This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds. More...
#include <OversaturatedHbondAcceptorFilter.hh>
Public Member Functions | |
| OversaturatedHbondAcceptorFilter () | |
| Default constructor. More... | |
| OversaturatedHbondAcceptorFilter (OversaturatedHbondAcceptorFilter const &src) | |
| Copy constructor. More... | |
| ~OversaturatedHbondAcceptorFilter () override | |
| Destructor (important for properly forward-declaring smart-pointer members) More... | |
| protocols::filters::FilterOP | clone () const override |
| Required in the context of the parser/scripting scheme. More... | |
| protocols::filters::FilterOP | fresh_instance () const override |
| Required in the context of the parser/scripting scheme. More... | |
| virtual std::string | get_name () const |
| bool | apply (core::pose::Pose const &pose) const override |
| Returns true if the structure passes the filter, false otherwise. More... | |
| core::Real | report_sm (core::pose::Pose const &pose) const override |
| Required for reporting score values. More... | |
| void | report (std::ostream &os, core::pose::Pose const &pose) const override |
| Allows printing a summary of this filter to a stream. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Parse XML tag (to use this Mover in RosettaScripts). More... | |
| void | set_max_allowed_oversaturated (core::Size const max_allowed) |
| Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More... | |
| core::Size | max_allowed_oversaturated () const |
| Get the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More... | |
| void | set_hbond_energy_cutoff (core::Real const &input_value) |
| Set the threshold for considering something to be a hydrogen bond. More... | |
| core::Real const & | hbond_energy_cutoff () const |
| Get the threshold for considering something to be a hydrogen bond. More... | |
| void | set_consider_mainchain_only (bool const input_setting) |
| Set whether we only consider mainchain hydrogen bond donors and acceptors. More... | |
| bool | consider_mainchain_only () const |
| Get whether we only consider mainchain hydrogen bond donors and acceptors. More... | |
| void | set_donor_selector (core::select::residue_selector::ResidueSelectorCOP donor_selector_in) |
| Set the residue selector for donor residues. More... | |
| core::select::residue_selector::ResidueSelectorCOP | donor_selector () const |
| Get the residue selector for donor residues. More... | |
| void | set_acceptor_selector (core::select::residue_selector::ResidueSelectorCOP acceptor_selector_in) |
| Set the residue selector for acceptor residues. More... | |
| core::select::residue_selector::ResidueSelectorCOP | acceptor_selector () const |
| Get the residue selector for acceptor residues. More... | |
| void | set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in) |
| Set the scorefunction. More... | |
| core::scoring::ScoreFunctionCOP | scorefxn () const |
| Get the scorefunction. More... | |
| std::string | name () const override |
 Public Member Functions inherited from protocols::filters::Filter | |
| Filter () | |
| Filter (std::string const &) | |
| ~Filter () override | |
| 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 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 void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
Private Member Functions | |
| core::Size | max_allowed_hbonds (core::pose::Pose const &pose, core::Size const res_index, core::Size const atom_index) const |
| Given an atom, return the maximum number of hydrogen bonds that an atom of this type is allowed to receive. More... | |
| core::Size | compute (core::pose::Pose const &pose) const |
| The function that actually calculates the value that this filter returns, called by the apply(), report(), and report_sm() functions. More... | |
Private Attributes | |
| core::Size | max_allowed_oversaturated_ |
| What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor? More... | |
| core::Real | hbond_energy_cutoff_ |
| The energy cutoff for considering something to be a hydrogen bond. More... | |
| bool | consider_mainchain_only_ |
| Should we only consider mainchain hydrogen bond donors and acceptors? More... | |
| core::select::residue_selector::ResidueSelectorCOP | donor_selector_ |
| Optional residue selector for the residues that could possibly be donating hydrogen bonds. More... | |
| core::select::residue_selector::ResidueSelectorCOP | acceptor_selector_ |
| Optional residue selector for the residues that could possibly be accepting hydrogen bonds. More... | |
| core::scoring::ScoreFunctionOP | scorefxn_ |
| The scorefunction to use for hydrogen bond scoring. More... | |
Additional Inherited Members | |
| Protected Attributes inherited from protocols::filters::Filter | |
| std::string | scorename_ |
Detailed Description
This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds.
