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protocols::sewing::hashing::AlignmentFileGeneratorMover Class Reference

Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover. More...

#include <AlignmentFileGeneratorMover.hh>

Inheritance diagram for protocols::sewing::hashing::AlignmentFileGeneratorMover:
Inheritance graph
[legend]

Public Member Functions

 AlignmentFileGeneratorMover ()
 
 AlignmentFileGeneratorMover (AlignmentFileGeneratorMover const &src)
 
 AlignmentFileGeneratorMover (EdgeMapGeneratorOP edge_file_reader, std::string model_file_name, std::string alignment_file_name)
 
 AlignmentFileGeneratorMover (EdgeMapGeneratorOP edge_file_reader, std::string model_file_name)
 
 AlignmentFileGeneratorMover (std::string model_file_name, std::string edge_file_name, utility::vector1< core::Size > match_segments, utility::vector1< core::Size > pose_segment_starts, utility::vector1< core::Size > pose_segment_ends, core::Size recursive_depth)
 
 AlignmentFileGeneratorMover (BasisMapGeneratorOP bmg)
 
 ~AlignmentFileGeneratorMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
BasisMapGeneratorOP basis_map_generator () const
 
std::string get_required_resnums () const
 
void set_required_resnums (std::string)
 
core::select::residue_selector::ResidueSelectorCOP get_required_selector () const
 
void set_required_selector (core::select::residue_selector::ResidueSelectorCOP)
 
void basis_map_generator (BasisMapGeneratorOP bmg)
 
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...
 
- 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 class_name ()
 
static core::Size add_pose_segments_to_segment_vector (core::pose::Pose const &pose, core::pose::PoseOP partner_pose, SegmentVectorCOP segvec, std::map< core::Size, data_storage::SmartSegmentOP > &pdb_segments, std::string pose_segment_starts_string, std::string pose_segment_ends_string, std::string pose_segment_dssp, utility::vector1< data_storage::LigandDescription > &ligands, std::map< core::Size, data_storage::LigandResidueCOP > &partner_ligands, utility::vector1< data_storage::LigandDescription > &expanded_ligands, std::string required_resnums, core::select::residue_selector::ResidueSelectorCOP required_selector, bool strict_dssp_changes)
 
static core::Size add_pose_segments_to_segment_vector (core::pose::Pose const &pose, core::pose::PoseOP partner_pose, BasisMapGeneratorOP bmg, utility::vector1< data_storage::LigandDescription > &ligands, std::map< core::Size, data_storage::LigandResidueCOP > &partner_ligands, utility::vector1< data_storage::LigandDescription > &expanded_ligands, std::string required_resnums, core::select::residue_selector::ResidueSelectorCOP required_selector, bool set_segments_from_dssp)
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void append_ligands_subelement (utility::tag::XMLSchemaSimpleSubelementList &subs, utility::tag::XMLSchemaDefinition &xsd, bool include_coord)
 
static void parse_ligands_tag (utility::tag::TagCOP ligands_tag, basic::datacache::DataMap const &data, utility::vector1< data_storage::LigandDescription > &ligands)
 
static std::string ligands_subtag_ct_namer (std::string)
 
static AlignmentFGMSettingsOP alignment_settings_from_tag (utility::tag::TagCOP tag)
 
static void basis_map_from_alignment (AlignmentFGMSettings const &alignment, core::pose::Pose const &pose, BasisMapGeneratorOP bmg)
 
static void parse_ligand_conformers (utility::vector1< data_storage::LigandDescription > &ligands)
 
- 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

BasisMapGeneratorOP basis_map_generator_
 
AlignmentFGMSettingsOP align_settings_
 
utility::vector1
< data_storage::LigandDescription
ligands_
 
std::string required_resnums_
 
core::select::residue_selector::ResidueSelectorCOP required_selector_
 
bool set_segments_from_dssp_
 

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

Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover.

Constructor & Destructor Documentation

protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover ( )

References basis_map_generator_.

protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover ( AlignmentFileGeneratorMover const &  src)
default
protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover ( EdgeMapGeneratorOP  edge_file_reader,
std::string  model_file_name,
std::string  alignment_file_name 
)

References basis_map_generator_.

protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover ( EdgeMapGeneratorOP  edge_file_reader,
std::string  model_file_name 
)

References basis_map_generator_.

protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover ( std::string  model_file_name,
std::string  edge_file_name,
utility::vector1< core::Size match_segments,
utility::vector1< core::Size pose_segment_starts,
utility::vector1< core::Size pose_segment_ends,
core::Size  recursive_depth 
)

References basis_map_generator_.

protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover ( BasisMapGeneratorOP  bmg)
protocols::sewing::hashing::AlignmentFileGeneratorMover::~AlignmentFileGeneratorMover ( )
override

Member Function Documentation

core::Size protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector ( core::pose::Pose const &  pose,
core::pose::PoseOP  partner_pose,
SegmentVectorCOP  segvec,
std::map< core::Size, data_storage::SmartSegmentOP > &  pdb_segments,
std::string  pose_segment_starts_string,
std::string  pose_segment_ends_string,
std::string  pose_segment_dssp,
utility::vector1< data_storage::LigandDescription > &  ligands,
std::map< core::Size, data_storage::LigandResidueCOP > &  partner_ligands,
utility::vector1< data_storage::LigandDescription > &  expanded_ligands,
std::string  required_resnums,
core::select::residue_selector::ResidueSelectorCOP  required_selector,
bool  strict_dssp_changes 
)
static

References core::pose::append_pose_to_pose(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::conformation::Residue::atoms(), core::chemical::ResidueTypeBase::base_name(), core::conformation::Conformation::bonded_neighbor_all_res(), core::conformation::Residue::chi(), core::pose::Pose::conformation(), protocols::sewing::data_storage::ContactDescription::contact_atom_name, protocols::sewing::data_storage::ContactDescription::contact_atom_num, protocols::sewing::data_storage::ContactDescription::contact_resnum, protocols::sewing::data_storage::ContactDescription::contact_resnum_string, core::util::find_metalbinding_atoms_for_complex(), core::scoring::dssp::Dssp::get_dssp_reduced_IG_as_L_secstruct(), core::pose::get_resnum_list(), core::pose::get_resnum_list_ordered(), core::conformation::Residue::is_protein(), protocols::sewing::data_storage::ligand, protocols::sewing::data_storage::ContactDescription::ligand_atom_name, protocols::sewing::data_storage::ContactDescription::ligand_atom_num, protocols::sewing::data_storage::LigandDescription::ligand_resnum, protocols::sewing::data_storage::SmartSegment::link_to(), protocols::mean_field::min(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::natoms(), core::scoring::pair, core::pose::parse_resnum(), protocols::sewing::data_storage::ContactDescription::partner_contact, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::id::to_string(), core::pose::Pose::total_residue(), protocols::TR(), core::conformation::Atom::type(), protocols::moves::Mover::type(), and core::conformation::Residue::type().

Referenced by apply(), protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly(), and protocols::sewing::movers::AppendAssemblyMover::set_up_assembly().

core::Size protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector ( core::pose::Pose const &  pose,
core::pose::PoseOP  partner_pose,
BasisMapGeneratorOP  bmg,
utility::vector1< data_storage::LigandDescription > &  ligands,
std::map< core::Size, data_storage::LigandResidueCOP > &  partner_ligands,
utility::vector1< data_storage::LigandDescription > &  expanded_ligands,
std::string  required_resnums,
core::select::residue_selector::ResidueSelectorCOP  required_selector,
bool  set_segments_from_dssp 
)
static

