Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::simple_moves::SetupMetalsMover Class Reference

A protocols::moves::Mover that. More...

#include <SetupMetalsMover.hh>

Inheritance diagram for protocols::simple_moves::SetupMetalsMover:
Inheritance graph
[legend]

Public Member Functions

 SetupMetalsMover ()
 Constructs a SetupMetalsMover. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing. More...
 
bool get_constraints_only () const
 
core::Real get_metals_detection_LJ_multiplier () const
 
core::Real get_metals_distance_constraint_multiplier () const
 
core::Real get_metals_angle_constraint_multiplier () const
 
core::select::residue_selector::ResidueSelectorCOP get_metal_selector () const
 
std::string get_metal_resnums_string () const
 
bool get_remove_hydrogens () const
 
bool get_add_constraints () const
 
core::select::residue_selector::ResidueSelectorCOP get_contact_selector () const
 
std::string get_contact_resnums_string () const
 
void set_constraints_only (bool)
 
void set_metals_detection_LJ_multiplier (core::Real)
 
void set_metals_distance_constraint_multiplier (core::Real)
 
void set_metals_angle_constraint_multiplier (core::Real)
 
void set_metal_selector (core::select::residue_selector::ResidueSelectorCOP)
 
void set_metal_resnums_string (std::string)
 
void set_remove_hydrogens (bool)
 
void set_add_constraints (bool)
 
void set_contact_selector (core::select::residue_selector::ResidueSelectorCOP)
 
void set_contact_resnums_string (std::string)
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? Returns false. 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 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 void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string mover_name ()
 
- 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

utility::vector1< core::Sizefind_metal_resnums (core::pose::Pose const &)
 If a residue selector or resnum string is provided, returns any metal ions within the selection. Otherwise returns an empty vector. More...
 
std::set< core::Sizefind_contact_resnums (core::pose::Pose const &)
 
void set_defaults_from_command_line ()
 
- 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 Attributes

bool remove_hydrogens_ = true
 
bool constraints_only_ = false
 
bool add_constraints_ = true
 
core::Real metals_detection_LJ_multiplier_ = 1.0
 
core::Real metals_distance_constraint_multiplier_ = 1.0
 
core::Real metals_angle_constraint_multiplier_ = 1.0
 
core::select::residue_selector::ResidueSelectorCOP metal_selector_ = nullptr
 
std::string metal_resnums_string_ = ""
 
core::select::residue_selector::ResidueSelectorCOP contact_selector_ = nullptr
 
std::string contact_resnums_string_ = ""
 

Additional Inherited Members

- 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
 

Detailed Description

A protocols::moves::Mover that.

Constructor & Destructor Documentation

protocols::simple_moves::SetupMetalsMover::SetupMetalsMover ( )

Member Function Documentation

void protocols::simple_moves::SetupMetalsMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::simple_moves::SetupMetalsMover::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.

std::set< core::Size > protocols::simple_moves::SetupMetalsMover::find_contact_resnums ( core::pose::Pose const &  pose)
protected
utility::vector1< core::Size > protocols::simple_moves::SetupMetalsMover::find_metal_resnums ( core::pose::Pose const &  pose)
protected

If a residue selector or resnum string is provided, returns any metal ions within the selection. Otherwise returns an empty vector.

If a residue selector or resnum string is provided, returns any metal ions within the selection. Otherwise returns an empty vector (it shouldn't be called in this situation, though)

References core::pose::get_resnum_list(), core::conformation::Residue::is_metal(), metal_resnums_string_, metal_selector_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by apply().

protocols::moves::MoverOP protocols::simple_moves::SetupMetalsMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

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.

bool protocols::simple_moves::SetupMetalsMover::get_add_constraints ( ) const

References add_constraints_.

bool protocols::simple_moves::SetupMetalsMover::get_constraints_only ( ) const

References constraints_only_.

std::string protocols::simple_moves::SetupMetalsMover::get_contact_resnums_string ( ) const
core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::get_contact_selector ( ) const

References contact_selector_.

std::string protocols::simple_moves::SetupMetalsMover::get_metal_resnums_string ( ) const

References metal_resnums_string_.

