core::conformation::Conformation::membrane_info(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::show(), core::pose::Pose::size(), and protocols::TR().
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overridevirtual |
Rosetta Scripts Methods ///.
Create a Clone of this mover
Reimplemented from protocols::moves::Mover.
References AddMPLigandMover().
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overridevirtual |
Create a Fresh Instance of this Mover.
Reimplemented from protocols::moves::Mover.
References AddMPLigandMover().
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overridevirtual |
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static |
Referenced by get_name(), protocols::membrane::AddMPLigandMoverCreator::keyname(), and provide_xml_schema().
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overridevirtual |
Pase Rosetta Scripts Options for this Mover.
Reimplemented from protocols::moves::Mover.
References closest_rsd_, and ligand_seqpos_.
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static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::membrane::AddMPLigandMoverCreator::provide_xml_schema().
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private |
Referenced by apply(), and parse_my_tag().
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private |
Referenced by apply(), and parse_my_tag().