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protocols::struct_fragment::StructFragmentMover Class Reference

#include <StructFragmentMover.hh>

Inheritance diagram for protocols::struct_fragment::StructFragmentMover:
Inheritance graph
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Public Member Functions

 StructFragmentMover ()
 Empty Constructor. More...
 
 ~StructFragmentMover () override
 Destructor. More...
 
void apply (core::pose::Pose &pose) override
 Apply Mover. More...
 
protocols::moves::MoverOP clone () const override
 Create clone of this mover. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Create a fresh instance of this mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Parse RosettaScripts options for this mover. More...
 
std::string get_name () const override
 Get mover name. More...
 
core::Size get_n_candidates () const
 Get the number of fragment candidates per position. More...
 
core::Size get_n_frags () const
 Get the number of fragments per position. More...
 
core::Real get_loop_angle_conf () const
 Get the confidence for phi and psi angles. More...
 
core::Size get_small_frag_size () const
 Get the size of small fragments. More...
 
core::Size get_large_frag_size () const
 Get the size of large fragments. More...
 
std::string get_small_frag_file () const
 Get the path to the small fragment file. More...
 
std::string get_large_frage_file () const
 Get the parth to the large fragment file. More...
 
std::string get_prefix () const
 Get the prefix for the fragment file output. More...
 
bool get_output_frag_files () const
 Check if fragment files should be outputted. More...
 
bool get_steal_small_frags () const
 Check if small fragments are being stolen. More...
 
bool get_steal_large_frags () const
 Check if large fragments are being stolen. More...
 
std::string get_frag_weight_file () const
 Get the path to the fragment weight file. More...
 
std::string get_sequence_profile () const
 Get the path to a sequence profile. More...
 
std::string get_vall_file () const
 Get the path to the vall file. More...
 
void set_n_candidates (core::Size n_candidates)
 Set the number of fragment candidates per position. More...
 
void set_n_frags (core::Size n_frags)
 Set the number of fragments per position. More...
 
void set_loop_angle_conf (core::Real loop_angle_conf)
 Set the confidence for phi and psi angles. More...
 
void set_small_frag_size (core::Size small_frag_size)
 Set the size of small fragments. More...
 
void set_large_frag_size (core::Size large_frag_size)
 Set the size of large fragments. More...
 
void set_small_frag_file (std::string small_frag_file)
 Set the path to the small fragment file. More...
 
void set_large_frag_file (std::string large_frag_file)
 Set the parth to the large fragment file. More...
 
void set_prefix (std::string prefix)
 Set the prefix for the fragment file output. More...
 
void set_output_frag_files (bool output_frag_files)
 Set whether fragment files should be outputted. More...
 
void set_steal_small_frags (bool steal_small_frags)
 Set whether small fragments are being stolen. More...
 
void set_steal_large_frags (bool steal_large_frags)
 Set whether large fragments are being stolen. More...
 
void set_frag_weight_file (std::string frag_weight_file)
 Set the path to the fragment weight file. More...
 
void set_sequence_profile (std::string sequence_profile)
 Set the path to a sequence profile. More...
 
void set_vall_file (std::string vall_file)
 Set the path to the vall file. More...
 
void set_secstruct (std::string const &ss)
 sets the secondary structure to be used for constraint generation More...
 
void set_use_dssp (bool const use_dssp)
 If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used. 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...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string mover_name ()
 Return mover name. More...
 
- 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

std::string get_secstruct (core::pose::Pose const &pose) const
 returns secondary structure to be used in this constraint generator More...
 
- 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::Size evaluate_job ()
 evaluates which process to run More...
 
utility::vector1
< core::fragment::FragSetOP
get_fragments (core::pose::Pose const &pose)
 Collect fragments for the specified input structure. More...
 
protocols::frag_picker::FragmentPickerOP make_fragment_picker (core::pose::Pose pose, std::string vall_file_name)
 Create fragment picker for the specified input structure. More...
 
core::fragment::FragSetOP steal_fragments_by_size (core::pose::Pose const &pose, core::fragment::FragSetOP fset, core::Size size)
 
utility::vector1
< core::fragment::FragSetOP
steal_fragments (core::pose::Pose const &pose, utility::vector1< core::fragment::FragSetOP > fsets)
 
void collector_to_picker (protocols::frag_picker::FragmentPickerOP pickIt, core::Size size, core::Size seqlength)
 
core::fragment::FragSetOP get_fragset (protocols::frag_picker::FragmentPickerOP pickIt, core::Size position, core::Size size)
 
core::fragment::FragSetOP shift_fragset (core::fragment::FragSetOP fset, core::id::SequenceMapping const &seqmap)
 
core::fragment::FragSetOP read_frag_file (std::string frag_file)
 Read existing fragment file. More...
 
utility::vector1
< core::fragment::FragSetOP
read_frag_files (std::string small_frag_file, std::string large_frag_file)
 Read small and large fragment file and combine the fragments. More...
 