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::get_metal_selector ( ) const

References metal_selector_.

core::Real protocols::simple_moves::SetupMetalsMover::get_metals_angle_constraint_multiplier ( ) const
core::Real protocols::simple_moves::SetupMetalsMover::get_metals_detection_LJ_multiplier ( ) const
core::Real protocols::simple_moves::SetupMetalsMover::get_metals_distance_constraint_multiplier ( ) const
std::string protocols::simple_moves::SetupMetalsMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::simple_moves::SetupMetalsMover::get_remove_hydrogens ( ) const

References remove_hydrogens_.

bool protocols::simple_moves::SetupMetalsMover::mover_is_unpublished ( ) const
overridevirtual

Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?

Returns true. This mover is unpublished.

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.

std::string protocols::simple_moves::SetupMetalsMover::mover_name ( )
static
bool protocols::simple_moves::SetupMetalsMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it? Returns false.

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::simple_moves::SetupMetalsMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::simple_moves::SetupMetalsMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Returns
Sharon Guffy's authorship information.
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 contact_selector_, and metal_selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::simple_moves::SetupMetalsMover::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
Nothing for this mover, since it is unpublished. Can return citations for residue selectors that this mover links.
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 contact_selector_, and metal_selector_.

void protocols::simple_moves::SetupMetalsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::SetupMetalsMover::set_add_constraints ( bool  input)

References add_constraints_.

void protocols::simple_moves::SetupMetalsMover::set_constraints_only ( bool  input)

References constraints_only_.

void protocols::simple_moves::SetupMetalsMover::set_contact_resnums_string ( std::string  input)
void protocols::simple_moves::SetupMetalsMover::set_contact_selector ( core::select::residue_selector::ResidueSelectorCOP  input)

References contact_selector_.

void protocols::simple_moves::SetupMetalsMover::set_defaults_from_command_line ( )
protected
void protocols::simple_moves::SetupMetalsMover::set_metal_resnums_string ( std::string  input)

References metal_resnums_string_.

void protocols::simple_moves::SetupMetalsMover::set_metal_selector ( core::select::residue_selector::ResidueSelectorCOP  input)

References metal_selector_.

void protocols::simple_moves::SetupMetalsMover::set_metals_angle_constraint_multiplier ( core::Real  input)
void protocols::simple_moves::SetupMetalsMover::set_metals_detection_LJ_multiplier ( core::Real  input)
void protocols::simple_moves::SetupMetalsMover::set_metals_distance_constraint_multiplier ( core::Real  input)
void protocols::simple_moves::SetupMetalsMover::set_remove_hydrogens ( bool  input)

References remove_hydrogens_.

void protocols::simple_moves::SetupMetalsMover::show ( std::ostream &  output = std::cout) const
overridevirtual

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 constraints_only_, metal_resnums_string_, metal_selector_, metals_angle_constraint_multiplier_, metals_detection_LJ_multiplier_, metals_distance_constraint_multiplier_, remove_hydrogens_, and protocols::moves::Mover::show().

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

Member Data Documentation

bool protocols::simple_moves::SetupMetalsMover::add_constraints_ = true
private
bool protocols::simple_moves::SetupMetalsMover::constraints_only_ = false
private
std::string protocols::simple_moves::SetupMetalsMover::contact_resnums_string_ = ""
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::contact_selector_ = nullptr
private
std::string protocols::simple_moves::SetupMetalsMover::metal_resnums_string_ = ""
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::metal_selector_ = nullptr
private
core::Real protocols::simple_moves::SetupMetalsMover::metals_angle_constraint_multiplier_ = 1.0
private
core::Real protocols::simple_moves::SetupMetalsMover::metals_detection_LJ_multiplier_ = 1.0
private
core::Real protocols::simple_moves::SetupMetalsMover::metals_distance_constraint_multiplier_ = 1.0
private
bool protocols::simple_moves::SetupMetalsMover::remove_hydrogens_ = true
private

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