Public Member Functions | Static Public Member Functions | Private Types | Private Attributes | Static Private Attributes | List of all members
protocols::protein_interface_design::filters::DisulfideFilter Class Reference

Filters for structures which could form a disulfide bond across the docking interface. More...

#include <DisulfideFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::DisulfideFilter:
Inheritance graph

Public Member Functions

 DisulfideFilter ()
 default ctor More...
 DisulfideFilter (DisulfideFilter const &df)
 copy ctor More...
 DisulfideFilter (core::Size targetResidue)
 Constructor with a single target residue. More...
 DisulfideFilter (core::select::residue_selector::ResidueSelectorCOP targetResidues)
 Constructor with multiple target residues. More...
bool apply (core::pose::Pose const &pose) const override
void report (std::ostream &out, core::pose::Pose const &pose) const override
core::Real report_sm (core::pose::Pose const &pose) const override
protocols::filters::FilterOP clone () const override
protocols::filters::FilterOP fresh_instance () const override
 ~DisulfideFilter () override
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
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 Types

typedef protocols::filters::Filter parent

Private Attributes

core::select::residue_selector::ResidueSelectorCOP targets_
 residues which may participate in the disulfide. More...
core::Size rb_jump_
 Which jump defines the interface where the targets lie? More...

Static Private Attributes

static const core::scoring::disulfides::CentroidDisulfidePotential potential_
 for calculating centroid disulfide energies More...

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_

Detailed Description

Filters for structures which could form a disulfide bond across the docking interface.

Use this filter when you are trying to design one docking member so that it forms a disulfide bond to one or more target residues of the other docking partner. The filter does not consider the indentities of the residues involved, only their Cb position.

This filter only applies to centroid poses. Calling it with a full atom pose will result in everything failing.

Spencer Bliven blive.nosp@m.ns@u.nosp@m..wash.nosp@m.ingt.nosp@m.on.ed.nosp@m.u

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ DisulfideFilter() [1/4]

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( )

default ctor

◆ DisulfideFilter() [2/4]

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( DisulfideFilter const &  df)

copy ctor

◆ DisulfideFilter() [3/4]

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( core::Size  targetResidue)

Constructor with a single target residue.

◆ DisulfideFilter() [4/4]

protocols::protein_interface_design::filters::DisulfideFilter::DisulfideFilter ( core::select::residue_selector::ResidueSelectorCOP  targetResidues)

Constructor with multiple target residues.

targets may come from either binding partner. If no targets are specified for one target, all residues on the interface will be concidered.

◆ ~DisulfideFilter()

protocols::protein_interface_design::filters::DisulfideFilter::~DisulfideFilter ( )

Member Function Documentation

◆ apply()

bool protocols::protein_interface_design::filters::DisulfideFilter::apply ( core::pose::Pose const &  pose) const

◆ class_name()

std::string protocols::protein_interface_design::filters::DisulfideFilter::class_name ( )

◆ clone()

protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::clone ( ) const

◆ fresh_instance()

protocols::filters::FilterOP protocols::protein_interface_design::filters::DisulfideFilter::fresh_instance ( ) const

◆ name()

std::string protocols::protein_interface_design::filters::DisulfideFilter::name ( ) const

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::protein_interface_design::filters::DisulfideFilter::parse_my_tag ( utility::tag::TagCOP  tag,

Parameters recognized:

  • targets. A list of possible target residues, seperated by commas.

Reimplemented from protocols::filters::Filter.

References core::pose::get_resnum_selector(), and targets_.

◆ provide_xml_schema()

void protocols::protein_interface_design::filters::DisulfideFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ report()

void protocols::protein_interface_design::filters::DisulfideFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const

◆ report_sm()

Real protocols::protein_interface_design::filters::DisulfideFilter::report_sm ( core::pose::Pose const &  pose) const

Member Data Documentation

◆ potential_

const core::scoring::disulfides::CentroidDisulfidePotential protocols::protein_interface_design::filters::DisulfideFilter::potential_

for calculating centroid disulfide energies

◆ rb_jump_

core::Size protocols::protein_interface_design::filters::DisulfideFilter::rb_jump_

Which jump defines the interface where the targets lie?

Referenced by apply(), report(), and report_sm().

◆ targets_

core::select::residue_selector::ResidueSelectorCOP protocols::protein_interface_design::filters::DisulfideFilter::targets_

residues which may participate in the disulfide.

If either docking partner has no target residues specified, all interface residues will be allowed to disulfide bond.

Referenced by apply(), parse_my_tag(), report(), and report_sm().

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