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:

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.

Author

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

Member Typedef Documentation

parent

typedef protocols::filters::Filter protocols::protein_interface_design::filters::DisulfideFilter::parent

private

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 )

default

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 ( )

overridedefault

Member Function Documentation

apply()

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

overridevirtual

Returns

Whether a disulfide bond is possible between any of the targets

Implements protocols::filters::Filter.

References protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), core::select::get_residues_from_subset(), rb_jump_, targets_, and protocols::protein_interface_design::filters::TR().

class_name()

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

static

Referenced by protocols::protein_interface_design::filters::DisulfideFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

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, basic::datacache::DataMap &    )

overridevirtual

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 )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::protein_interface_design::filters::DisulfideFilterCreator::provide_xml_schema().

report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), core::select::get_residues_from_subset(), core::conformation::membrane::out, rb_jump_, and targets_.

report_sm()

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

overridevirtual

Returns

The number of disulfides possible

Reimplemented from protocols::filters::Filter.

References protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), core::select::get_residues_from_subset(), rb_jump_, and targets_.

Member Data Documentation

potential_

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

staticprivate

for calculating centroid disulfide energies

rb_jump_

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

private

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_

private

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().

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

• src/protocols/protein_interface_design/filters/DisulfideFilter.hh
• src/protocols/protein_interface_design/filters/DisulfideFilter.cc