Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo Class Reference

#include <MatchConstraintFileInfo.hh>

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

List of all members.

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
utility::vector1< std::string >
const & 
allowed_res_name3s (core::Size which_cstres) const
 what type of amino acids/ligands make this constraint
core::Size num_enz_cst_template_res () const
bool is_backbone (core::Size which_cstres) const
 is this interaction a backbone interaction
utility::vector1
< core::chemical::ResidueTypeCAP
allowed_restypes (core::Size which_cstres) const
 all chemically non-redundant restypes of the given restypes
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
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
std::map< std::string,
utility::vector1< std::string >
> const & 
algorithm_inputs () const
 holds information read from ALGORITHM_INFO blocks in the input file
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
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
bool read_data (utility::io::izstream &data)
 data reading routine
void process_data ()
 processes the read data right now this only generates the template atomnos for every restype
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
std::list
< core::conformation::ResidueCOP
inverse_rotamers_against_residue (core::conformation::Residue const &target_conf, core::chemical::ResidueTypeCAP invrot_restype, utility::vector1< core::Size > const &target_ats, utility::vector1< core::Size > const &invrot_ats, bool const flip_exgs_upstream_downstream_samples) const

Protected Member Functions

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

Member Typedef Documentation


Constructor & Destructor Documentation

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

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::ResidueTypeCAP > protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_restypes ( core::Size  which_cstres) const

all chemically non-redundant restypes of the given restypes

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

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::ang_U1D2 ( ) const [inline]
GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::ang_U2D1 ( ) const [inline]
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

References protocols::toolbox::match_enzdes_util::tr().

Referenced by inverse_rotamers_against_residue().

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::dis_U1D1 ( ) const [inline]
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
core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::index ( ) const [inline]
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(), is_backbone(), 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::ResidueTypeCAP  invrot_restype,
utility::vector1< core::Size > const &  target_ats,
utility::vector1< core::Size > const &  invrot_ats,
bool const  flip_exgs_upstream_downstream_samples 
) const
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]
bool protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::native ( ) const [inline]
core::Size protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::num_enz_cst_template_res ( ) const [inline]
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 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().

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

data reading routine

References process_algorithm_info().

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

Referenced by inverse_rotamers_against_residue().

GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U1D3 ( ) const [inline]
GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U2D2 ( ) const [inline]
GeomSampleInfoCOP protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::tor_U3D1 ( ) const [inline]
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().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines