Rosetta 3.4
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes
protocols::relax::RelaxProtocolBase Class Reference

#include <RelaxProtocolBase.hh>

Inheritance diagram for protocols::relax::RelaxProtocolBase:
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List of all members.

Public Types

typedef moves::Mover parent

Public Member Functions

 RelaxProtocolBase (core::scoring::ScoreFunctionOP)
 RelaxProtocolBase (std::string const &movername="RelaxProtocol")
 RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)
 ~RelaxProtocolBase ()
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
void set_defaults ()
void set_default_minimization_settings ()
void set_default_coordinate_settings ()
void set_default_movemap ()
void minimize_bond_lengths (bool setting)
void minimize_bond_angles (bool setting)
void minimize_mainchain_bond_lengths (bool setting)
void minimize_mainchain_bond_angles (bool setting)
bool minimize_bond_lengths () const
bool minimize_bond_angles () const
bool minimize_mainchain_bond_lengths () const
bool minimize_mainchain_bond_angles () const
bool constrain_relax_to_native_coords () const
bool constrain_relax_to_start_coords () const
bool constrain_coords () const
bool explicit_ramp_constraints () const
bool ramp_down_constraints () const
bool constrain_relax_segments () const
bool limit_aroma_chi2 () const
void constrain_relax_to_native_coords (bool constrain_relax_to_native_coords)
void constrain_relax_to_start_coords (bool constrain_relax_to_start_coords)
void constrain_coords (bool constrain_coords)
void ramp_down_constraints (bool ramp_down_constraints)
void constrain_relax_segments (bool constrain_relax_segments)
void cartesian (bool newval)
bool cartesian () const
core::kinematics::MoveMapOP get_movemap ()
void set_movemap (core::kinematics::MoveMapOP movemap)
void set_min_type (std::string min_type)
void set_scorefxn (core::scoring::ScoreFunctionOP score)
const
core::scoring::ScoreFunctionCOP 
get_scorefxn () const
void set_task_factory (core::pack::task::TaskFactoryOP taskf)
core::pack::task::TaskFactoryOP
const & 
get_task_factory () const
void set_dry_run (bool setting)
bool dry_run () const
void apply_disulfides (core::pose::Pose &pose)

Static Public Member Functions

static void register_options ()
 overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.

Protected Member Functions

void initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)
core::scoring::ScoreFunctionOP get_scorefxn ()
void set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)
void output_debug_structure (core::pose::Pose &pose, std::string prefix)

Protected Attributes

bool constrain_relax_to_native_coords_
bool constrain_relax_to_start_coords_
bool constrain_coords_
bool coord_constrain_sidechains_
bool explicit_ramp_constraints_
bool ramp_down_constraints_
bool constrain_relax_segments_
std::string min_type_
bool cartesian_
 Do cartesian-space minimization?
bool limit_aroma_chi2_

Member Typedef Documentation


Constructor & Destructor Documentation

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( core::scoring::ScoreFunctionOP  score_in)

References set_defaults().

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( std::string const &  movername = "RelaxProtocol")

References set_defaults().

protocols::relax::RelaxProtocolBase::RelaxProtocolBase ( std::string const &  movername,
core::scoring::ScoreFunctionOP  score_in 
)

References set_defaults().

protocols::relax::RelaxProtocolBase::~RelaxProtocolBase ( )

Member Function Documentation

void protocols::relax::RelaxProtocolBase::apply_disulfides ( core::pose::Pose pose)
void protocols::relax::RelaxProtocolBase::cartesian ( bool  newval) [inline]

References cartesian_.

bool protocols::relax::RelaxProtocolBase::cartesian ( ) const [inline]
bool protocols::relax::RelaxProtocolBase::constrain_coords ( ) const [inline]
void protocols::relax::RelaxProtocolBase::constrain_coords ( bool  constrain_coords) [inline]
bool protocols::relax::RelaxProtocolBase::constrain_relax_segments ( ) const [inline]
void protocols::relax::RelaxProtocolBase::constrain_relax_segments ( bool  constrain_relax_segments) [inline]
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( ) const [inline]
void protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords ( bool  constrain_relax_to_native_coords) [inline]
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( ) const [inline]
void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords ( bool  constrain_relax_to_start_coords) [inline]
bool protocols::relax::RelaxProtocolBase::dry_run ( ) const [inline]
bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints ( ) const [inline]
virtual protocols::moves::MoverOP protocols::relax::RelaxProtocolBase::fresh_instance ( ) const [inline, virtual]

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

References protocols::moves::Mover::clone().

core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::get_movemap ( )
const core::scoring::ScoreFunctionCOP protocols::relax::RelaxProtocolBase::get_scorefxn ( ) const
core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::get_scorefxn ( ) [protected]
core::pack::task::TaskFactoryOP const & protocols::relax::RelaxProtocolBase::get_task_factory ( ) const
void protocols::relax::RelaxProtocolBase::initialize_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMap movemap 
) [protected]
bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2 ( ) const [inline]
void protocols::relax::RelaxProtocolBase::minimize_bond_angles ( bool  setting)
bool protocols::relax::RelaxProtocolBase::minimize_bond_angles ( ) const
void protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( bool  setting)
bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths ( ) const
void protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_angles ( bool  setting)
bool protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_angles ( ) const
void protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_lengths ( bool  setting)
bool protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_lengths ( ) const
void protocols::relax::RelaxProtocolBase::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
) [protected]
void protocols::relax::RelaxProtocolBase::ramp_down_constraints ( bool  ramp_down_constraints) [inline]
bool protocols::relax::RelaxProtocolBase::ramp_down_constraints ( ) const [inline]
void protocols::relax::RelaxProtocolBase::register_options ( ) [static]

overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::relax::ClassicRelax.

void protocols::relax::RelaxProtocolBase::set_default_coordinate_settings ( )
void protocols::relax::RelaxProtocolBase::set_default_minimization_settings ( )
void protocols::relax::RelaxProtocolBase::set_default_movemap ( )
void protocols::relax::RelaxProtocolBase::set_defaults ( )
void protocols::relax::RelaxProtocolBase::set_dry_run ( bool  setting) [inline]
void protocols::relax::RelaxProtocolBase::set_min_type ( std::string  min_type)
void protocols::relax::RelaxProtocolBase::set_movemap ( core::kinematics::MoveMapOP  movemap)
void protocols::relax::RelaxProtocolBase::set_scorefxn ( core::scoring::ScoreFunctionOP  score)
void protocols::relax::RelaxProtocolBase::set_task_factory ( core::pack::task::TaskFactoryOP  taskf)
void protocols::relax::RelaxProtocolBase::set_up_constraints ( core::pose::Pose pose,
core::kinematics::MoveMap local_movemap 
) [protected]

Member Data Documentation


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