Rosetta 3.4
Public Types | Public Member Functions | Protected Attributes
protocols::simple_moves::BackboneMover Class Reference

#include <BackboneMover.hh>

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List of all members.

Public Types

typedef core::Real Real

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 overloaded or called from the inheriting classes
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
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.
void nmoves (core::Size const nmoves_in)
core::kinematics::MoveMapCOP movemap ()
void movemap (core::kinematics::MoveMapOP new_movemap)
void angle_max (core::Real const angle)
 Sets the maximum angle of perturbation, independent of secondary structure.
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', and 'L')
void angle_max (std::map< char, core::Real > angle_max_in)
 sets the max angle of perturbation, for secondary structure 'H', 'E', and 'L'
core::Real new_phi ()
core::Real new_psi ()
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::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.
bool preserve_detailed_balance () const
 get whether detailed balance is preserved (i.e. no Ramachandran biasing)
void set_preserve_detailed_balance (bool preserve_detailed_balance)
 set whether detailed balance is preserved (i.e. no Ramachandran biasing)
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

Protected Attributes

core::kinematics::MoveMapOP movemap_
core::Real temperature_
 controls bias w/which uphill moves are accepted
Size nmoves_
 number of positions at which to make moves
std::map< char, core::Realangle_max_
 max allowed angle-change as a function of ss type
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_

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)

Sets the maximum angle of perturbation, independent of secondary structure.

example: bbmover.angle_max(25) See also: ShearMover SmallMover

Referenced by BackboneMover(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), and parse_my_tag().

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', and '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 structure '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::SmallMover, and protocols::simple_moves::ShearMover.

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

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

References movemap_.

core::kinematics::MoveMapCOP protocols::simple_moves::BackboneMover::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)
void protocols::simple_moves::BackboneMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::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::temperature ( core::Real const  temperature_in)

Properties set/get functions.

References temperature_.

Referenced by parse_my_tag().


Member Data Documentation

Referenced by apply(), and clear().

max allowed angle-change as a function of ss type

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

number of positions at which to make moves

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

Referenced by apply().

controls bias w/which uphill moves are accepted

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

Referenced by apply(), and clear().


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