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

#include <MergePDBMover.hh>

Inheritance diagram for protocols::pose_creation::MergePDBMover:
Inheritance graph
[legend]

Classes

struct  Overlap
 

Public Types

typedef
core::select::residue_selector::ResidueSelectorOP 
ResidueSelectorOP
 
typedef
core::select::residue_selector::ResidueSelectorCOP 
ResidueSelectorCOP
 
- 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
 

Public Member Functions

 MergePDBMover ()
 Constructor. More...
 
void determine_overlap (Pose const pose, core::Size chain_id)
 Determines the overlaps. stores the start and end position in the struct Overlap. More...
 
bool check_duplicate (Pose &pose)
 fast check to maake sure the pose isn't a structural duplicate More...
 
void generate_overlaps (Pose &pose, core::Size chain_id)
 Uses the overlap to generate poses. More...
 
core::Size closest_non_overlap_residue (core::pose::Pose const &pose, core::Size resid, core::Size start_overlap_resid, core::Size end_overlap_resid)
 Figures out the closest residue that's not part of the overlap. More...
 
void increase_range_to_ignore_ss_element (core::pose::Pose const &pose, core::Size init_start, core::Size init_end, core::Size &ss_start, core::Size &ss_end)
 Gets the entire SS element the match is on. More...
 
void copy_sequence (core::Size start_overlap_resid, core::Size end_overlap_resid, core::Size start_overlap_input_pose_resid, core::Size start_overlap_xml_pose_resid, core::pose::Pose const &input_pose, core::pose::Pose const &xml_pose, core::pose::Pose &output_pose)
 Copies the sequence in the overlap region as appropriate. This sets the initial residues before the pack and minimize is called. More...
 
void pack_and_minimize (Pose const pose, core::Real baseline_score)
 packs and minimizes if no clashes as determined by score0 More...
 
core::pose::PoseOP get_additional_output () override
 any poses that score lower than the input files is output More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
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 std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Attributes

utility::vector1
< MergePDBMover::Overlap
overlaps_
 
core::pose::PoseOP xml_input_pose_
 
std::string overlap_location_pose_
 
core::Real overlap_max_rmsd_
 
core::Size overlap_length_
 
core::Size overlap_scan_range_cmdLine_
 
core::Size overlap_scan_range_xml_
 
core::Real design_range_
 
core::Real packing_range_
 
core::scoring::ScoreFunctionOP sfxn_
 
core::scoring::ScoreFunctionOP asymm_score_
 
core::pack::task::TaskFactoryOP task_factory_
 
bool do_minimize_
 
std::string chain_
 
std::string symm_file_
 
std::string no_design_label_
 
std::string init_overlap_sequence_
 
core::Real duplicate_rmsd_pose_threshold_
 
bool detect_disulf_before_repack_
 
bool output_only_first_
 
bool output_overlap_positions_
 
bool do_design_
 
core::Real clash_threshold_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::pose_creation::MergePDBMover::MergePDBMover ( )

Constructor.

Member Function Documentation

void protocols::pose_creation::MergePDBMover::apply ( core::pose::Pose )
overridevirtual
bool protocols::pose_creation::MergePDBMover::check_duplicate ( Pose pose)
moves::MoverOP protocols::pose_creation::MergePDBMover::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.

Size protocols::pose_creation::MergePDBMover::closest_non_overlap_residue ( core::pose::Pose const &  pose,
core::Size  resid,
core::Size  start_overlap_resid,
core::Size  end_overlap_resid 
)

Figures out the closest residue that's not part of the overlap.

References core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by copy_sequence().

void protocols::pose_creation::MergePDBMover::copy_sequence ( core::Size  start_overlap_resid,
core::Size  end_overlap_resid,
core::Size  start_overlap_input_pose_resid,
core::Size  start_overlap_xml_pose_resid,
core::pose::Pose const &  input_pose,
core::pose::Pose const &  xml_pose,
core::pose::Pose output_pose 
)

Copies the sequence in the overlap region as appropriate. This sets the initial residues before the pack and minimize is called.

References protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), closest_non_overlap_residue(), increase_range_to_ignore_ss_element(), init_overlap_sequence_, overlap_location_pose_, and protocols::pose_creation::TR().

Referenced by generate_overlaps().

void protocols::pose_creation::MergePDBMover::determine_overlap ( Pose const  pose,
core::Size  chain_id 
)
moves::MoverOP protocols::pose_creation::MergePDBMover::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.

void protocols::pose_creation::MergePDBMover::generate_overlaps ( Pose pose,
core::Size  chain_id 
)
core::pose::PoseOP protocols::pose_creation::MergePDBMover::get_additional_output ( )
overridevirtual
std::string protocols::pose_creation::MergePDBMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::pose_creation::MergePDBMover::increase_range_to_ignore_ss_element ( core::pose::Pose const &  pose,
core::Size  init_start,
core::Size  init_end,
core::Size ss_start,
core::Size ss_end 
)

Gets the entire SS element the match is on.

increases the range to ignore to include the entire secondary structure element

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::scoring::dssp::Dssp::get_dssp_secstruct(), and core::pose::Pose::total_residue().

Referenced by copy_sequence().

std::string protocols::pose_creation::MergePDBMover::mover_name ( )
static
void protocols::pose_creation::MergePDBMover::pack_and_minimize ( Pose const  pose,
core::Real  baseline_score 
)
void protocols::pose_creation::MergePDBMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References chain_, clash_threshold_, design_range_, detect_disulf_before_repack_, do_design_, do_minimize_, duplicate_rmsd_pose_threshold_, init_overlap_sequence_, no_design_label_, output_only_first_, output_overlap_positions_, overlap_length_, overlap_location_pose_, overlap_max_rmsd_, overlap_scan_range_cmdLine_, overlap_scan_range_xml_, packing_range_, core::pack::task::parse_task_operations(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), sfxn_, symm_file_, task_factory_, and xml_input_pose_.

void protocols::pose_creation::MergePDBMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::pose_creation::MergePDBMover::asymm_score_
private

Referenced by apply(), and generate_overlaps().

std::string protocols::pose_creation::MergePDBMover::chain_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::pose_creation::MergePDBMover::clash_threshold_
private

Referenced by generate_overlaps(), and parse_my_tag().

core::Real protocols::pose_creation::MergePDBMover::design_range_
private

Referenced by generate_overlaps(), and parse_my_tag().

bool protocols::pose_creation::MergePDBMover::detect_disulf_before_repack_
private

Referenced by pack_and_minimize(), and parse_my_tag().

bool protocols::pose_creation::MergePDBMover::do_design_
private

Referenced by apply(), and parse_my_tag().

bool protocols::pose_creation::MergePDBMover::do_minimize_
private

Referenced by pack_and_minimize(), and parse_my_tag().

core::Real protocols::pose_creation::MergePDBMover::duplicate_rmsd_pose_threshold_
private

Referenced by check_duplicate(), and parse_my_tag().

std::string protocols::pose_creation::MergePDBMover::init_overlap_sequence_
private

Referenced by copy_sequence(), and parse_my_tag().

std::string protocols::pose_creation::MergePDBMover::no_design_label_
private
bool protocols::pose_creation::MergePDBMover::output_only_first_
private

Referenced by pack_and_minimize(), and parse_my_tag().

bool protocols::pose_creation::MergePDBMover::output_overlap_positions_
private
core::Size protocols::pose_creation::MergePDBMover::overlap_length_
private

Referenced by determine_overlap(), and parse_my_tag().

std::string protocols::pose_creation::MergePDBMover::overlap_location_pose_
private
core::Real protocols::pose_creation::MergePDBMover::overlap_max_rmsd_
private

Referenced by determine_overlap(), and parse_my_tag().

core::Size protocols::pose_creation::MergePDBMover::overlap_scan_range_cmdLine_
private

Referenced by determine_overlap(), and parse_my_tag().

core::Size protocols::pose_creation::MergePDBMover::overlap_scan_range_xml_
private

Referenced by determine_overlap(), and parse_my_tag().

utility::vector1<MergePDBMover::Overlap> protocols::pose_creation::MergePDBMover::overlaps_
private
core::Real protocols::pose_creation::MergePDBMover::packing_range_
private

Referenced by pack_and_minimize(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::pose_creation::MergePDBMover::sfxn_
private
std::string protocols::pose_creation::MergePDBMover::symm_file_
private

Referenced by generate_overlaps(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::pose_creation::MergePDBMover::task_factory_
private

Referenced by pack_and_minimize(), and parse_my_tag().

core::pose::PoseOP protocols::pose_creation::MergePDBMover::xml_input_pose_
private

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