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protocols::pdbinfo_manipulations::AlignPDBInfoToSequences Class Reference

Realign poses to sequences after losing pdb_info. More...

#include <AlignPDBInfoToSequences.hh>

Inheritance diagram for protocols::pdbinfo_manipulations::AlignPDBInfoToSequences:
Inheritance graph
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Public Member Functions

 AlignPDBInfoToSequences ()
 Constructors ///. More...
 
 AlignPDBInfoToSequences (AlignPDBInfoToSequences const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~AlignPDBInfoToSequences () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
AlignPDBInfoToSequencesoperator= (AlignPDBInfoToSequences const &src)
 = operator More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
void set_target_sequences (utility::vector1< SequenceSpecification > const &target_sequences)
 
utility::vector1
< SequenceSpecification >
const & 
get_target_sequences () const
 
utility::vector1
< SequenceSpecification > & 
get_target_sequences ()
 
void set_mode (AlignPDBInfoToSequencesMode const &mode)
 
void set_mode_from_string (std::string const &mode)
 
AlignPDBInfoToSequencesMode const & get_mode () const
 
std::string get_mode_as_string () const
 
void set_throw_on_fail (bool const throw_on_fail)
 
bool get_throw_on_fail () const
 
void set_sequence_alignment_cut_max (core::Size const sequence_alignment_cut_max)
 
core::Size get_sequence_alignment_cut_max () const
 
SequenceSpecification parse_target_tag (utility::tag::TagCOP const &tag) const
 Rosetta Scripts Support ///. More...
 
void load_json_file (std::string const &json_fn)
 Rosetta Scripts Support ///. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme 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...
 
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...
 
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 Member Functions

void apply_multi_sequence (core::pose::Pose &pose)
 This method tries to align every sequence of the pose to every target sequence by applying a SWAligner to them, and if we find a perfect alignment we use that target sequence as the reference. More...
 
void apply_single_sequence (core::pose::Pose &pose)
 This method tries to align the pose to a target sequence that is generated by appending all target_sequences_ together. This allows for more residue-level control of the residue numbers/chainIDs but uses more memory (larger SWAligner). Most of the time you should probably use apply_multi_sequence, but sometimes you just crave that control!!! More...
 

Private Attributes

utility::vector1
< SequenceSpecification
target_sequences_
 
AlignPDBInfoToSequencesMode mode_
 
bool throw_on_fail_ = false
 
core::Size sequence_alignment_cut_max_ = 10
 

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
 
- 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

Realign poses to sequences after losing pdb_info.

Constructor & Destructor Documentation

protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::AlignPDBInfoToSequences ( )

Constructors ///.

Default constructor

protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::AlignPDBInfoToSequences ( AlignPDBInfoToSequences const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::~AlignPDBInfoToSequences ( )
override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply ( core::pose::Pose pose)
overridevirtual
void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence ( core::pose::Pose pose)
private
void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_single_sequence ( core::pose::Pose pose)
private

This method tries to align the pose to a target sequence that is generated by appending all target_sequences_ together. This allows for more residue-level control of the residue numbers/chainIDs but uses more memory (larger SWAligner). Most of the time you should probably use apply_multi_sequence, but sometimes you just crave that control!!!

Mover Methods ///.

References core::sequence::SWAligner::align(), protocols::pdbinfo_manipulations::pad_sequences(), core::pose::Pose::pdb_info(), core::pose::Pose::sequence(), target_sequences_, and protocols::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

AlignPDBInfoToSequencesMode const& protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode ( ) const
inline

References mode_.

Referenced by apply(), get_mode_as_string(), operator=(), and parse_my_tag().

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode_as_string ( ) const
std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_sequence_alignment_cut_max ( ) const
inline
utility::vector1<SequenceSpecification> const& protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_target_sequences ( ) const
inline
utility::vector1<SequenceSpecification>& protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_target_sequences ( )
inline

References target_sequences_.

bool protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_throw_on_fail ( ) const
inline

References throw_on_fail_.

Referenced by operator=().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::load_json_file ( std::string const &  json_fn)

Rosetta Scripts Support ///.

References core::sequence::end, and get_target_sequences().

Referenced by parse_my_tag().

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::mover_name ( )
static
AlignPDBInfoToSequences & protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::operator= ( AlignPDBInfoToSequences const &  src)
void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
SequenceSpecification protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_target_tag ( utility::tag::TagCOP const &  tag) const

Rosetta Scripts Support ///.

References protocols::kinmatch::str().

Referenced by parse_my_tag().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode ( AlignPDBInfoToSequencesMode const &  mode)
inline

References mode_.

Referenced by operator=(), parse_my_tag(), and set_mode_from_string().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode_from_string ( std::string const &  mode)
void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_sequence_alignment_cut_max ( core::Size const  sequence_alignment_cut_max)
inline

References sequence_alignment_cut_max_.

Referenced by parse_my_tag().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_target_sequences ( utility::vector1< SequenceSpecification > const &  target_sequences)
inline

References target_sequences_.

Referenced by operator=().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_throw_on_fail ( bool const  throw_on_fail)
inline

References throw_on_fail_.

Referenced by operator=(), and parse_my_tag().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

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

Member Data Documentation

AlignPDBInfoToSequencesMode protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::mode_
private

Referenced by get_mode(), and set_mode().

core::Size protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::sequence_alignment_cut_max_ = 10
private
utility::vector1<SequenceSpecification> protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::target_sequences_
private
bool protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::throw_on_fail_ = false
private

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