Static Private Member Functions

static core::Real default_value_for_loop_angle_conf ()
 Default value for the confidence of phi and psi angles. More...
 
static core::Size default_value_for_small_frag_size ()
 Default value for the small fragment size. More...
 
static core::Size default_value_for_large_frag_size ()
 Default value for the large fragment size. More...
 
static bool default_value_for_output_frag_files ()
 Default value for outputting fragment files. More...
 
static bool default_value_for_steal_small_frags ()
 Default value for stealing small fragments. More...
 
static bool default_value_for_steal_large_frags ()
 Default value for stealing large fragments. More...
 
static std::string default_value_for_empty_file ()
 Default value for empty file. More...
 
static core::Size default_value_for_n_candidates ()
 Default value for fragment candidates per position. More...
 
static core::Size default_value_for_n_frags ()
 Default value for the number of fragments per position. More...
 
static std::string default_value_for_prefix ()
 Default prefix for fragment output files. More...
 
static std::string default_value_for_secstruct ()
 Default value for empty file. More...
 

Private Attributes

protocols::frag_picker::FragmentPickerOP structPicker_
 
core::Real loop_angle_conf_
 
core::Size small_frag_size_
 
core::Size large_frag_size_
 
std::string small_frag_file_
 
std::string large_frag_file_
 
bool output_frag_files_
 
bool steal_small_frags_
 
bool steal_large_frags_
 
bool changed_frags_
 
std::string frag_weight_file_
 
std::string sequence_profile_
 
std::string vall_file_
 
core::fragment::FragSetOP smallF_
 
core::fragment::FragSetOP largeF_
 
bool use_dssp_
 
std::string secstruct_
 

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
 

Constructor & Destructor Documentation

protocols::struct_fragment::StructFragmentMover::StructFragmentMover ( )
protocols::struct_fragment::StructFragmentMover::~StructFragmentMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::struct_fragment::StructFragmentMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::struct_fragment::StructFragmentMover::clone ( ) const
inlineoverridevirtual

Create clone of this mover.

Reimplemented from protocols::moves::Mover.

void protocols::struct_fragment::StructFragmentMover::collector_to_picker ( protocols::frag_picker::FragmentPickerOP  pickIt,
core::Size  size,
core::Size  seqlength 
)
private

Referenced by get_fragments().

static std::string protocols::struct_fragment::StructFragmentMover::default_value_for_empty_file ( )
inlinestaticprivate

Default value for empty file.

Referenced by parse_my_tag().

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_large_frag_size ( )
inlinestaticprivate

Default value for the large fragment size.

Referenced by parse_my_tag(), and provide_xml_schema().

static core::Real protocols::struct_fragment::StructFragmentMover::default_value_for_loop_angle_conf ( )
inlinestaticprivate

Default value for the confidence of phi and psi angles.

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_n_candidates ( )
inlinestaticprivate

Default value for fragment candidates per position.

Referenced by parse_my_tag(), provide_xml_schema(), and StructFragmentMover().

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_n_frags ( )
inlinestaticprivate

Default value for the number of fragments per position.

Referenced by parse_my_tag(), provide_xml_schema(), and StructFragmentMover().

static bool protocols::struct_fragment::StructFragmentMover::default_value_for_output_frag_files ( )
inlinestaticprivate

Default value for outputting fragment files.

Referenced by parse_my_tag(), and provide_xml_schema().

static std::string protocols::struct_fragment::StructFragmentMover::default_value_for_prefix ( )
inlinestaticprivate

Default prefix for fragment output files.

Referenced by parse_my_tag(), provide_xml_schema(), and StructFragmentMover().

static std::string protocols::struct_fragment::StructFragmentMover::default_value_for_secstruct ( )
inlinestaticprivate

Default value for empty file.

Referenced by provide_xml_schema().

static core::Size protocols::struct_fragment::StructFragmentMover::default_value_for_small_frag_size ( )
inlinestaticprivate

Default value for the small fragment size.

Referenced by parse_my_tag(), and provide_xml_schema().

static bool protocols::struct_fragment::StructFragmentMover::default_value_for_steal_large_frags ( )
inlinestaticprivate

Default value for stealing large fragments.

Referenced by parse_my_tag(), and provide_xml_schema().

static bool protocols::struct_fragment::StructFragmentMover::default_value_for_steal_small_frags ( )
inlinestaticprivate

Default value for stealing small fragments.

Referenced by parse_my_tag(), and provide_xml_schema().

core::Size protocols::struct_fragment::StructFragmentMover::evaluate_job ( )
private

evaluates which process to run

References large_frag_file_, small_frag_file_, steal_large_frags_, steal_small_frags_, and vall_file_.

