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protocols::protein_interface_design::movers::SetAtomTree Class Reference

a mover that sets a user-defined atom tree More...

#include <SetAtomTree.hh>

Inheritance diagram for protocols::protein_interface_design::movers::SetAtomTree:
Inheritance graph
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Public Member Functions

 SetAtomTree ()
 
 ~SetAtomTree () override
 Commenting out to fix PyRosetta build SetAtomTree( core::kinematics::FoldTreeOP ft );. More...
 
void apply (core::pose::Pose &pose) override
 
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...
 
core::kinematics::FoldTreeOP create_atom_tree (core::pose::Pose const &pose, core::Size const host_chain, core::Size const resnum, core::Size const anchor_num_=0, std::string const &connect_to="", std::string const &connect_from="")
 
bool simple_ft () const
 
void simple_ft (bool const s)
 
void set_ab_fold_tree (core::pose::Pose &pose)
 
void two_parts_chain1 (bool const t)
 
bool two_parts_chain1 () const
 
core::kinematics::FoldTreeOP fold_tree () const
 
void fold_tree (core::kinematics::FoldTreeOP ft_)
 
char start_tree_at_chain () const
 
void start_tree_at_chain (char const c)
 
void ab_fold_tree (bool b)
 
bool ab_fold_tree ()
 
void update_residue_variants (bool b)
 
bool update_residue_variants ()
 
void add_cutpoint_variants (core::pose::Pose &pose)
 
void chain (core::Size i)
 
core::Size chain ()
 
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 Attributes

bool docking_ft_
 
bool simple_ft_
 
bool two_parts_chain1_
 
char start_tree_at_chain_
 
core::Size jump_
 
std::string resnum_
 
std::string connect_to_
 
std::string anchor_res_
 
std::string connect_from_
 
core::Size host_chain_
 
core::kinematics::FoldTreeOP fold_tree_
 
bool ab_fold_tree_
 
bool update_residue_variants_
 
std::string remark_foldtree_
 

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

a mover that sets a user-defined atom tree

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::SetAtomTree::SetAtomTree ( )

References start_tree_at_chain_.

protocols::protein_interface_design::movers::SetAtomTree::~SetAtomTree ( )
overridedefault

Commenting out to fix PyRosetta build SetAtomTree( core::kinematics::FoldTreeOP ft );.

Member Function Documentation

void protocols::protein_interface_design::movers::SetAtomTree::ab_fold_tree ( bool  b)
inline
bool protocols::protein_interface_design::movers::SetAtomTree::ab_fold_tree ( )
inline

References ab_fold_tree_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants ( core::pose::Pose pose)
void protocols::protein_interface_design::movers::SetAtomTree::apply ( core::pose::Pose pose)
overridevirtual

Commenting out to fix PyRosetta build void fold_tree( core::kinematics::FoldTreeOP ft ); Commenting out to fix PyRosetta build core::kinematics::FoldTreeOP fold_tree() const;

Implements protocols::moves::Mover.

References ab_fold_tree_, add_cutpoint_variants(), core::kinematics::FoldTree::add_edge(), protocols::protein_interface_design::movers::anchor_num, anchor_res_, protocols::simple_moves::CutChainMover::bond_length(), chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::connect_from(), connect_from_, protocols::protein_interface_design::movers::connect_to(), connect_to_, create_atom_tree(), docking_ft_, core::pose::Pose::fold_tree(), fold_tree_, core::pose::get_comment(), host_chain_, jump_, protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::name3(), core::conformation::Conformation::num_chains(), protocols::protein_interface_design::optimal_connection_point(), core::pose::parse_resnum(), core::pose::Pose::pdb_info(), remark_foldtree_, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::conformation::symmetry::residue_center_of_mass(), core::pose::residue_center_of_mass(), resnum_, set_ab_fold_tree(), protocols::docking::setup_foldtree(), simple_ft(), start_tree_at_chain(), protocols::protein_interface_design::movers::TR(), two_parts_chain1(), and update_residue_variants_.

