protocols::ligand_docking::InterfaceBuilder Class Reference

#include <InterfaceBuilder.hh>

Inheritance diagram for protocols::ligand_docking::InterfaceBuilder:

Public Member Functions
	InterfaceBuilder ()
	~InterfaceBuilder () override
	InterfaceBuilder (utility::vector1< LigandAreaOP > ligand_areas, core::Size extension_window=0)
	InterfaceBuilder (InterfaceBuilder const &that)
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
ligand_options::Interface	build (core::pose::Pose const &pose) const
LigandAreas	get_ligand_areas () const

Static Public Member Functions
static std::string	element_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	enforce_minimum_length (ligand_options::Interface &interface, core::pose::Pose const &pose) const
void	find_interface_residues (ligand_options::Interface &interface, core::pose::Pose const &pose) const
void	find_protein_residues (ligand_options::Interface &interface, core::Size ligand_residue_id, core::pose::Pose const &pose) const
	First call find_ligand_residues. More...
void	set_interface_residue (ligand_options::Interface &interface, core::Size const potential_interface_residue_id, core::Size const ligand_interface_residue_id, core::pose::Pose const &pose) const
bool	is_interface_residue (core::conformation::Residue const &potential_interface_residue, core::conformation::Residue const &ligand_interface_residue, char const chain) const

Private Attributes
LigandAreas	ligand_areas_
core::Size	extension_window_

Constructor & Destructor Documentation

InterfaceBuilder() [1/3]

protocols::ligand_docking::InterfaceBuilder::InterfaceBuilder

(

)

~InterfaceBuilder()

protocols::ligand_docking::InterfaceBuilder::~InterfaceBuilder ( )

overridedefault

InterfaceBuilder() [2/3]

protocols::ligand_docking::InterfaceBuilder::InterfaceBuilder	(	utility::vector1< LigandAreaOP >	ligand_areas,
		core::Size	extension_window = 0
	)

References ligand_areas_.

InterfaceBuilder() [3/3]

protocols::ligand_docking::InterfaceBuilder::InterfaceBuilder

(

InterfaceBuilder const &

that

)

Member Function Documentation

build()

ligand_options::Interface protocols::ligand_docking::InterfaceBuilder::build

(

core::pose::Pose const &

pose

)

const

References enforce_minimum_length(), extension_window_, find_interface_residues(), protocols::ligand_docking::interface_builder_tracer(), and core::pose::Pose::size().

element_name()

std::string protocols::ligand_docking::InterfaceBuilder::element_name ( )

static

Referenced by protocols::ligand_docking::InterfaceBuilderLoader::load_data(), provide_xml_schema(), and protocols::ligand_docking::InterfaceBuilderLoader::provide_xml_schema().

enforce_minimum_length()

void protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length ( ligand_options::Interface &  interface, core::pose::Pose const &  pose  ) const

private

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::end, protocols::ligand_docking::ligand_options::Interface::enforce_minimum_length(), extension_window_, core::conformation::Residue::is_polymer(), core::pose::Pose::residue(), and protocols::loops::start.

Referenced by build().

find_interface_residues()

void protocols::ligand_docking::InterfaceBuilder::find_interface_residues ( ligand_options::Interface &  interface, core::pose::Pose const &  pose  ) const

private

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::end, find_protein_residues(), core::pose::get_chain_ids_from_chain(), protocols::ligand_docking::interface_builder_tracer(), protocols::ligand_docking::ligand_options::InterfaceInfo::is_interface, and ligand_areas_.

Referenced by build().

find_protein_residues()

void protocols::ligand_docking::InterfaceBuilder::find_protein_residues ( ligand_options::Interface &  interface, core::Size  ligand_residue_id, core::pose::Pose const &  pose  ) const

private

First call find_ligand_residues.

References protocols::ligand_docking::ligand_options::InterfaceInfo::is_interface, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), set_interface_residue(), and core::pose::Pose::size().

Referenced by find_interface_residues().

get_ligand_areas()

LigandAreas protocols::ligand_docking::InterfaceBuilder::get_ligand_areas

(

)

const

References ligand_areas_.

is_interface_residue()

bool protocols::ligand_docking::InterfaceBuilder::is_interface_residue ( core::conformation::Residue const &  potential_interface_residue, core::conformation::Residue const &  ligand_interface_residue, char const  chain  ) const

private

References protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), ligand_areas_, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), and core::conformation::Residue::xyz().

Referenced by set_interface_residue().

parse_my_tag()

void protocols::ligand_docking::InterfaceBuilder::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

References extension_window_, and ligand_areas_.

provide_xml_schema()

void protocols::ligand_docking::InterfaceBuilder::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References element_name(), and protocols::ligand_docking::InterfaceBuilderLoader::interface_builder_ct_namer().

Referenced by protocols::ligand_docking::InterfaceBuilderLoader::provide_xml_schema().

set_interface_residue()

void protocols::ligand_docking::InterfaceBuilder::set_interface_residue ( ligand_options::Interface &  interface, core::Size const  potential_interface_residue_id, core::Size const  ligand_interface_residue_id, core::pose::Pose const &  pose  ) const

private

References protocols::ligand_docking::ligand_options::InterfaceInfo::is_interface, is_interface_residue(), and core::pose::Pose::residue().

Referenced by find_protein_residues().

Member Data Documentation

extension_window_

core::Size protocols::ligand_docking::InterfaceBuilder::extension_window_

private

Referenced by build(), enforce_minimum_length(), and parse_my_tag().

ligand_areas_

LigandAreas protocols::ligand_docking::InterfaceBuilder::ligand_areas_

private

Referenced by find_interface_residues(), get_ligand_areas(), InterfaceBuilder(), is_interface_residue(), and parse_my_tag().

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

• src/protocols/ligand_docking/InterfaceBuilder.hh
• src/protocols/ligand_docking/InterfaceBuilder.cc