#include <MatchConstraintFileInfo.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo:

Public Types
typedef numeric::HomogeneousTransform< core::Real >	HTReal

Public Member Functions
	MatchConstraintFileInfo (core::Size index, core::chemical::ResidueTypeSetCOP restype_set)

	~MatchConstraintFileInfo () override

core::Size	index () const

utility::vector1< core::Size > const &	allowed_seqpos () const
	all positions where a residue for this geometry can be placed More...

utility::vector1< std::string > const &	allowed_res_name3s (core::Size which_cstres) const
	what type of amino acids/ligands make this constraint More...

core::Size	num_enz_cst_template_res () const

bool	is_backbone (core::Size which_cstres) const
	is this interaction a backbone interaction More...

utility::vector1< core::chemical::ResidueTypeCOP > const	allowed_restypes (core::Size which_cstres) const
	all chemically non-redundant restypes of the given restypes. Note – now sorted by name! More...

core::Size	upstream_res () const
	which one of the residues (1 or 2 ) in this block is the upstream res. used for classic match algorithm hardcoded 2 for now More...

core::Size	downstream_res () const
	which one of the residues (1 or 2 ) in this block is the upstream res. used for classic match algorithm hardcoded 1 for now More...

std::map< std::string, utility::vector1< std::string > > const &	algorithm_inputs () const
	holds information read from ALGORITHM_INFO blocks in the input file More...

bool	is_covalent () const

utility::vector1< SingleConstraint >	constraints () const

utility::vector1< core::Size > const &	template_atom_inds (core::Size which_cstres, core::Size which_template_atom, core::chemical::ResidueType const &restype) const
	all atoms of restype to be used as template_atom in the matcher/constraints More...

EnzCstTemplateResCOP	enz_cst_template_res (core::Size template_res) const

bool	native () const

utility::vector1< ExternalGeomSamplerOP >	create_exgs () const
	returns ExternalGeomSampler only if the user has specified all six degrees of freedom, otherwise null pointer is returned More...

void	initialize_from_tag (utility::tag::TagCOP tag)

bool	read_data (utility::io::izstream &data)
	data reading routine More...

void	process_data ()
	processes the read data right now this only generates the template atomnos for every restype More...

std::list< core::conformation::ResidueCOP >	inverse_rotamers_against_residue (core::Size const target_template, core::conformation::ResidueCOP target_conf) const
	function that takes all rotamers for the ResidueType(s) that interact with the target residues and places them according according to the geometry specified More...

std::list< core::conformation::ResidueCOP >	inverse_rotamers_against_residue (core::conformation::Residue const &target_conf, core::chemical::ResidueTypeCOP invrot_restype, utility::vector1< core::Size > const &target_ats, utility::vector1< core::Size > const &invrot_ats, bool const flip_exgs_upstream_downstream_samples, bool const backbone_interaction) const

void	diversify_backbone_only_rotamers (utility::vector1< core::conformation::ResidueCOP > &rotamers) const

Static Public Member Functions
static void	return_complex_type_for_MatcherConstraint (utility::tag::XMLSchemaSimpleSubelementList &ssl, utility::tag::XMLSchemaDefinition &xsd)

Protected Member Functions
bool	process_algorithm_info (std::string const &tag, utility::io::izstream &data)
	reads and stores arbitrary algorithm specific input More...

Private Member Functions
void	add_enzyme_template (core::Size index, utility::tag::TagCOP tag)

Private Attributes
core::Size	index_

utility::vector1< core::Size >	allowed_seqpos_

std::map< core::Size, EnzCstTemplateResOP >	enz_template_res_

bool	is_covalent_

utility::vector1< SingleConstraint >	constraints_

std::map< std::string, utility::vector1< std::string > >	algorithm_inputs_

core::chemical::ResidueTypeSetCOP	restype_set_

bool	native_

Member Typedef Documentation

◆ HTReal

typedef numeric::HomogeneousTransform< core::Real > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::HTReal

Constructor & Destructor Documentation

◆ MatchConstraintFileInfo()

protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::MatchConstraintFileInfo	(	core::Size	index,
		core::chemical::ResidueTypeSetCOP	restype_set
	)

References allowed_seqpos_, constraints_, and enz_template_res_.

◆ ~MatchConstraintFileInfo()

protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::~MatchConstraintFileInfo ( )

overridedefault

Member Function Documentation

◆ add_enzyme_template()

void protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::add_enzyme_template	(	core::Size	index,
		utility::tag::TagCOP	tag
	)

private

References enz_template_res_, index(), and restype_set_.

Referenced by initialize_from_tag().

◆ algorithm_inputs()

std::map< std::string, utility::vector1< std::string > > const& protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::algorithm_inputs ( ) const

inline

holds information read from ALGORITHM_INFO blocks in the input file

References algorithm_inputs_.

◆ allowed_res_name3s()

utility::vector1< std::string > const& protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_res_name3s ( core::Size which_cstres ) const

inline

what type of amino acids/ligands make this constraint

References enz_cst_template_res().