Constructor & Destructor Documentation
◆ OversaturatedHbondAcceptorFilter() [1/2]
| protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::OversaturatedHbondAcceptorFilter | ( | ) |
Default constructor.
◆ OversaturatedHbondAcceptorFilter() [2/2]
| protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::OversaturatedHbondAcceptorFilter | ( | OversaturatedHbondAcceptorFilter const & | src | ) |
Copy constructor.
References acceptor_selector_, donor_selector_, and scorefxn_.
◆ ~OversaturatedHbondAcceptorFilter()
|
overridedefault |
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ acceptor_selector()
| core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::acceptor_selector | ( | ) | const |
Get the residue selector for acceptor residues.
References acceptor_selector_.
◆ apply()
|
overridevirtual |
Returns true if the structure passes the filter, false otherwise.
Implements protocols::filters::Filter.
References compute(), and max_allowed_oversaturated().
◆ class_name()
|
static |
◆ clone()
|
overridevirtual |
Required in the context of the parser/scripting scheme.
Make a copy of this object and return an owning pointer to the copy.
Implements protocols::filters::Filter.
Referenced by compute().
◆ compute()
|
private |
The function that actually calculates the value that this filter returns, called by the apply(), report(), and report_sm() functions.
Returns the number of atoms receiving more than the allowed number of hydrogen bonds.
References core::scoring::hbonds::HBond::acc_atm(), acceptor_selector_, core::scoring::hbonds::HBondSet::allow_hbond(), core::conformation::Residue::atom_name(), core::scoring::hbonds::calculate_intra_res_hbonds(), clone(), consider_mainchain_only(), consider_mainchain_only_, donor_selector_, core::scoring::hbonds::HBond::energy(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), hbond_energy_cutoff(), core::scoring::hbonds::HBondSet::hbond_options(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), max_allowed_hbonds(), core::conformation::Residue::natoms(), core::scoring::hbonds::HBondSet::nbrs(), core::scoring::hbonds::HBondSet::nhbonds(), core::scoring::hbonds::HBondOptions::params_database_tag(), core::pose::Pose::residue(), scorefxn(), scorefxn_, core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::pose::Pose::size(), protocols::cyclic_peptide::TR(), and core::scoring::hbonds::HBond::weight().
Referenced by apply(), report(), and report_sm().
◆ consider_mainchain_only()
| bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::consider_mainchain_only | ( | ) | const |
Get whether we only consider mainchain hydrogen bond donors and acceptors.
References consider_mainchain_only_.
Referenced by compute(), and parse_my_tag().
◆ donor_selector()
| core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::donor_selector | ( | ) | const |
Get the residue selector for donor residues.
References donor_selector_.
◆ fresh_instance()
|
overridevirtual |
Required in the context of the parser/scripting scheme.
Implements protocols::filters::Filter.
◆ get_name()
|
virtual |
References class_name().
◆ hbond_energy_cutoff()
| core::Real const & protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::hbond_energy_cutoff | ( | ) | const |
Get the threshold for considering something to be a hydrogen bond.
References hbond_energy_cutoff_.
Referenced by compute(), and parse_my_tag().
◆ max_allowed_hbonds()
|
private |
Given an atom, return the maximum number of hydrogen bonds that an atom of this type is allowed to receive.
For now, this function returns 0 if this is not an acceptor, 2 if it is. This is crude, of course. Ultimately, it should figure out how many hbonds an atom can actually receive.
References core::chemical::ResidueType::heavyatom_is_an_acceptor(), core::pose::Pose::residue(), and core::conformation::Residue::type().
Referenced by compute().
◆ max_allowed_oversaturated()
| core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_oversaturated | ( | ) | const |
Get the maximum allowed number of instances of an oversaturated hydrogen bond acceptor.
