Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover. More...
#include <AlignmentFileGeneratorMover.hh>
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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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
◆ AlignmentFileGeneratorMover() [1/6]
| protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover | ( | ) |
References basis_map_generator_.
◆ AlignmentFileGeneratorMover() [2/6]
|
default |
◆ AlignmentFileGeneratorMover() [3/6]
| protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover | ( | EdgeMapGeneratorOP | edge_file_reader, |
| std::string | model_file_name, | ||
| std::string | alignment_file_name | ||
| ) |
References basis_map_generator_.
◆ AlignmentFileGeneratorMover() [4/6]
| protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover | ( | EdgeMapGeneratorOP | edge_file_reader, |
| std::string | model_file_name | ||
| ) |
References basis_map_generator_.
◆ AlignmentFileGeneratorMover() [5/6]
| 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_.
◆ AlignmentFileGeneratorMover() [6/6]
| protocols::sewing::hashing::AlignmentFileGeneratorMover::AlignmentFileGeneratorMover | ( | BasisMapGeneratorOP | bmg | ) |
◆ ~AlignmentFileGeneratorMover()
|
override |
Member Function Documentation
◆ add_pose_segments_to_segment_vector() [1/2]
|
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::Residue::type(), protocols::moves::Mover::type(), and core::conformation::Atom::type().
◆ add_pose_segments_to_segment_vector() [2/2]
|
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::Residue::type(), protocols::moves::Mover::type(), and core::conformation::Atom::type().
Referenced by apply(), protocols::sewing::movers::AppendAssemblyMover::set_up_assembly(), and protocols::sewing::movers::LigandBindingAssemblyMover::set_up_assembly().
◆ alignment_settings_from_tag()
|
static |
Referenced by parse_my_tag(), and protocols::sewing::movers::AppendAssemblyMover::parse_my_tag().
◆ append_ligands_subelement()
|
static |
References protocols::sewing::movers::AssemblyMover::assembly_mover_subtag_ct_namer(), core::select::residue_selector::attributes_for_parse_residue_selector(), protocols::sewing::hashing::LigandBindingResPlacer::define_ideal_contacts_subelement(), and ligands_subtag_ct_namer().
Referenced by protocols::sewing::movers::AppendAssemblyMover::provide_xml_schema(), protocols::sewing::movers::LigandBindingAssemblyMover::provide_xml_schema(), and provide_xml_schema().
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References add_pose_segments_to_segment_vector(), align_settings_, basis_map_from_alignment(), basis_map_generator_, protocols::sewing::data_storage::SmartSegment::get_c_most_segment(), protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), ligands_, core::pose::Pose::pdb_info(), required_resnums_, required_selector_, set_segments_from_dssp_, and core::id::to_string().
◆ basis_map_from_alignment()
|
static |
◆ basis_map_generator() [1/2]
| BasisMapGeneratorOP protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_generator | ( | ) | const |
References basis_map_generator_.
◆ basis_map_generator() [2/2]
| void protocols::sewing::hashing::AlignmentFileGeneratorMover::basis_map_generator | ( | BasisMapGeneratorOP | bmg | ) |
References basis_map_generator_.
◆ class_name()
|
static |
Referenced by get_name(), and protocols::sewing::hashing::AlignmentFileGeneratorMoverCreator::keyname().
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References class_name().
◆ get_required_resnums()
| std::string protocols::sewing::hashing::AlignmentFileGeneratorMover::get_required_resnums | ( | ) | const |
References required_resnums_.
◆ get_required_selector()
| core::select::residue_selector::ResidueSelectorCOP protocols::sewing::hashing::AlignmentFileGeneratorMover::get_required_selector | ( | ) | const |
References required_selector_.
◆ ligands_subtag_ct_namer()
|
static |
Referenced by append_ligands_subelement().
◆ parse_ligand_conformers()
|
static |
References core::import_pose::read_all_poses().
Referenced by protocols::sewing::movers::AppendAssemblyMover::parse_my_tag().
◆ parse_ligands_tag()
|
static |
References protocols::sewing::data_storage::LigandDescription::alignment_atoms_str, protocols::sewing::data_storage::LigandDescription::auto_detect_contacts, core::select::residue_selector::get_residue_selector(), protocols::sewing::data_storage::LigandDescription::ligand_contacts, protocols::sewing::data_storage::LigandDescription::ligand_resnum_string, protocols::sewing::data_storage::LigandDescription::ligand_selector, protocols::sewing::data_storage::ContactDescription::partner_contact, protocols::sewing::data_storage::LigandDescription::partner_ligand, protocols::sewing::data_storage::LigandDescription::pdb_conformers_string, core::id::to_string(), and protocols::TR().
Referenced by parse_my_tag(), and protocols::sewing::movers::AppendAssemblyMover::parse_my_tag().
◆ parse_my_tag()
|
overridevirtual |
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
References align_settings_, alignment_settings_from_tag(), basis_map_generator_, core::select::residue_selector::get_residue_selector(), ligands_, parse_ligands_tag(), required_resnums_, required_selector_, and set_segments_from_dssp_.
◆ provide_xml_schema()
|
static |
References append_ligands_subelement(), core::select::residue_selector::attributes_for_parse_residue_selector(), protocols::moves::complex_type_name_for_mover(), and protocols::sewing::hashing::AlignmentFileGeneratorMoverCreator::mover_name().
Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMoverCreator::provide_xml_schema().
◆ set_required_resnums()
| void protocols::sewing::hashing::AlignmentFileGeneratorMover::set_required_resnums | ( | std::string | req | ) |
References required_resnums_.
◆ set_required_selector()
| void protocols::sewing::hashing::AlignmentFileGeneratorMover::set_required_selector | ( | core::select::residue_selector::ResidueSelectorCOP | sel | ) |
References required_selector_.
◆ show()
|
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
◆ align_settings_
|
private |
Referenced by apply(), and parse_my_tag().
◆ basis_map_generator_
|
private |
Referenced by AlignmentFileGeneratorMover(), apply(), basis_map_generator(), and parse_my_tag().
◆ ligands_
|
private |
Referenced by apply(), and parse_my_tag().
◆ required_resnums_
|
private |
Referenced by apply(), get_required_resnums(), parse_my_tag(), and set_required_resnums().
◆ required_selector_
|
private |
Referenced by apply(), get_required_selector(), parse_my_tag(), and set_required_selector().
◆ set_segments_from_dssp_
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private |
Referenced by apply(), and parse_my_tag().
The documentation for this class was generated from the following files:
- src/protocols/sewing/hashing/AlignmentFileGeneratorMover.hh
- src/protocols/sewing/hashing/AlignmentFileGeneratorMover.cc
