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protocols::toolbox::match_enzdes_util::EnzCstTemplateRes Class Reference

helper class for class EnzConstraintParameters, gathers information More...

#include <EnzCstTemplateRes.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::EnzCstTemplateRes:
Inheritance graph
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Public Types

typedef std::map
< core::chemical::ResidueTypeCOP,
utility::vector1
< utility::vector1< core::Size > > > 
RestypeToTemplateAtomsMap
 
typedef std::map
< core::chemical::ResidueTypeCOP,
utility::vector1
< utility::vector1< core::Size > > > 
AtomIndsForRestypeMap
 

Public Member Functions

 ~EnzCstTemplateRes () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 EnzCstTemplateRes (core::chemical::ResidueTypeSetCOP src_restype_set)
 
 EnzCstTemplateRes (core::chemical::ResidueTypeSetCOP src_restype_set, EnzConstraintParametersCAP src_enzio_param)
 
 EnzCstTemplateRes (EnzCstTemplateResCOP other, EnzConstraintParametersCAP new_ref_param)
 WARNING: currently doesn't copy the template atoms in the respos map. More...
 
void initialize_from_params (std::string const &a1, std::string const &a2, std::string const &a3, utility::vector1< std::string > const &allowed_3res)
 
void read_params (std::istringstream &line_stream)
 read and set up the general information for one residue of one pair block in a cstfile More...
 
void show_params () const
 show the contents of a particular instance More...
 
void get_pose_data (core::pose::Pose &pose) const
 check whether the data gathered from the cst file and the pdbfile/pose is consistent in itself and with one another More...
 
void set_enzio_param (EnzConstraintParametersCAP src_enz_io_param)
 
void set_param_index (core::Size index)
 
core::Size param_index () const
 
EnzCstTemplateResAtomsCOP get_template_atoms_at_pos (core::pose::Pose const &pose, core::Size seqpos) const
 
bool rb_minimizable () const
 
bool is_backbone () const
 
core::Size corresponding_res_block () const
 
bool find_in_pose_if_missing_from_header (core::pose::Pose &pose)
 
void set_external_position (core::Size resnum)
 
utility::vector1< std::string >
const & 
allowed_res_types () const
 
utility::vector1
< core::chemical::ResidueTypeCOP >
const & 
allowed_res_types_pointers () const
 
RestypeToTemplateAtomsMap::const_iterator atom_inds_for_restype_begin () const
 Iterator to the map from ResidueType pointers (addresses) to the set of atoms that are used to build from; this returns ResidueTypes in an indeterminant order as they are going to be sorted based on where in memory the ResidueTypes happened to be allocated. More...
 
RestypeToTemplateAtomsMap::const_iterator atom_inds_for_restype_end () const
 End iterator to the map from ResidueType pointers to the set of atoms that are used to build from. More...
 
void clear_all ()
 
void remap_resid (core::id::SequenceMapping const &smap)
 
bool compatible_restype (core::chemical::ResidueTypeCOP restype) const
 
void determine_atom_inds_for_restype (core::chemical::ResidueTypeCOP restype) const
 
utility::vector1< core::Size >
const & 
atom_inds_for_restype (core::Size template_atom, core::chemical::ResidueTypeCOP restype) const
 
bool residue_conformations_redundant (core::conformation::Residue const &res1, core::conformation::Residue const &res2) const
 checks whether the distance between any of the template res atoms of res1 and res2 is below a certain cutoff. More...
 
void identical_info_consistency_check () const
 

Private Attributes

utility::vector1< std::string > atom1_
 
utility::vector1< std::string > atom2_
 
utility::vector1< std::string > atom3_
 
std::string at1_type_
 
std::string at2_type_
 
std::string at3_type_
 
utility::vector1< std::string > allowed_res_types_
 
utility::vector1
< core::chemical::ResidueTypeCOP
allowed_res_types_pointers_
 
RestypeToTemplateAtomsMap atom_inds_for_restype_
 
bool rb_minimizable_
 
bool is_backbone_
 
utility::vector1< core::Sizerespos_from_external_
 
bool identical_tag_found_
 
core::Size corresponding_res_block_
 
core::Size corresponding_res_num_in_block_
 
core::chemical::ResidueTypeSetCOP restype_set_
 
EnzConstraintParametersCAP enz_io_param_
 
core::Size param_index_
 

Detailed Description

helper class for class EnzConstraintParameters, gathers information

from cst input and pdb input

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::~EnzCstTemplateRes ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes ( core::chemical::ResidueTypeSetCOP  src_restype_set)

References clear_all().