References max_allowed_oversaturated_.
Referenced by apply(), parse_my_tag(), and report().
◆ name()
|
overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
◆ parse_my_tag()
|
overridevirtual |
Parse XML tag (to use this Mover in RosettaScripts).
Reimplemented from protocols::filters::Filter.
References consider_mainchain_only(), hbond_energy_cutoff(), max_allowed_oversaturated(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), set_acceptor_selector(), set_consider_mainchain_only(), set_donor_selector(), set_hbond_energy_cutoff(), set_max_allowed_oversaturated(), and set_scorefxn().
◆ provide_xml_schema()
|
static |
References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().
Referenced by protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::provide_xml_schema().
◆ report()
|
overridevirtual |
Allows printing a summary of this filter to a stream.
Reimplemented from protocols::filters::Filter.
References compute(), and max_allowed_oversaturated().
◆ report_sm()
|
overridevirtual |
Required for reporting score values.
Reimplemented from protocols::filters::Filter.
References compute().
◆ scorefxn()
| core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::scorefxn | ( | ) | const |
◆ set_acceptor_selector()
| void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_acceptor_selector | ( | core::select::residue_selector::ResidueSelectorCOP | acceptor_selector_in | ) |
Set the residue selector for acceptor residues.
Clones the input.
References acceptor_selector_.
Referenced by parse_my_tag().
◆ set_consider_mainchain_only()
| void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_consider_mainchain_only | ( | bool const | input_setting | ) |
Set whether we only consider mainchain hydrogen bond donors and acceptors.
References consider_mainchain_only_.
Referenced by parse_my_tag().
◆ set_donor_selector()
| void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_donor_selector | ( | core::select::residue_selector::ResidueSelectorCOP | donor_selector_in | ) |
Set the residue selector for donor residues.
Clones the input.
References donor_selector_.
Referenced by parse_my_tag().
◆ set_hbond_energy_cutoff()
| void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_hbond_energy_cutoff | ( | core::Real const & | input_value | ) |
Set the threshold for considering something to be a hydrogen bond.
References hbond_energy_cutoff_.
Referenced by parse_my_tag().
◆ set_max_allowed_oversaturated()
| void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_max_allowed_oversaturated | ( | core::Size const | max_allowed | ) |
Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor.
References max_allowed_oversaturated_.
Referenced by parse_my_tag().
◆ set_scorefxn()
| void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_scorefxn | ( | core::scoring::ScoreFunctionCOP | sfxn_in | ) |
Member Data Documentation
◆ acceptor_selector_
|
private |
Optional residue selector for the residues that could possibly be accepting hydrogen bonds.
Referenced by acceptor_selector(), compute(), OversaturatedHbondAcceptorFilter(), and set_acceptor_selector().
◆ consider_mainchain_only_
|
private |
Should we only consider mainchain hydrogen bond donors and acceptors?
Defaults to true.
Referenced by compute(), consider_mainchain_only(), and set_consider_mainchain_only().
◆ donor_selector_
|
private |
Optional residue selector for the residues that could possibly be donating hydrogen bonds.
Referenced by compute(), donor_selector(), OversaturatedHbondAcceptorFilter(), and set_donor_selector().
◆ hbond_energy_cutoff_
|
private |
The energy cutoff for considering something to be a hydrogen bond.
Defaults to -0.1.
Referenced by hbond_energy_cutoff(), and set_hbond_energy_cutoff().
◆ max_allowed_oversaturated_
|
private |
What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor?
Defaults to 0.
Referenced by max_allowed_oversaturated(), and set_max_allowed_oversaturated().
◆ scorefxn_
|
private |
The scorefunction to use for hydrogen bond scoring.
If no scorefunction is provided, then the default scorefunction is used.
Referenced by compute(), OversaturatedHbondAcceptorFilter(), scorefxn(), and set_scorefxn().
The documentation for this class was generated from the following files:
- src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.hh
- src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.cc
