Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Attributes | List of all members
protocols::simple_moves::BackboneMover Class Referenceabstract

BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.). More...

#include <BackboneMover.hh>

Public Types

typedef core::Real Real
 
- 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
 

Public Member Functions

 BackboneMover ()
 
 BackboneMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in)
 
 ~BackboneMover ()
 
virtual void apply (core::pose::Pose &)
 virtual functions that get overridden or called from the inheriting classes More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual void setup_list (core::pose::Pose &)=0
 
virtual void set_angles (core::Real)=0
 
virtual bool make_move (core::pose::Pose &)=0
 
void clear ()
 
bool check_rama ()
 
void temperature (core::Real const temperature_in)
 Properties set/get functions. More...
 
core::Real temperature () const
 
void nmoves (core::Size const nmoves_in)
 
core::Size nmoves () const
 
core::kinematics::MoveMapCOP movemap () const
 
void movemap (core::kinematics::MoveMapOP new_movemap)
 
void angle_max (core::Real const angle)
 Sets the maximum angle of perturbation, independent of secondary structure. More...
 
void angle_max (char const type, core::Real const angle)
 Sets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More...
 
void angle_max (std::map< char, core::Real > angle_max_in)
 Sets the max angle of perturbation, for secondary structures 'H', 'E', and 'L'. More...
 
core::Real get_angle_max (char const type) const
 Gets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More...
 
core::Real new_phi ()
 
core::Real new_psi ()
 
virtual void 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)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
bool preserve_detailed_balance () const
 get whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
 
void set_preserve_detailed_balance (bool preserve_detailed_balance)
 set whether detailed balance is preserved (i.e. no Ramachandran biasing) More...
 
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)=0
 get the DOF_IDs perturbed by the mover during moves, along with their ranges More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 Default constructor. More...
 
virtual ~ThermodynamicMover ()
 Default destructor. More...
 
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 Callback executed before any Monte Carlo trials are attempted. More...
 
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after the Metropolis criterion is evaluated. More...
 
virtual core::Real last_proposal_density_ratio ()
 Return the proposal density ratio for last apply method. More...
 
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after all Monte Carlo trials are completed. More...
 
virtual bool is_multi_trial ()
 Return true if the move performs multiple trials on each apply. More...
 
virtual core::Real last_inner_score_temperature_delta ()
 If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...
 
virtual
protocols::canonical_sampling::MetropolisHastingsMoverAP 
metropolis_hastings_mover ()
 If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...
 
virtual void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
 If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...
 
virtual utility::vector1
< core::id::TorsionID_Range
torsion_id_ranges (core::pose::Pose &pose)=0
 Return a list specifying which torsions may be perturbed by apply(), and the in what range each perturbation may be. More...
 
- 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...
 
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)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Attributes

core::kinematics::MoveMapOP movemap_
 
core::Real temperature_
 controls bias w/which uphill moves are accepted More...
 
Size nmoves_
 number of positions at which to make moves More...
 
std::map< char, core::Realangle_max_
 max allowed angle-change as a function of ss type More...
 
int num_
 
int resnum_
 
int tries_
 
core::Real big_angle_
 
core::Real small_angle_
 
utility::vector1< std::pair
< int, core::Real > > 
pos_list_
 
utility::vector1< intalready_moved_
 
core::Real old_phi_
 
core::Real new_phi_
 
core::Real old_psi_
 
core::Real new_psi_
 
core::Real old_rama_score_
 
core::Real new_rama_score_
 
bool preserve_detailed_balance_
 

Additional Inherited Members

- 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

BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.).

Todo:
change this to some kind of 'protocol' so the MC is managed separately from conformational moves

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::BackboneMover::BackboneMover ( )
protocols::simple_moves::BackboneMover::BackboneMover ( core::kinematics::MoveMapOP  movemap_in,
core::Real  temperature_in,
core::Size  nmoves_in 
)
protocols::simple_moves::BackboneMover::~BackboneMover ( )

Member Function Documentation

void protocols::simple_moves::BackboneMover::angle_max ( core::Real const  angle)
void protocols::simple_moves::BackboneMover::angle_max ( char const  type,
core::Real const  angle 
)

Sets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.)

Example: bbmover.angle_max('H', 25)

See also: ShearMover SmallMover

References angle_max_, and protocols::moves::Mover::type().

void protocols::simple_moves::BackboneMover::angle_max ( std::map< char, core::Real angle_max_in)

Sets the max angle of perturbation, for secondary structures 'H', 'E', and 'L'.

