#include <MatchConstraintFileInfo.hh>

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

Collaboration 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::ResidueTypeSetCAP restype_set)

virtual	~MatchConstraintFileInfo ()

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 >	allowed_restypes (core::Size which_cstres) const
	all chemically non-redundant restypes of the given restypes 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

GeomSampleInfoCOP	dis_U1D1 () const

GeomSampleInfoCOP	ang_U1D2 () const

GeomSampleInfoCOP	ang_U2D1 () const

GeomSampleInfoCOP	tor_U1D3 () const

GeomSampleInfoCOP	tor_U3D1 () const

GeomSampleInfoCOP	tor_U2D2 () 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

ExternalGeomSamplerCOP	create_exgs () const
	returns ExternalGeomSampler only if the user has specified all six degrees of freedom, otherwise null pointer is returned More...

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

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

Private Attributes
core::Size	index_

utility::vector1< core::Size >	allowed_seqpos_

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

bool	is_covalent_

GeomSampleInfoOP	dis_U1D1_

GeomSampleInfoOP	ang_U1D2_

GeomSampleInfoOP	ang_U2D1_

GeomSampleInfoOP	tor_U1D3_

GeomSampleInfoOP	tor_U3D1_

GeomSampleInfoOP	tor_U2D2_

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

core::chemical::ResidueTypeSetCAP	restype_set_

bool	native_

Detailed Description

Definition at line 144 of file MatchConstraintFileInfo.hh.

Member Typedef Documentation

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

Definition at line 150 of file MatchConstraintFileInfo.hh.

Constructor & Destructor Documentation

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

Definition at line 264 of file MatchConstraintFileInfo.cc.

References allowed_seqpos_, and enz_template_res_.

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

virtual

Definition at line 276 of file MatchConstraintFileInfo.cc.

Member Function Documentation

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

Definition at line 212 of file MatchConstraintFileInfo.hh.

References algorithm_inputs_.

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

Definition at line 177 of file MatchConstraintFileInfo.hh.

References enz_cst_template_res().

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

all chemically non-redundant restypes of the given restypes

Definition at line 280 of file MatchConstraintFileInfo.cc.

References enz_cst_template_res().

Referenced by inverse_rotamers_against_residue().

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

Definition at line 170 of file MatchConstraintFileInfo.hh.

References allowed_seqpos_.

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::ang_U1D2 ( ) const

inline

Definition at line 224 of file MatchConstraintFileInfo.hh.

References ang_U1D2_.

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

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::ang_U2D1 ( ) const

inline

Definition at line 228 of file MatchConstraintFileInfo.hh.

References ang_U2D1_.

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

ExternalGeomSamplerCOP 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

Definition at line 696 of file MatchConstraintFileInfo.cc.

References ang_U1D2_, ang_U2D1_, dis_U1D1_, tor_U1D3_, tor_U2D2_, tor_U3D1_, and protocols::toolbox::match_enzdes_util::tr().

Referenced by inverse_rotamers_against_residue().

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::dis_U1D1 ( ) const

inline

Definition at line 220 of file MatchConstraintFileInfo.hh.

References dis_U1D1_.

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

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

Definition at line 628 of file MatchConstraintFileInfo.cc.

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().

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

Definition at line 206 of file MatchConstraintFileInfo.hh.

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

Definition at line 314 of file MatchConstraintFileInfo.cc.

References enz_template_res_.

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

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

inline

Definition at line 163 of file MatchConstraintFileInfo.hh.

References index_.

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

Definition at line 477 of file MatchConstraintFileInfo.cc.

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

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

Definition at line 536 of file MatchConstraintFileInfo.cc.

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

inline

is this interaction a backbone interaction

Definition at line 186 of file MatchConstraintFileInfo.hh.

References enz_cst_template_res().

Referenced by inverse_rotamers_against_residue().

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

inline

Definition at line 216 of file MatchConstraintFileInfo.hh.

References is_covalent_.

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

inline

Definition at line 256 of file MatchConstraintFileInfo.hh.

References native_.

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

inline

Definition at line 181 of file MatchConstraintFileInfo.hh.

References enz_template_res_.

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

protected

reads and stores arbitrary algorithm specific input

Definition at line 641 of file MatchConstraintFileInfo.cc.

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

Referenced by read_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

Definition at line 444 of file MatchConstraintFileInfo.cc.

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

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

data reading routine

Definition at line 335 of file MatchConstraintFileInfo.cc.

References ang_U1D2_, ang_U2D1_, dis_U1D1_, enz_template_res_, is_covalent_, native_, process_algorithm_info(), restype_set_, tor_U1D3_, tor_U2D2_, and tor_U3D1_.

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

Definition at line 297 of file MatchConstraintFileInfo.cc.

References enz_template_res_.

Referenced by inverse_rotamers_against_residue().

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U1D3 ( ) const

inline

Definition at line 232 of file MatchConstraintFileInfo.hh.

References tor_U1D3_.

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

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U2D2 ( ) const

inline

Definition at line 240 of file MatchConstraintFileInfo.hh.

References tor_U2D2_.

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

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U3D1 ( ) const

inline

Definition at line 236 of file MatchConstraintFileInfo.hh.

References tor_U3D1_.

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

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

Definition at line 199 of file MatchConstraintFileInfo.hh.

Referenced by inverse_rotamers_against_residue().

Member Data Documentation

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

private

Definition at line 331 of file MatchConstraintFileInfo.hh.

Referenced by algorithm_inputs(), and process_algorithm_info().

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

private

Definition at line 321 of file MatchConstraintFileInfo.hh.

Referenced by allowed_seqpos(), and MatchConstraintFileInfo().

GeomSampleInfoOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::ang_U1D2_

private

Definition at line 328 of file MatchConstraintFileInfo.hh.

Referenced by ang_U1D2(), create_exgs(), and read_data().

GeomSampleInfoOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::ang_U2D1_

private

Definition at line 328 of file MatchConstraintFileInfo.hh.

Referenced by ang_U2D1(), create_exgs(), and read_data().

GeomSampleInfoOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::dis_U1D1_

private

Definition at line 328 of file MatchConstraintFileInfo.hh.

Referenced by create_exgs(), dis_U1D1(), and read_data().

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

private

Definition at line 323 of file MatchConstraintFileInfo.hh.

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

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

private

Definition at line 318 of file MatchConstraintFileInfo.hh.

Referenced by index().

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

private

Definition at line 325 of file MatchConstraintFileInfo.hh.

Referenced by is_covalent(), and read_data().

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

private

Definition at line 336 of file MatchConstraintFileInfo.hh.

Referenced by native(), and read_data().

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

private

Definition at line 333 of file MatchConstraintFileInfo.hh.

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

GeomSampleInfoOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U1D3_

private

Definition at line 328 of file MatchConstraintFileInfo.hh.

Referenced by create_exgs(), read_data(), and tor_U1D3().

GeomSampleInfoOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U2D2_

private

Definition at line 328 of file MatchConstraintFileInfo.hh.

Referenced by create_exgs(), read_data(), and tor_U2D2().

GeomSampleInfoOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U3D1_

private

Definition at line 328 of file MatchConstraintFileInfo.hh.

Referenced by create_exgs(), read_data(), and tor_U3D1().

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

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation