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protocols::denovo_design::movers::FastDesign Class Reference

#include <FastDesign.hh>

Inheritance diagram for protocols::denovo_design::movers::FastDesign:
Inheritance graph
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Public Member Functions

 FastDesign ()
 default constructor More...
 
 FastDesign (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)
 Constructor with some options. More...
 
 FastDesign (core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)
 Constructor with some options. More...
 
 ~FastDesign () override
 virtual constructor to allow derivation More...
 
void set_up_default_task_factory ()
 Create the default task factory. Must be called before design can occur. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Parses the FastDesignTags. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Return the name of this mover. More...
 
protocols::moves::MoverOP clone () const override
 return a copy of this class in an owning pointer More...
 
void apply (core::pose::Pose &pose) override
 Apply the FastDesign. Overloaded apply function from mover base class. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
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...
 
- Public Member Functions inherited from protocols::relax::FastRelax
 FastRelax (core::Size standard_repeats=0)
 Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied. More...
 
 FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)
 Initialize FastRelax using the default script with a varying number of rounds, defined by the standard_repeats repeats paramter. By default, 5. More...
 
 FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)
 Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied. More...
 
 FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats, const std::string &script_file)
 Initialize FastRelax with a specific script file, and allows fastrelax to only use a subset of the number of stages in the scriptfile. More...
 
void set_script_to_batchrelax_default (core::Size standard_repeats=0)
 Override the stored script with the default script for batchrelax Ignores '-default_repeat' value. More...
 
void set_script_from_lines (std::vector< std::string > const &filelines)
 replace schedule by providing lines of commands explicitly More...
 
void set_force_nonideal (bool val)
 Force us to batchrelax with nonideal geometry (using additional memory) More...
 
void dualspace (bool val)
 Use the dualspace (Dihedral + Cartesian) relax protocol (Default false) More...
 
bool dualspace ()
 
core::Size default_repeats () const
 Return the number of repeats. More...
 
void set_movemap_disables_packing_of_fixed_chi_positions (bool const setting)
 Set whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...
 
bool movemap_disables_packing_of_fixed_chi_positions () const
 Get whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...
 
 ~FastRelax () override
 virtual constructor to allow derivation More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Parses the FastRelaxTags. More...
 
void set_to_default ()
 Initializes class using option system. This is called by the constructors. More...
 
protocols::moves::MoverOP clone () const override
 return a fresh instance of this class in an owning pointer More...
 
void apply (core::pose::Pose &pose) override
 Apply the FastRelax. Overloaded apply function from mover base class. More...
 
void batch_apply (std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=nullptr, core::Real decay_rate=0.5)
 Batch Relax, a new even faster way to relax entire batches of structures. More...
 
void set_enable_design (bool const val)
 sets the enable_design option. Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.) More...
 
std::string get_name () const override
 Return the name of this mover. More...
 
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...
 
- 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
 
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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::relax::FastRelax
static std::string mover_name ()
 Return the name of this mover. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_fast_relax (utility::tag::XMLSchemaDefinition &)
 
- 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

void set_constraint_weight (core::scoring::ScoreFunctionOP local_scorefxn, core::scoring::EnergyMap const &full_weights, core::Real const weight, core::pose::Pose &pose) const override
 sets constraint weights – used with constraint ramping More...
 
- Protected Member Functions inherited from protocols::relax::FastRelax
void cmd_accept_to_best (const core::scoring::ScoreFunctionOP local_scorefxn, core::pose::Pose &pose, core::pose::Pose &best_pose, const core::pose::Pose &start_pose, core::Real &best_score, core::Size &accept_count)
 
void do_minimize (core::pose::Pose &pose, core::Real tolerance, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)
 
void do_md (core::pose::Pose &pose, core::Real nstep, core::Real temp0, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)
 
std::string determine_default_relax_script ()
 default is currently MonomerDesign2019 or MonomerRelax2019, depending on the state of enable_design_ More...
 
core::pack::task::TaskFactoryOP setup_local_tf (core::pose::Pose const &pose, core::kinematics::MoveMapOP const &local_movemap)
 helper function for apply(). Helps setup the task factory 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...
 

Private Member Functions

core::pack::task::TaskFactoryOP create_default_task_factory () const
 

Private Attributes

bool clear_designable_residues_
 Should we clear designable residues (sets them to ALA so that they can be rebuilt) More...
 
core::Size run_count_
 
protocols::constraint_generator::ConstraintGeneratorCOPs cgs_
 

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
 

Constructor & Destructor Documentation

protocols::denovo_design::movers::FastDesign::FastDesign ( )

default constructor


FastDesign main code:

References protocols::relax::FastRelax::set_enable_design().

protocols::denovo_design::movers::FastDesign::FastDesign ( core::scoring::ScoreFunctionOP  scorefxn_in,
core::Size  standard_repeats = 0 
)

Constructor with some options.

References protocols::relax::FastRelax::set_enable_design().

protocols::denovo_design::movers::FastDesign::FastDesign ( core::scoring::ScoreFunctionOP  scorefxn_in,
std::string const &  script_file 
)

Constructor with some options.

References protocols::relax::FastRelax::set_enable_design().

protocols::denovo_design::movers::FastDesign::~FastDesign ( )
overridedefault

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.

Member Function Documentation

void protocols::denovo_design::movers::FastDesign::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::denovo_design::movers::FastDesign::clone ( ) const
overridevirtual

return a copy of this class in an owning pointer

Return a copy of ourselves.

Reimplemented from protocols::moves::Mover.

Referenced by apply().

core::pack::task::TaskFactoryOP protocols::denovo_design::movers::FastDesign::create_default_task_factory ( ) const
private
protocols::moves::MoverOP protocols::denovo_design::movers::FastDesign::fresh_instance ( ) const
overridevirtual

Return the name of this mover.

return an blank version of ourselves

return a fresh instance of this class in an owning pointer

Reimplemented from protocols::moves::Mover.

std::string protocols::denovo_design::movers::FastDesign::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by provide_citation_info().

std::string protocols::denovo_design::movers::FastDesign::mover_name ( )
static
bool protocols::denovo_design::movers::FastDesign::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

void protocols::denovo_design::movers::FastDesign::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Parses the FastDesignTags.

Reimplemented from protocols::moves::Mover.

References cgs_, clear_designable_residues_, and set_up_default_task_factory().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::denovo_design::movers::FastDesign::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

This function provides citations for the task operations in the task factory and for FastDesign.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)
Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

This function provides citations for the task operations in the task factory and for FastRelax.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References get_name().

void protocols::denovo_design::movers::FastDesign::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::denovo_design::movers::FastDesign::set_constraint_weight ( core::scoring::ScoreFunctionOP  local_scorefxn,
core::scoring::EnergyMap const &  full_weights,
core::Real const  weight,
core::pose::Pose pose 
) const
overrideprotectedvirtual
void protocols::denovo_design::movers::FastDesign::set_up_default_task_factory ( )

Create the default task factory. Must be called before design can occur.

References create_default_task_factory(), and protocols::relax::RelaxProtocolBase::set_task_factory().

Referenced by parse_my_tag().

Member Data Documentation

protocols::constraint_generator::ConstraintGeneratorCOPs protocols::denovo_design::movers::FastDesign::cgs_
private
bool protocols::denovo_design::movers::FastDesign::clear_designable_residues_
private

Should we clear designable residues (sets them to ALA so that they can be rebuilt)

Referenced by apply(), and parse_my_tag().

core::Size protocols::denovo_design::movers::FastDesign::run_count_
private

Referenced by apply().


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