Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::protein_interface_design::movers::SetAtomTree Class Reference

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

#include <SetAtomTree.hh>

Public Member Functions

 SetAtomTree ()
 
virtual ~SetAtomTree ()
 Commenting out to fix PyRosetta build SetAtomTree( core::kinematics::FoldTreeOP ft );. More...
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 &)
 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 connect_from="")
 
bool simple_ft () const
 
void simple_ft (bool const s)
 
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)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (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...
 
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 Stringsinfo ()
 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...
 

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_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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...
 
- 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_.

Referenced by clone().

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

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

Member Function Documentation

void protocols::protein_interface_design::movers::SetAtomTree::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::protein_interface_design::movers::SetAtomTree::clone ( ) const
virtual

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.

References SetAtomTree().

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  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
inlinevirtual

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
virtual

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

Implements protocols::moves::Mover.

References protocols::protein_interface_design::movers::SetAtomTreeCreator::mover_name().

void protocols::protein_interface_design::movers::SetAtomTree::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References anchor_res_, connect_from_, connect_to_, docking_ft_, fold_tree_, host_chain_, jump_, resnum_, runtime_assert, simple_ft(), start_tree_at_chain(), protocols::protein_interface_design::movers::TR, two_parts_chain1(), and utility_exit_with_message.

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

References start_tree_at_chain_.

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

References two_parts_chain1_.

bool protocols::protein_interface_design::movers::SetAtomTree::two_parts_chain1 ( ) const
inline

References two_parts_chain1_.

Referenced by apply(), and parse_my_tag().

Member Data Documentation

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

Referenced by apply(), and parse_my_tag().

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::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().


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