Referenced by apply().

protocols::moves::MoverOP protocols::struct_fragment::StructFragmentMover::fresh_instance ( ) const
inlineoverridevirtual

Create a fresh instance of this mover.

Reimplemented from protocols::moves::Mover.

std::string protocols::struct_fragment::StructFragmentMover::get_frag_weight_file ( ) const
inline

Get the path to the fragment weight file.

References frag_weight_file_.

utility::vector1< cf::FragSetOP > protocols::struct_fragment::StructFragmentMover::get_fragments ( core::pose::Pose const &  pose)
private
cf::FragSetOP protocols::struct_fragment::StructFragmentMover::get_fragset ( protocols::frag_picker::FragmentPickerOP  pickIt,
core::Size  position,
core::Size  size 
)
private
core::Size protocols::struct_fragment::StructFragmentMover::get_large_frag_size ( ) const
inline

Get the size of large fragments.

References large_frag_size_.

std::string protocols::struct_fragment::StructFragmentMover::get_large_frage_file ( ) const
inline

Get the parth to the large fragment file.

References large_frag_file_.

core::Real protocols::struct_fragment::StructFragmentMover::get_loop_angle_conf ( ) const
inline

Get the confidence for phi and psi angles.

References loop_angle_conf_.

core::Size protocols::struct_fragment::StructFragmentMover::get_n_candidates ( ) const
inline

Get the number of fragment candidates per position.

References structPicker_.

core::Size protocols::struct_fragment::StructFragmentMover::get_n_frags ( ) const
inline

Get the number of fragments per position.

References structPicker_.

std::string protocols::struct_fragment::StructFragmentMover::get_name ( ) const
inlineoverridevirtual

Get mover name.

Implements protocols::moves::Mover.

References mover_name().

bool protocols::struct_fragment::StructFragmentMover::get_output_frag_files ( ) const
inline

Check if fragment files should be outputted.

References output_frag_files_.

std::string protocols::struct_fragment::StructFragmentMover::get_prefix ( ) const
inline

Get the prefix for the fragment file output.

References structPicker_.

std::string protocols::struct_fragment::StructFragmentMover::get_secstruct ( core::pose::Pose const &  pose) const
protected

returns secondary structure to be used in this constraint generator

Parameters
[in]poseInput pose
Returns
Secondary stucture of the pose according to the following rules:
  1. secstruct_ if it is non-empty
  2. DSSP secondary structure of the input pose if use_dssp_ is true
  3. Pose secondary structure if use_dssp_ is false

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_, and use_dssp_.

Referenced by make_fragment_picker().

std::string protocols::struct_fragment::StructFragmentMover::get_sequence_profile ( ) const
inline

Get the path to a sequence profile.

References sequence_profile_.

std::string protocols::struct_fragment::StructFragmentMover::get_small_frag_file ( ) const
inline

Get the path to the small fragment file.

References small_frag_file_.

core::Size protocols::struct_fragment::StructFragmentMover::get_small_frag_size ( ) const
inline

Get the size of small fragments.

References small_frag_size_.

bool protocols::struct_fragment::StructFragmentMover::get_steal_large_frags ( ) const
inline

Check if large fragments are being stolen.

References steal_large_frags_.

bool protocols::struct_fragment::StructFragmentMover::get_steal_small_frags ( ) const
inline

Check if small fragments are being stolen.

References steal_small_frags_.

std::string protocols::struct_fragment::StructFragmentMover::get_vall_file ( ) const
inline

Get the path to the vall file.

References vall_file_.

pfp::FragmentPickerOP protocols::struct_fragment::StructFragmentMover::make_fragment_picker ( core::pose::Pose  pose,
std::string  vall_file_name 
)
private
static std::string protocols::struct_fragment::StructFragmentMover::mover_name ( )
inlinestatic
void protocols::struct_fragment::StructFragmentMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::struct_fragment::StructFragmentMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
cf::FragSetOP protocols::struct_fragment::StructFragmentMover::read_frag_file ( std::string  frag_file)
private

Read existing fragment file.

References core::fragment::FragmentIO::read_data().

Referenced by read_frag_files().

utility::vector1< cf::FragSetOP > protocols::struct_fragment::StructFragmentMover::read_frag_files ( std::string  small_frag_file,
std::string  large_frag_file 
)
private

Read small and large fragment file and combine the fragments.

References read_frag_file().

Referenced by apply().

void protocols::struct_fragment::StructFragmentMover::set_frag_weight_file ( std::string  frag_weight_file)
inline

Set the path to the fragment weight file.

References frag_weight_file_.

void protocols::struct_fragment::StructFragmentMover::set_large_frag_file ( std::string  large_frag_file)
inline

Set the parth to the large fragment file.

