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protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo Class Reference

#include <MatchConstraintFileInfo.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo:
Inheritance graph
[legend]

Public Types

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

Public Member Functions

 MatchConstraintFileInfo (core::Size index, core::chemical::ResidueTypeSetCOP 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 >
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
 
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
 
ExternalGeomSamplerOP 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::ResidueTypeSetCOP restype_set_
 
bool native_
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

References allowed_seqpos_, and enz_template_res_.

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

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

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

References enz_cst_template_res().

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().

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_.

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

References ang_U1D2_.

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

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

References ang_U2D1_.

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

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 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

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

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

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().

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

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

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

References core::pack::rotamer_set::bb_independent_rotamers(), create_exgs(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::dis_U1D1_samples(), diversify_backbone_only_rotamers(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::flip_upstream_downstream_samples(), 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, protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U1D2_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U2D1_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_dis_U1D1_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U1D3_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U2D2_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U3D1_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::precompute_transforms(), rot(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_ang_D1D2D3(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D2D3(), protocols::toolbox::match_enzdes_util::tr(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::transform(), and core::conformation::Residue::xyz().

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().

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

References is_covalent_.

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

References native_.

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

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

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

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

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

data reading routine

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

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

Referenced by inverse_rotamers_against_residue().

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

References tor_U1D3_.

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

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

References tor_U2D2_.

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

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

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

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

Referenced by algorithm_inputs(), and process_algorithm_info().

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

Referenced by allowed_seqpos(), and MatchConstraintFileInfo().

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

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

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

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

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

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

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

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

Referenced by index(), and process_data().

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

Referenced by is_covalent(), and read_data().

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

Referenced by native(), and read_data().

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

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

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

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

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

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

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

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

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