References angle_max_.

void protocols::simple_moves::BackboneMover::apply ( core::pose::Pose pose)
virtual
bool protocols::simple_moves::BackboneMover::check_rama ( )
void protocols::simple_moves::BackboneMover::clear ( )
virtual utility::vector1<core::id::DOF_ID_Range> protocols::simple_moves::BackboneMover::dof_id_ranges ( core::pose::Pose pose)
pure virtual

get the DOF_IDs perturbed by the mover during moves, along with their ranges

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Implemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

core::Real protocols::simple_moves::BackboneMover::get_angle_max ( char const  type) const

Gets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.)

Example: bbmover.angle_max('H')

See also: ShearMover SmallMover

References angle_max_.

Referenced by show().

std::string protocols::simple_moves::BackboneMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

virtual bool protocols::simple_moves::BackboneMover::make_move ( core::pose::Pose )
pure virtual
core::kinematics::MoveMapCOP protocols::simple_moves::BackboneMover::movemap ( ) const
void protocols::simple_moves::BackboneMover::movemap ( core::kinematics::MoveMapOP  new_movemap)

References movemap_.

core::Real protocols::simple_moves::BackboneMover::new_phi ( )

References new_phi_.

core::Real protocols::simple_moves::BackboneMover::new_psi ( )

References new_psi_.

void protocols::simple_moves::BackboneMover::nmoves ( core::Size const  nmoves_in)
core::Size protocols::simple_moves::BackboneMover::nmoves ( ) const

References nmoves_.

Referenced by parse_my_tag(), and show().

void protocols::simple_moves::BackboneMover::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 angle_max(), movemap(), nmoves(), nmoves_, protocols::rosetta_scripts::parse_movemap(), preserve_detailed_balance_, set_preserve_detailed_balance(), temperature(), and temperature_.

bool protocols::simple_moves::BackboneMover::preserve_detailed_balance ( ) const
virtual

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance_.

Referenced by set_preserve_detailed_balance().

virtual void protocols::simple_moves::BackboneMover::set_angles ( core::Real  )
pure virtual
void protocols::simple_moves::BackboneMover::set_preserve_detailed_balance ( bool  preserve_detailed_balance)
virtual

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance(), and preserve_detailed_balance_.

Referenced by parse_my_tag().

virtual void protocols::simple_moves::BackboneMover::setup_list ( core::pose::Pose )
pure virtual
void protocols::simple_moves::BackboneMover::show ( std::ostream &  output = std::cout) const
virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References get_angle_max(), movemap(), nmoves(), protocols::moves::Mover::show(), and temperature().

Referenced by protocols::simple_moves::operator<<().

void protocols::simple_moves::BackboneMover::temperature ( core::Real const  temperature_in)

Properties set/get functions.

References temperature_.

core::Real protocols::simple_moves::BackboneMover::temperature ( ) const

References temperature_.

Referenced by parse_my_tag(), and show().

Member Data Documentation

utility::vector1< int > protocols::simple_moves::BackboneMover::already_moved_
protected

Referenced by apply(), and clear().

std::map< char, core::Real > protocols::simple_moves::BackboneMover::angle_max_
protected

max allowed angle-change as a function of ss type

Referenced by angle_max(), get_angle_max(), and protocols::simple_moves::SmallMover::setup_list().

core::Real protocols::simple_moves::BackboneMover::big_angle_
protected
core::kinematics::MoveMapOP protocols::simple_moves::BackboneMover::movemap_
protected
core::Real protocols::simple_moves::BackboneMover::new_phi_
protected
core::Real protocols::simple_moves::BackboneMover::new_psi_
protected
core::Real protocols::simple_moves::BackboneMover::new_rama_score_
protected
Size protocols::simple_moves::BackboneMover::nmoves_
protected

number of positions at which to make moves

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

int protocols::simple_moves::BackboneMover::num_
protected

Referenced by apply().

core::Real protocols::simple_moves::BackboneMover::old_phi_
protected
core::Real protocols::simple_moves::BackboneMover::old_psi_
protected
core::Real protocols::simple_moves::BackboneMover::old_rama_score_
protected
utility::vector1< std::pair< int, core::Real > > protocols::simple_moves::BackboneMover::pos_list_
protected
bool protocols::simple_moves::BackboneMover::preserve_detailed_balance_
protected
int protocols::simple_moves::BackboneMover::resnum_
protected
core::Real protocols::simple_moves::BackboneMover::small_angle_
protected
core::Real protocols::simple_moves::BackboneMover::temperature_
protected

controls bias w/which uphill moves are accepted

Referenced by check_rama(), parse_my_tag(), and temperature().

int protocols::simple_moves::BackboneMover::tries_
protected

Referenced by apply(), and clear().


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