◆ allowed_restypes()

utility::vector1< core::chemical::ResidueTypeCOP > const protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_restypes ( core::Size which_cstres ) const

all chemically non-redundant restypes of the given restypes. Note – now sorted by name!

References enz_cst_template_res(), and protocols::toolbox::match_enzdes_util::sort_residue_type_pointers_by_name().

Referenced by inverse_rotamers_against_residue().

◆ allowed_seqpos()

utility::vector1< core::Size > const& protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_seqpos ( ) const

inline

all positions where a residue for this geometry can be placed

References allowed_seqpos_.

◆ constraints()

utility::vector1< SingleConstraint > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::constraints ( ) const

inline

References constraints_.

Referenced by protocols::match::downstream::GeometrySecMatchRPE::GeometrySecMatchRPE().

◆ create_exgs()

utility::vector1< ExternalGeomSamplerOP > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::create_exgs ( ) const

returns ExternalGeomSampler only if the user has specified all six degrees of freedom, otherwise null pointer is returned

References constraints_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by inverse_rotamers_against_residue().

◆ diversify_backbone_only_rotamers()

void protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers ( utility::vector1< core::conformation::ResidueCOP > & rotamers ) const

helper function to keep code readable for rotamers that make backbone interactions, as opposed to sidechain interactions only, the default phi (-150) that comes out of the bb-indep rotamers function has an influence on what fragments in sampling can overlap with this rotamer. thus we'll put in more samples to allow for more diversity the implementation is quite clumsy, make a one residue pose add the chainbreak variant, set the chi, return the residue but there's no easier way to simply rotate around a bond. additional samples will be put at a phi of -60 and 70, i.e. other regions observed in ramachandran plot

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), core::chemical::CUTPOINT_UPPER, core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), and core::pose::Pose::set_phi().

Referenced by inverse_rotamers_against_residue().

◆ downstream_res()

core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::downstream_res ( ) const

inline

which one of the residues (1 or 2 ) in this block is the upstream res. used for classic match algorithm hardcoded 1 for now

◆ enz_cst_template_res()

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::enz_cst_template_res ( core::Size template_res ) const

References enz_template_res_.

Referenced by allowed_res_name3s(), allowed_restypes(), and is_backbone().

◆ index()

core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::index ( ) const

inline

References index_.

Referenced by add_enzyme_template().

◆ initialize_from_tag()

void protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::initialize_from_tag ( utility::tag::TagCOP tag )

References add_enzyme_template(), protocols::toolbox::match_enzdes_util::SingleConstraint::ang_U1D2, protocols::toolbox::match_enzdes_util::SingleConstraint::ang_U2D1, constraints_, protocols::toolbox::match_enzdes_util::SingleConstraint::dis_U1D1, protocols::toolbox::match_enzdes_util::SingleConstraint::tor_U1D3, protocols::toolbox::match_enzdes_util::SingleConstraint::tor_U2D2, and protocols::toolbox::match_enzdes_util::SingleConstraint::tor_U3D1.

◆ inverse_rotamers_against_residue() [1/2]

std::list< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue	(	core::conformation::Residue const &	target_conf,
		core::chemical::ResidueTypeCOP	invrot_restype,
		utility::vector1< core::Size > const &	target_ats,
		utility::vector1< core::Size > const &	invrot_ats,
		bool const	flip_exgs_upstream_downstream_samples,
		bool const	backbone_interaction
	)		const

References core::pack::rotamer_set::bb_independent_rotamers(), create_exgs(), diversify_backbone_only_rotamers(), protocols::toolbox::match_enzdes_util::HT_ang_U1D2, protocols::toolbox::match_enzdes_util::HT_ang_U2D1, protocols::toolbox::match_enzdes_util::HT_tor_U1D3, protocols::toolbox::match_enzdes_util::HT_tor_U2D2, protocols::toolbox::match_enzdes_util::HT_tor_U3D1, rot(), protocols::toolbox::match_enzdes_util::tr(), and core::conformation::Residue::xyz().

◆ inverse_rotamers_against_residue() [2/2]

std::list< core::conformation::ResidueCOP > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue	(	core::Size const	target_template,
		core::conformation::ResidueCOP	target_conf
	)		const

function that takes all rotamers for the ResidueType(s) that interact with the target residues and places them according according to the geometry specified

References allowed_restypes(), enz_template_res_, is_backbone(), restype_set_, template_atom_inds(), protocols::toolbox::match_enzdes_util::tr(), and upstream_res().

◆ is_backbone()

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::is_backbone ( core::Size which_cstres ) const

inline

is this interaction a backbone interaction

References enz_cst_template_res().

Referenced by inverse_rotamers_against_residue().

◆ is_covalent()

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::is_covalent ( ) const

inline

References is_covalent_.

◆ native()

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::native ( ) const

inline

References native_.

◆ num_enz_cst_template_res()

core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::num_enz_cst_template_res ( ) const

inline

References enz_template_res_.

