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protocols::ligand_docking::MinimizeBackbone Class Reference

#include <MinimizeBackbone.hh>

Inheritance diagram for protocols::ligand_docking::MinimizeBackbone:
Inheritance graph
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Public Member Functions

 MinimizeBackbone ()
 
 MinimizeBackbone (InterfaceBuilderOP interface_builder)
 
 ~MinimizeBackbone () override
 
 MinimizeBackbone (MinimizeBackbone const &that)
 
void apply (core::pose::Pose &pose) override
 setting up backbone_minimization foldtree More...
 
virtual void remove_constraints (core::pose::Pose &pose)
 Remove any constraints which were added during the apply() call. More...
 
virtual void remove_cutpoints (core::pose::Pose &pose)
 Remove any cutpoint variants which were added during the apply() call. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::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 &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. 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 Member Functions

void reorder_foldtree_around_mobile_regions (ligand_options::Interface const &interface, core::pose::Pose &pose)
 
core::kinematics::FoldTreeOP create_fold_tree_with_ligand_jumps_from_attach_pts (core::kinematics::FoldTree const &, ligand_options::Interface const &interface, core::pose::Pose &pose) const
 
core::kinematics::FoldTreeOP create_fold_tree_with_cutpoints (core::kinematics::FoldTreeCOP f, ligand_options::Interface const &interface, core::pose::Pose &pose)
 
utility::vector1
< protocols::loops::Loop
add_cut_points (core::kinematics::Edge const &edge, ligand_options::Interface const &interface, core::pose::Pose &pose)
 
std::map< core::Size, core::Sizefind_attach_pts (const ligand_options::Interface &interface, core::pose::Pose const &pose) const
 
void restrain_protein_Calphas (ligand_options::Interface const &interface, core::pose::Pose &pose)
 : residues that are near the interface residues will be allowed to move with restraint More...
 
void restrain_protein_Calpha (ligand_options::Interface const &interface, core::pose::Pose &pose, core::Size residue_id, core::id::AtomID const &fixed_pt)
 

Private Attributes

InterfaceBuilderOP interface_builder_
 map of ligand chains to minimize backbone around and how much minimization around each chain Real is the Size of one standard deviation. For restraints placed on C-alphas More...
 
core::scoring::constraints::ConstraintCOPs constraints_
 The constraints which were added to the pose in apply() Stored in case we want to remove them later. More...
 
utility::vector1< core::Sizecutpoints_
 The cutpoints for which we added cutpoint variants - remove them when we're done with them. More...
 

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...
 

Constructor & Destructor Documentation

protocols::ligand_docking::MinimizeBackbone::MinimizeBackbone ( )
protocols::ligand_docking::MinimizeBackbone::MinimizeBackbone ( InterfaceBuilderOP  interface_builder)
protocols::ligand_docking::MinimizeBackbone::~MinimizeBackbone ( )
overridedefault
protocols::ligand_docking::MinimizeBackbone::MinimizeBackbone ( MinimizeBackbone const &  that)
default

Member Function Documentation

utility::vector1< protocols::loops::Loop > protocols::ligand_docking::MinimizeBackbone::add_cut_points ( core::kinematics::Edge const &  edge,
ligand_options::Interface const &  interface,
core::pose::Pose pose 
)
private
void protocols::ligand_docking::MinimizeBackbone::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::ligand_docking::MinimizeBackbone::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.

core::kinematics::FoldTreeOP protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints ( core::kinematics::FoldTreeCOP  f,
ligand_options::Interface const &  interface,
core::pose::Pose pose 
)
private
core::kinematics::FoldTreeOP protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts ( core::kinematics::FoldTree const &  f_const,
ligand_options::Interface const &  interface,
core::pose::Pose pose 
) const
private
std::map< core::Size, core::Size > protocols::ligand_docking::MinimizeBackbone::find_attach_pts ( const ligand_options::Interface interface,
core::pose::Pose const &  pose 
) const
private
protocols::moves::MoverOP protocols::ligand_docking::MinimizeBackbone::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::ligand_docking::MinimizeBackbone::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::ligand_docking::MinimizeBackbone::mover_name ( )
static
void protocols::ligand_docking::MinimizeBackbone::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 interface_builder_.

void protocols::ligand_docking::MinimizeBackbone::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::ligand_docking::MinimizeBackbone::remove_constraints ( core::pose::Pose pose)
virtual

Remove any constraints which were added during the apply() call.

References constraints_, and core::pose::Pose::remove_constraint().

Referenced by protocols::ligand_docking::FinalMinimizer::apply().

void protocols::ligand_docking::MinimizeBackbone::remove_cutpoints ( core::pose::Pose pose)
virtual
void protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions ( ligand_options::Interface const &  interface,
core::pose::Pose pose 
)
private
void protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha ( ligand_options::Interface const &  interface,
core::pose::Pose pose,
core::Size  residue_id,
core::id::AtomID const &  fixed_pt 
)
private
void protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calphas ( ligand_options::Interface const &  interface,
core::pose::Pose pose 
)
private

Member Data Documentation

core::scoring::constraints::ConstraintCOPs protocols::ligand_docking::MinimizeBackbone::constraints_
private

The constraints which were added to the pose in apply() Stored in case we want to remove them later.

Referenced by apply(), remove_constraints(), and restrain_protein_Calpha().

utility::vector1< core::Size > protocols::ligand_docking::MinimizeBackbone::cutpoints_
private

The cutpoints for which we added cutpoint variants - remove them when we're done with them.

Referenced by add_cut_points(), apply(), and remove_cutpoints().

InterfaceBuilderOP protocols::ligand_docking::MinimizeBackbone::interface_builder_
private

map of ligand chains to minimize backbone around and how much minimization around each chain Real is the Size of one standard deviation. For restraints placed on C-alphas

Referenced by apply(), find_attach_pts(), parse_my_tag(), and restrain_protein_Calpha().


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