Referenced by protocols::splice::SpliceInAntibody::adjust_template_jump().

void protocols::protein_interface_design::movers::SetAtomTree::chain ( core::Size  i)
inline
core::Size protocols::protein_interface_design::movers::SetAtomTree::chain ( )
inline

References host_chain_.

Referenced by apply().

protocols::moves::MoverOP protocols::protein_interface_design::movers::SetAtomTree::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::protein_interface_design::movers::SetAtomTree::create_atom_tree ( core::pose::Pose const &  pose,
core::Size const  host_chain,
core::Size const  resnum,
core::Size const  anchor_num_ = 0,
std::string const &  connect_to = "",
std::string const &  connect_from = "" 
)
core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::SetAtomTree::fold_tree ( ) const

References fold_tree_.

Referenced by create_atom_tree().

void protocols::protein_interface_design::movers::SetAtomTree::fold_tree ( core::kinematics::FoldTreeOP  ft_)

References fold_tree_.

protocols::moves::MoverOP protocols::protein_interface_design::movers::SetAtomTree::fresh_instance ( ) const
inlineoverridevirtual

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::protein_interface_design::movers::SetAtomTree::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::protein_interface_design::movers::SetAtomTree::mover_name ( )
static
void protocols::protein_interface_design::movers::SetAtomTree::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 ab_fold_tree(), anchor_res_, connect_from_, connect_to_, docking_ft_, fold_tree_, host_chain_, jump_, remark_foldtree_, resnum_, simple_ft(), start_tree_at_chain(), protocols::protein_interface_design::movers::TR(), two_parts_chain1(), and update_residue_variants().

void protocols::protein_interface_design::movers::SetAtomTree::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree ( core::pose::Pose pose)
bool protocols::protein_interface_design::movers::SetAtomTree::simple_ft ( ) const
inline

References simple_ft_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::SetAtomTree::simple_ft ( bool const  s)
inline

References simple_ft_.

char protocols::protein_interface_design::movers::SetAtomTree::start_tree_at_chain ( ) const
inline

References start_tree_at_chain_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::SetAtomTree::start_tree_at_chain ( char const  c)
inline
void protocols::protein_interface_design::movers::SetAtomTree::two_parts_chain1 ( bool const  t)
inline
bool protocols::protein_interface_design::movers::SetAtomTree::two_parts_chain1 ( ) const
inline

References two_parts_chain1_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::SetAtomTree::update_residue_variants ( bool  b)
inline
bool protocols::protein_interface_design::movers::SetAtomTree::update_residue_variants ( )
inline

References update_residue_variants_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::protein_interface_design::movers::SetAtomTree::ab_fold_tree_
private

Referenced by ab_fold_tree(), and apply().

std::string protocols::protein_interface_design::movers::SetAtomTree::anchor_res_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::SetAtomTree::connect_from_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::SetAtomTree::connect_to_
private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::SetAtomTree::docking_ft_
private

Referenced by apply(), and parse_my_tag().

core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::SetAtomTree::fold_tree_
private

Referenced by apply(), fold_tree(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::SetAtomTree::host_chain_
private
core::Size protocols::protein_interface_design::movers::SetAtomTree::jump_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::SetAtomTree::remark_foldtree_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::SetAtomTree::resnum_
private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::SetAtomTree::simple_ft_
private

Referenced by simple_ft().

char protocols::protein_interface_design::movers::SetAtomTree::start_tree_at_chain_
private

Referenced by SetAtomTree(), and start_tree_at_chain().

bool protocols::protein_interface_design::movers::SetAtomTree::two_parts_chain1_
private

Referenced by two_parts_chain1().

bool protocols::protein_interface_design::movers::SetAtomTree::update_residue_variants_
private

Referenced by apply(), and update_residue_variants().


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