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protocols::relax::CentroidRelax Class Reference

Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization. More...

#include <CentroidRelax.hh>

Inheritance diagram for protocols::relax::CentroidRelax:
Inheritance graph
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Classes

struct  parameters
 Container for ramp settings. More...
 

Public Member Functions

 CentroidRelax ()
 
 CentroidRelax (core::kinematics::MoveMapOP mm)
 
 CentroidRelax (core::kinematics::MoveMapOP mm, core::scoring::ScoreFunctionOP cen_scorefxn_in)
 
 ~CentroidRelax () override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void set_defaults ()
 
void set_rounds (core::Size rounds)
 
void set_use_increased_vdw_radii (bool use)
 use larger VDW radii for atoms - bb for now - default True (Courtesy of Frank Dimaio) More...
 
void set_use_rama2b (bool use)
 Sets to use Rama2b instead of Rama - default True. More...
 
void set_ramp_rama (bool use)
 Ramp Rama according to centroid relax parameters. More...
 
void set_ramp_vdw (bool use)
 Ramp VDW according to centroid relax parameters. More...
 
void set_score_function (core::scoring::ScoreFunctionOP cen_score)
 Sets main scorefunction used for centroid minimization. More...
 
void set_fa_score_function (core::scoring::ScoreFunctionOP fa_score)
 Sets fullatom scorefunction - only used for scoring the full atom pose before and after protocol. More...
 
void set_min_type (std::string min)
 Sets the minimizer type. More...
 
void set_cartesian (bool cart)
 Sets to use the cartesian minimizer. More...
 
void do_final_repack (bool repack_sc)
 If a fullatom pose is passed, should we repack sidechains according to movemap? More...
 
void apply (core::pose::Pose &pose) override
 Applies the protocol, See notes. More...
 
- Public Member Functions inherited from protocols::relax::RelaxProtocolBase
 RelaxProtocolBase (core::scoring::ScoreFunctionOP)
 
 RelaxProtocolBase (std::string const &movername="RelaxProtocol")
 
 RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)
 
 ~RelaxProtocolBase () override
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void apply_disulfides (core::pose::Pose &pose)
 
void set_defaults ()
 
void set_default_minimization_settings ()
 
void set_default_coordinate_settings ()
 
void set_default_movemap ()
 
core::kinematics::MoveMapCOP get_movemap () const
 
core::kinematics::MoveMapOP get_movemap ()
 
const
core::scoring::ScoreFunctionCOP 
get_scorefxn () const
 
core::pack::task::TaskFactoryOP
const & 
get_task_factory () const
 
bool cartesian () const
 
std::string min_type () const
 
core::Size max_iter () const
 
bool dry_run () const
 
bool constrain_relax_to_native_coords () const
 
bool constrain_relax_to_start_coords () const
 
bool constrain_coords () const
 
bool coord_constrain_sidechains () const
 
bool ramp_down_constraints () const
 
bool constrain_relax_segments () const
 
bool minimize_bond_lengths () const
 
bool minimize_bond_angles () const
 
void set_movemap (core::kinematics::MoveMapOP movemap)
 
void set_movemap_factory (core::select::movemap::MoveMapFactoryOP mm_factory)
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
void set_task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void cartesian (bool newval)
 Use cartesian (minimization step) More...
 
void min_type (std::string min_type)
 
void max_iter (core::Size max_iter)
 
void dry_run (bool setting)
 
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 coord_constrain_sidechains (bool coord_constrain_sidechains)
 
void constrain_relax_segments (bool constrain_relax_segments)
 
void ramp_down_constraints (bool ramp_down_constraints)
 
void minimize_bond_lengths (bool minimize_bond_lengths)
 
void minimize_bond_angles (bool minimize_bond_angles)
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
bool mover_is_unpublished () const override
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Private Member Functions

void read_default_parameters ()
 Load the default parameters from the default file. More...
 
void setup_class_movemap_and_constraints (Pose &pose)
 used internally to setup extra stuff for movemap. More...
 
void setup_increased_vdw_radii ()
 increase VDW radii for backbone to help geometry and decrease rmsd More...
 

Private Attributes

bool use_increased_vdw_radii_
 
bool ramp_rama_
 
bool ramp_vdw_
 
core::Size rounds_
 
bool repack_sc_
 
core::scoring::ScoreFunctionOP cen_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
core::kinematics::MoveMapOP movemap_
 
core::scoring::ScoreType rama_type_
 
parameters def_parameters
 

Additional Inherited Members

- Public Types inherited from protocols::relax::RelaxProtocolBase
typedef moves::Mover parent
 
- 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
 
- Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
static void register_options ()
 
- 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::relax::RelaxProtocolBase
core::scoring::ScoreFunctionOP get_scorefxn ()
 
bool fix_omega () const
 
int minimize_bondlength_subset () const
 
int minimize_bondangle_subset () const
 
bool limit_aroma_chi2 () const
 
std::string cst_files (core::Size const i) const
 
void fix_omega (bool fix_omega)
 
void minimize_bondangle_subset (int minimize_bondangle_subset)
 
void minimize_bondlength_subset (int minimize_bondlength_subset)
 
void initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)
 
void set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
void add_cst_files (std::string const &cstfile)
 
- 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

Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization.