◆ process_algorithm_info()

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_algorithm_info	(	std::string const &	tag,
		utility::io::izstream &	data
	)

protected

reads and stores arbitrary algorithm specific input

References algorithm_inputs_, core::scoring::pair, and protocols::toolbox::match_enzdes_util::tr().

Referenced by read_data().

◆ process_data()

void protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_data ( )

processes the read data right now this only generates the template atomnos for every restype

References protocols::toolbox::match_enzdes_util::add_relevant_restypes_to_subset(), enz_template_res_, index_, restype_set_, and protocols::toolbox::match_enzdes_util::tr().

◆ read_data()

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::read_data ( utility::io::izstream & data )

data reading routine

References protocols::toolbox::match_enzdes_util::SingleConstraint::ang_U1D2, protocols::toolbox::match_enzdes_util::SingleConstraint::ang_U2D1, constraints_, protocols::toolbox::match_enzdes_util::SingleConstraint::dis_U1D1, enz_template_res_, is_covalent_, native_, process_algorithm_info(), restype_set_, protocols::toolbox::match_enzdes_util::SingleConstraint::tor_U1D3, protocols::toolbox::match_enzdes_util::SingleConstraint::tor_U2D2, and protocols::toolbox::match_enzdes_util::SingleConstraint::tor_U3D1.

◆ return_complex_type_for_MatcherConstraint()

void protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::return_complex_type_for_MatcherConstraint	(	utility::tag::XMLSchemaSimpleSubelementList &	ssl,
		utility::tag::XMLSchemaDefinition &	xsd
	)

static

References protocols::toolbox::match_enzdes_util::add_subelement_for_constraint_combination(), and protocols::toolbox::match_enzdes_util::matcher_constraint_name_mangler().

Referenced by protocols::match::MatcherMover::provide_xml_schema().

◆ template_atom_inds()

utility::vector1< core::Size > const & protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::template_atom_inds	(	core::Size	which_cstres,
		core::Size	which_template_atom,
		core::chemical::ResidueType const &	restype
	)		const

all atoms of restype to be used as template_atom in the matcher/constraints

References enz_template_res_, and core::chemical::ResidueType::get_self_ptr().

Referenced by inverse_rotamers_against_residue().

◆ upstream_res()

core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::upstream_res ( ) const

inline

which one of the residues (1 or 2 ) in this block is the upstream res. used for classic match algorithm hardcoded 2 for now

Referenced by inverse_rotamers_against_residue().

Member Data Documentation

◆ algorithm_inputs_

std::map< std::string, utility::vector1< std::string > > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::algorithm_inputs_

private

Referenced by algorithm_inputs(), and process_algorithm_info().

◆ allowed_seqpos_

utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_seqpos_

private

Referenced by allowed_seqpos(), and MatchConstraintFileInfo().

◆ constraints_

utility::vector1< SingleConstraint > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::constraints_

private

Referenced by constraints(), create_exgs(), initialize_from_tag(), MatchConstraintFileInfo(), and read_data().

◆ enz_template_res_

std::map< core::Size, EnzCstTemplateResOP > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::enz_template_res_

private

Referenced by add_enzyme_template(), enz_cst_template_res(), inverse_rotamers_against_residue(), MatchConstraintFileInfo(), num_enz_cst_template_res(), process_data(), read_data(), and template_atom_inds().

◆ index_

core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::index_

private

Referenced by index(), and process_data().

◆ is_covalent_

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::is_covalent_

private

Referenced by is_covalent(), and read_data().

◆ native_

bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::native_

private

Referenced by native(), and read_data().

◆ restype_set_

core::chemical::ResidueTypeSetCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::restype_set_

private

Referenced by add_enzyme_template(), inverse_rotamers_against_residue(), process_data(), and read_data().

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

src/protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.hh
src/protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ HTReal

Constructor & Destructor Documentation

◆ MatchConstraintFileInfo()

◆ ~MatchConstraintFileInfo()

Member Function Documentation

◆ add_enzyme_template()

◆ algorithm_inputs()

◆ allowed_res_name3s()

◆ allowed_restypes()

◆ allowed_seqpos()

◆ constraints()

◆ create_exgs()

◆ diversify_backbone_only_rotamers()

◆ downstream_res()

◆ enz_cst_template_res()

◆ index()

◆ initialize_from_tag()

◆ inverse_rotamers_against_residue() [1/2]

◆ inverse_rotamers_against_residue() [2/2]

◆ is_backbone()

◆ is_covalent()

◆ native()

◆ num_enz_cst_template_res()

◆ process_algorithm_info()

◆ process_data()

◆ read_data()

◆ return_complex_type_for_MatcherConstraint()

◆ template_atom_inds()

◆ upstream_res()

Member Data Documentation

◆ algorithm_inputs_

◆ allowed_seqpos_

◆ constraints_

◆ enz_template_res_

◆ index_

◆ is_covalent_

◆ native_

◆ restype_set_