References large_frag_file_.

void protocols::struct_fragment::StructFragmentMover::set_large_frag_size ( core::Size  large_frag_size)
inline

Set the size of large fragments.

References large_frag_size_.

void protocols::struct_fragment::StructFragmentMover::set_loop_angle_conf ( core::Real  loop_angle_conf)
inline

Set the confidence for phi and psi angles.

References loop_angle_conf_.

void protocols::struct_fragment::StructFragmentMover::set_n_candidates ( core::Size  n_candidates)
inline

Set the number of fragment candidates per position.

References structPicker_.

void protocols::struct_fragment::StructFragmentMover::set_n_frags ( core::Size  n_frags)
inline

Set the number of fragments per position.

References structPicker_.

void protocols::struct_fragment::StructFragmentMover::set_output_frag_files ( bool  output_frag_files)
inline

Set whether fragment files should be outputted.

References output_frag_files_.

void protocols::struct_fragment::StructFragmentMover::set_prefix ( std::string  prefix)
inline

Set the prefix for the fragment file output.

References structPicker_.

void protocols::struct_fragment::StructFragmentMover::set_secstruct ( std::string const &  ss)

sets the secondary structure to be used for constraint generation

returns secondary structure to be used in this constraint generator

Parameters
[in]poseInput pose
Returns
Pose secondary structure

References secstruct_.

Referenced by parse_my_tag().

void protocols::struct_fragment::StructFragmentMover::set_sequence_profile ( std::string  sequence_profile)
inline

Set the path to a sequence profile.

References sequence_profile_.

void protocols::struct_fragment::StructFragmentMover::set_small_frag_file ( std::string  small_frag_file)
inline

Set the path to the small fragment file.

References small_frag_file_.

void protocols::struct_fragment::StructFragmentMover::set_small_frag_size ( core::Size  small_frag_size)
inline

Set the size of small fragments.

References small_frag_size_.

void protocols::struct_fragment::StructFragmentMover::set_steal_large_frags ( bool  steal_large_frags)
inline

Set whether large fragments are being stolen.

References steal_large_frags_.

void protocols::struct_fragment::StructFragmentMover::set_steal_small_frags ( bool  steal_small_frags)
inline

Set whether small fragments are being stolen.

References steal_small_frags_.

void protocols::struct_fragment::StructFragmentMover::set_use_dssp ( bool const  use_dssp)

If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used.

Parameters
[in]use_dsspDesired value

References use_dssp_.

Referenced by parse_my_tag().

void protocols::struct_fragment::StructFragmentMover::set_vall_file ( std::string  vall_file)
inline

Set the path to the vall file.

References vall_file_.

core::fragment::FragSetOP protocols::struct_fragment::StructFragmentMover::shift_fragset ( core::fragment::FragSetOP  fset,
core::id::SequenceMapping const &  seqmap 
)
private
utility::vector1< cf::FragSetOP > protocols::struct_fragment::StructFragmentMover::steal_fragments ( core::pose::Pose const &  pose,
utility::vector1< core::fragment::FragSetOP fsets 
)
private
cf::FragSetOP protocols::struct_fragment::StructFragmentMover::steal_fragments_by_size ( core::pose::Pose const &  pose,
core::fragment::FragSetOP  fset,
core::Size  size 
)
private

Member Data Documentation

bool protocols::struct_fragment::StructFragmentMover::changed_frags_
private
std::string protocols::struct_fragment::StructFragmentMover::frag_weight_file_
private
std::string protocols::struct_fragment::StructFragmentMover::large_frag_file_
private
core::Size protocols::struct_fragment::StructFragmentMover::large_frag_size_
private
core::fragment::FragSetOP protocols::struct_fragment::StructFragmentMover::largeF_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::struct_fragment::StructFragmentMover::loop_angle_conf_
private
bool protocols::struct_fragment::StructFragmentMover::output_frag_files_
private
std::string protocols::struct_fragment::StructFragmentMover::secstruct_
private
std::string protocols::struct_fragment::StructFragmentMover::sequence_profile_
private
std::string protocols::struct_fragment::StructFragmentMover::small_frag_file_
private
core::Size protocols::struct_fragment::StructFragmentMover::small_frag_size_
private
core::fragment::FragSetOP protocols::struct_fragment::StructFragmentMover::smallF_
private

Referenced by apply(), and parse_my_tag().

bool protocols::struct_fragment::StructFragmentMover::steal_large_frags_
private
bool protocols::struct_fragment::StructFragmentMover::steal_small_frags_
private
protocols::frag_picker::FragmentPickerOP protocols::struct_fragment::StructFragmentMover::structPicker_
private
bool protocols::struct_fragment::StructFragmentMover::use_dssp_
private
std::string protocols::struct_fragment::StructFragmentMover::vall_file_
private

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