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes ( core::chemical::ResidueTypeSetCOP  src_restype_set,
EnzConstraintParametersCAP  src_enzio_param 
)

References clear_all().

protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::EnzCstTemplateRes ( EnzCstTemplateResCOP  other,
EnzConstraintParametersCAP  new_ref_param 
)

WARNING: currently doesn't copy the template atoms in the respos map.

Member Function Documentation

utility::vector1< std::string > const& protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types ( ) const
inline

References allowed_res_types_.

utility::vector1< core::chemical::ResidueTypeCOP > const& protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_pointers ( ) const
inline
utility::vector1< core::Size > const & protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype ( core::Size  template_atom,
core::chemical::ResidueTypeCOP  restype 
) const
RestypeToTemplateAtomsMap::const_iterator protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_begin ( ) const
inline

Iterator to the map from ResidueType pointers (addresses) to the set of atoms that are used to build from; this returns ResidueTypes in an indeterminant order as they are going to be sorted based on where in memory the ResidueTypes happened to be allocated.

References atom_inds_for_restype_.

RestypeToTemplateAtomsMap::const_iterator protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_end ( ) const
inline

End iterator to the map from ResidueType pointers to the set of atoms that are used to build from.

References atom_inds_for_restype_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::clear_all ( )
bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::compatible_restype ( core::chemical::ResidueTypeCOP  restype) const
core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_block ( ) const
inline
void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype ( core::chemical::ResidueTypeCOP  restype) const
bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header ( core::pose::Pose pose)
void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data ( core::pose::Pose pose) const
EnzCstTemplateResAtomsCOP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_template_atoms_at_pos ( core::pose::Pose const &  pose,
core::Size  seqpos 
) const
void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_info_consistency_check ( ) const
void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::initialize_from_params ( std::string const &  a1,
std::string const &  a2,
std::string const &  a3,
utility::vector1< std::string > const &  allowed_3res 
)
bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::is_backbone ( ) const
inline

References is_backbone_.

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::param_index ( ) const
inline

References param_index_.

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::rb_minimizable ( ) const
inline

References rb_minimizable_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params ( std::istringstream &  line_stream)
void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::remap_resid ( core::id::SequenceMapping const &  smap)

References respos_from_external_.

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2 
) const

checks whether the distance between any of the template res atoms of res1 and res2 is below a certain cutoff.

References core::conformation::Residue::atom(), atom_inds_for_restype_, core::chemical::ResidueTypeBase::name(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::conformation::Atom::xyz().

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_enzio_param ( EnzConstraintParametersCAP  src_enz_io_param)
inline

References enz_io_param_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_external_position ( core::Size  resnum)

References respos_from_external_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_param_index ( core::Size  index)
inline

References param_index_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::show_params ( ) const

show the contents of a particular instance

References allowed_res_types_, at1_type_, atom1_, atom2_, atom3_, and protocols::toolbox::match_enzdes_util::tr().

Member Data Documentation

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_
private
utility::vector1< core::chemical::ResidueTypeCOP > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_pointers_
mutableprivate
std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at1_type_
private
std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at2_type_
private

Referenced by clear_all(), and read_params().

std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at3_type_
private

Referenced by clear_all(), and read_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom1_
private
utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom2_
private
utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom3_
private
RestypeToTemplateAtomsMap protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_
mutableprivate
core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_block_
private
core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_num_in_block_
private
EnzConstraintParametersCAP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::enz_io_param_
private
bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_tag_found_
private
bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::is_backbone_
private

Referenced by is_backbone(), and read_params().

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::param_index_
private
bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::rb_minimizable_
private

Referenced by rb_minimizable(), and read_params().

utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::respos_from_external_
private
core::chemical::ResidueTypeSetCOP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::restype_set_
private

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