|
| | SecondaryStructureFilter () |
| |
| | SecondaryStructureFilter (String const &ss) |
| |
| | ~SecondaryStructureFilter () override |
| |
| FilterOP | clone () const override |
| |
| FilterOP | fresh_instance () const override |
| |
| void | filtered_ss (String const &s) |
| |
| void | filtered_abego (String const &s) |
| |
| void | set_use_dssp (bool const use_ss) |
| | Should we use the secstruct in the pose (false), or compute via dssp (true)? default=false for historical reasons. More...
|
| |
| void | set_strand_pairings (String const &s) |
| | Sets sheet topology string. More...
|
| |
| void | set_blueprint (std::string const &blueprint_file) |
| | sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match. More...
|
| |
| void | set_residue_selector (core::select::residue_selector::ResidueSelector const &selector) |
| | sets the residue selector used to choose which residues to scan. Default is all protein residues More...
|
| |
| void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &) override |
| | parse xml More...
|
| |
| bool | apply (Pose const &pose) const override |
| | Returns true if the given pose passes the filter, false otherwise. More...
|
| |
| core::Real | report_sm (Pose const &pose) const override |
| | used to report filter internals through a score or silent file More...
|
| |
| std::string | name () const override |
| |
| | Filter () |
| |
| | Filter (std::string const &) |
| |
| | Filter (Filter const &) |
| |
| | ~Filter () override |
| |
| virtual void | report (std::ostream &, core::pose::Pose const &) const |
| |
| virtual std::string | get_type () const |
| |
| std::string | get_user_defined_name () const |
| |
| void | set_user_defined_name (std::string const &name) |
| |
| virtual void | clear () |
| | used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
|
| |
| virtual core::Real | score (core::pose::Pose &pose) |
| |
| virtual bool | filter_provides_citation_info () const |
| | Does this filter 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 | filter_is_unpublished () const |
| | Does this filter 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...
|
| |
returns the number of residues in the protein that have matching secondary structure
- Parameters
-
| [in] | pose | Pose to be analyzed |
| [in] | subset | Subset of the pose to be analyzed. Only residues that are true in the subset will be included in the computation. |
- Returns
- Number of protein residues in the residue subset that match the desired secondary structure WARNING: ignores abegos for now, since abegomanager only returns a bool The filter score will report only secondary structures, but if you specify abego, the 'apply' function will return false if abegos don't match
If impossible strand pairings exist (i.e a two-strand pose where one strand has 6 residues and the other has 5), either 'E' or 'L' will be allowed at the unpaired position
- Parameters
-
| [in] | pose | Pose to be analyzed |
| [in] | subset | Subset of the pose to be analyzed. Only residues that are true in the subset will be included in the computation. WARNING: ignores abegos for now, since abegomanager only returns a bool The filter score will report only secondary structures, but if you specify abego, the 'apply' function will return false if abegos don't match |
If impossible strand pairings exist (i.e a two-strand pose where one strand has 6 residues and the other has 5), either 'E' or 'L' will be allowed at the unpaired position
References core::scoring::abego, core::sequence::ABEGOManager::check_rama(), correct_for_incomplete_strand_pairings(), protocols::simple_filters::dssp(), filtered_abego_, core::sequence::ABEGOManager::get_abego_string(), core::scoring::dssp::Dssp::get_dssp_secstruct(), get_filtered_secstruct(), core::conformation::Residue::is_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), tr(), treat_L_as_D_, use_abego_, and use_dssp_.
Referenced by report_sm().
| void protocols::fldsgn::filters::SecondaryStructureFilter::correct_for_incomplete_strand_pairings |
( |
core::pose::Pose const & |
pose, |
|
|
std::string & |
secstruct |
|
) |
| const |
|
protected |
If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match.
- Parameters
-
| [in] | pose | Input pose to be tested. |
| in/out] | secstruct Desired secondary structure. It will be modified in-place |
| [in] | strand_pairings | Strand pairings to be used for modification |
If strand_pairings_ is user-specified, the specific residue pairings will be computed based on it. If strand_pairings_ is empty, residue pairings will be taken from the cached StructureData in the pose, if present. If strand_pairings is empty and no cached StructureData was found, this will do nothing. Any unpaired residues found in the sheet topology with 'E' secondary structure will be changed to 'h' (to allow either loop or strand)
- Parameters
-
| [in] | pose | Input pose to be tested. |
| in/out] | secstruct Desired secondary structure. It will be modified in-place |
| [in] | strand_pairings | Strand pairings to be used for modification |
If strand_pairings is user-specified, the specific residue pairings will be computed based on it. If strand_pairings is empty, residue pairings will be taken from the cached StructureData in the pose, if present. If strand_pairings_ is empty and no cached StructureData was found, this will do nothing. Any unpaired residues found in the sheet topology with 'E' secondary structure will be changed to 'h' (to allow either loop or strand)
References protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::set_secstruct(), core::pose::Pose::size(), strand_pairings_, and tr().
Referenced by compute().
| void protocols::fldsgn::filters::SecondaryStructureFilter::set_blueprint |
( |
std::string const & |
blueprint_file | ) |
|
sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match.
Sets the filtered_ss, filtered_abego, and strand_pairings from the blueprint file given.
References filtered_abego_, filtered_ss_, and strand_pairings_.
Referenced by parse_my_tag().
Public Member Functions inherited from protocols::filters::Filter
1.8.7