References core::pose::append_pose_to_pose(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::conformation::Residue::atoms(), core::chemical::ResidueTypeBase::base_name(), core::conformation::Conformation::bonded_neighbor_all_res(), core::conformation::Residue::chi(), core::pose::Pose::conformation(), protocols::sewing::data_storage::ContactDescription::contact_atom_name, protocols::sewing::data_storage::ContactDescription::contact_atom_num, protocols::sewing::data_storage::ContactDescription::contact_resnum, protocols::sewing::data_storage::ContactDescription::contact_resnum_string, core::util::find_metalbinding_atoms_for_complex(), core::scoring::dssp::Dssp::get_dssp_reduced_IG_as_L_secstruct(), core::pose::get_resnum_list(), core::conformation::Residue::is_protein(), protocols::sewing::data_storage::ligand, protocols::sewing::data_storage::ContactDescription::ligand_atom_name, protocols::sewing::data_storage::ContactDescription::ligand_atom_num, protocols::sewing::data_storage::LigandDescription::ligand_resnum, protocols::sewing::data_storage::SmartSegment::link_to(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::natoms(), core::scoring::pair, core::pose::parse_resnum(), protocols::sewing::data_storage::ContactDescription::partner_contact, core::pose::Pose::residue(), core::id::AtomID::rsd(), protocols::sewing::hashing::AlignmentSettings::segments_, core::id::to_string(), core::pose::Pose::total_residue(), protocols::TR(), core::conformation::Atom::type(), protocols::moves::Mover::type(), and core::conformation::Residue::type().

AlignmentFGMSettingsOP protocols::sewing::hashing::AlignmentFileGeneratorMover::alignment_settings_from_tag ( utility::tag::TagCOP  tag)
static
void protocols::sewing::hashing::AlignmentFileGeneratorMover::append_ligands_subelement ( utility::tag::XMLSchemaSimpleSubelementList &  subs,
utility::tag::XMLSchemaDefinition &  xsd,
bool  include_coord 
)
static
void protocols::sewing::hashing::AlignmentFileGeneratorMover::apply ( core::pose::Pose )
overridevirtual
void protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_from_alignment ( AlignmentFGMSettings const &  alignment,
core::pose::Pose const &  pose,
BasisMapGeneratorOP  bmg 
)
static
BasisMapGeneratorOP protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_generator ( ) const

References basis_map_generator_.

void protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_generator ( BasisMapGeneratorOP  bmg)

References basis_map_generator_.

std::string protocols::sewing::hashing::AlignmentFileGeneratorMover::class_name ( )
static
protocols::moves::MoverOP protocols::sewing::hashing::AlignmentFileGeneratorMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::sewing::hashing::AlignmentFileGeneratorMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::sewing::hashing::AlignmentFileGeneratorMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References class_name().

std::string protocols::sewing::hashing::AlignmentFileGeneratorMover::get_required_resnums ( ) const

References required_resnums_.

core::select::residue_selector::ResidueSelectorCOP protocols::sewing::hashing::AlignmentFileGeneratorMover::get_required_selector ( ) const

References required_selector_.

std::string protocols::sewing::hashing::AlignmentFileGeneratorMover::ligands_subtag_ct_namer ( std::string  tag_name)
static
void protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligand_conformers ( utility::vector1< data_storage::LigandDescription > &  ligands)
static
void protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligands_tag ( utility::tag::TagCOP  ligands_tag,
basic::datacache::DataMap const &  data,
utility::vector1< data_storage::LigandDescription > &  ligands 
)
static
void protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::sewing::hashing::AlignmentFileGeneratorMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::sewing::hashing::AlignmentFileGeneratorMover::set_required_resnums ( std::string  req)

References required_resnums_.

void protocols::sewing::hashing::AlignmentFileGeneratorMover::set_required_selector ( core::select::residue_selector::ResidueSelectorCOP  sel)

References required_selector_.

void protocols::sewing::hashing::AlignmentFileGeneratorMover::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 protocols::moves::Mover::show().

Referenced by protocols::sewing::hashing::operator<<().

Member Data Documentation

AlignmentFGMSettingsOP protocols::sewing::hashing::AlignmentFileGeneratorMover::align_settings_
private

Referenced by apply(), and parse_my_tag().

BasisMapGeneratorOP protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_generator_
private
utility::vector1< data_storage::LigandDescription > protocols::sewing::hashing::AlignmentFileGeneratorMover::ligands_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::sewing::hashing::AlignmentFileGeneratorMover::required_resnums_
private
core::select::residue_selector::ResidueSelectorCOP protocols::sewing::hashing::AlignmentFileGeneratorMover::required_selector_
private
bool protocols::sewing::hashing::AlignmentFileGeneratorMover::set_segments_from_dssp_
private

Referenced by apply(), and parse_my_tag().


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