Minimize a centroid representation of a pose. Ramp VDW/Rama or both.

May tweak structure by up to ~2.5 A without constraints. Use custom constraints or coordinate constraints through relax options for best results. Using starting coordinate constraints, structure is tweaked by ~.3/.4 A Use increased VDW radii option for bb to improve bb-geometry when not using constraints

Constructor & Destructor Documentation

protocols::relax::CentroidRelax::CentroidRelax ( )
protocols::relax::CentroidRelax::CentroidRelax ( core::kinematics::MoveMapOP  mm)
protocols::relax::CentroidRelax::CentroidRelax ( core::kinematics::MoveMapOP  mm,
core::scoring::ScoreFunctionOP  cen_scorefxn_in 
)
protocols::relax::CentroidRelax::~CentroidRelax ( )
overridedefault

Member Function Documentation

void protocols::relax::CentroidRelax::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::relax::CentroidRelax::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.

void protocols::relax::CentroidRelax::do_final_repack ( bool  repack_sc)

If a fullatom pose is passed, should we repack sidechains according to movemap?

References repack_sc_.

Referenced by set_defaults().

string protocols::relax::CentroidRelax::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::relax::CentroidRelax::read_default_parameters ( )
private
void protocols::relax::CentroidRelax::set_cartesian ( bool  cart)
void protocols::relax::CentroidRelax::set_defaults ( )
void protocols::relax::CentroidRelax::set_fa_score_function ( core::scoring::ScoreFunctionOP  fa_score)

Sets fullatom scorefunction - only used for scoring the full atom pose before and after protocol.

References fa_scorefxn_, and protocols::hybridization::score.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_min_type ( std::string  min)

Sets the minimizer type.

References protocols::relax::RelaxProtocolBase::min_type().

Referenced by set_cartesian().

void protocols::relax::CentroidRelax::set_ramp_rama ( bool  use)

Ramp Rama according to centroid relax parameters.

References ramp_rama_.

Referenced by apply(), and set_defaults().

void protocols::relax::CentroidRelax::set_ramp_vdw ( bool  use)

Ramp VDW according to centroid relax parameters.

References ramp_vdw_.

Referenced by apply(), and set_defaults().

void protocols::relax::CentroidRelax::set_rounds ( core::Size  rounds)

References rounds_.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_score_function ( core::scoring::ScoreFunctionOP  cen_score)
void protocols::relax::CentroidRelax::set_use_increased_vdw_radii ( bool  use)

use larger VDW radii for atoms - bb for now - default True (Courtesy of Frank Dimaio)

References use_increased_vdw_radii_.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::set_use_rama2b ( bool  use)

Sets to use Rama2b instead of Rama - default True.

References cen_scorefxn_, core::scoring::rama, core::scoring::rama2b, and rama_type_.

Referenced by set_defaults().

void protocols::relax::CentroidRelax::setup_class_movemap_and_constraints ( Pose pose)
private
void protocols::relax::CentroidRelax::setup_increased_vdw_radii ( )
private

increase VDW radii for backbone to help geometry and decrease rmsd

References core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name(), cen_scorefxn_, and protocols::relax::TR().

Referenced by apply().

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::relax::CentroidRelax::cen_scorefxn_
private
parameters protocols::relax::CentroidRelax::def_parameters
private

Referenced by apply(), and read_default_parameters().

core::scoring::ScoreFunctionOP protocols::relax::CentroidRelax::fa_scorefxn_
private

Referenced by apply(), and set_fa_score_function().

core::kinematics::MoveMapOP protocols::relax::CentroidRelax::movemap_
private
core::scoring::ScoreType protocols::relax::CentroidRelax::rama_type_
private

Referenced by apply(), and set_use_rama2b().

bool protocols::relax::CentroidRelax::ramp_rama_
private

Referenced by apply(), and set_ramp_rama().

bool protocols::relax::CentroidRelax::ramp_vdw_
private

Referenced by apply(), and set_ramp_vdw().

bool protocols::relax::CentroidRelax::repack_sc_
private

Referenced by apply(), and do_final_repack().

core::Size protocols::relax::CentroidRelax::rounds_
private

Referenced by apply(), and set_rounds().

bool protocols::relax::CentroidRelax::use_increased_vdw_radii_
private

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