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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:
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Collaboration diagram for protocols::toolbox::match_enzdes_util::EnzCstTemplateRes:
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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

virtual ~EnzCstTemplateRes ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 EnzCstTemplateRes (core::chemical::ResidueTypeSetCAP src_restype_set)
 
 EnzCstTemplateRes (core::chemical::ResidueTypeSetCAP 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 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
 
RestypeToTemplateAtomsMap::const_iterator atom_inds_for_restype_begin () const
 
RestypeToTemplateAtomsMap::const_iterator atom_inds_for_restype_end () const
 
void clear_all ()
 
void remap_resid (core::id::SequenceMapping const &smap)
 
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_
 
RestypeToTemplateAtomsMap atom_inds_for_restype_
 
bool rb_minimizable_
 
bool is_backbone_
 
utility::vector1< core::Size > respos_from_external_
 
bool identical_tag_found_
 
core::Size corresponding_res_block_
 
core::Size corresponding_res_num_in_block_
 
core::chemical::ResidueTypeSetCAP 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

Definition at line 87 of file EnzCstTemplateRes.hh.

Member Typedef Documentation

typedef std::map< core::chemical::ResidueTypeCOP, utility::vector1< utility::vector1< core::Size > > > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::AtomIndsForRestypeMap

Definition at line 97 of file EnzCstTemplateRes.hh.

typedef std::map< core::chemical::ResidueTypeCOP, utility::vector1< utility::vector1< core::Size > > > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::RestypeToTemplateAtomsMap

Definition at line 94 of file EnzCstTemplateRes.hh.

Constructor & Destructor Documentation

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

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 61 of file EnzCstTemplateRes.cc.

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

Definition at line 93 of file EnzCstTemplateRes.cc.

References clear_all().

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

Definition at line 104 of file EnzCstTemplateRes.cc.

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.

Definition at line 118 of file EnzCstTemplateRes.cc.

Member Function Documentation

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

Definition at line 159 of file EnzCstTemplateRes.hh.

References allowed_res_types_.

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

Definition at line 538 of file EnzCstTemplateRes.cc.

References atom_inds_for_restype_, and determine_atom_inds_for_restype().

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

Definition at line 164 of file EnzCstTemplateRes.hh.

References atom_inds_for_restype_.

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

Definition at line 168 of file EnzCstTemplateRes.hh.

References atom_inds_for_restype_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::clear_all ( )

Definition at line 411 of file EnzCstTemplateRes.cc.

References allowed_res_types_, at1_type_, at2_type_, at3_type_, atom1_, atom2_, atom3_, atom_inds_for_restype_, corresponding_res_block_, corresponding_res_num_in_block_, param_index_, and respos_from_external_.

Referenced by EnzCstTemplateRes().

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

Definition at line 148 of file EnzCstTemplateRes.hh.

References corresponding_res_block_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype ( core::chemical::ResidueTypeCOP  restype) const

Definition at line 443 of file EnzCstTemplateRes.cc.

References at1_type_, atom1_, atom2_, atom3_, atom_inds_for_restype_, core::chemical::AtomType::name(), core::scoring::pair, and protocols::toolbox::match_enzdes_util::tr().

Referenced by atom_inds_for_restype(), and get_pose_data().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header ( core::pose::Pose &  pose)

Definition at line 336 of file EnzCstTemplateRes.cc.

References allowed_res_types_, corresponding_res_block_, corresponding_res_num_in_block_, enz_io_param_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::name3(), param_index_, core::pose::Pose::residue(), respos_from_external_, core::pose::Pose::total_residue(), and protocols::toolbox::match_enzdes_util::tr().

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::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

Definition at line 251 of file EnzCstTemplateRes.cc.

References allowed_res_types_, atom_inds_for_restype_, determine_atom_inds_for_restype(), enz_io_param_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::name3(), param_index_, core::pose::Pose::residue(), and core::pose::Pose::residue_type().

EnzCstTemplateResAtomsCOP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_template_atoms_at_pos ( core::pose::Pose const &  pose,
core::Size  seqpos 
) const

Definition at line 321 of file EnzCstTemplateRes.cc.

References enz_io_param_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and param_index_.

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

Definition at line 622 of file EnzCstTemplateRes.cc.

References allowed_res_types_, corresponding_res_block_, corresponding_res_num_in_block_, enz_io_param_, and identical_tag_found_.

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

Definition at line 144 of file EnzCstTemplateRes.hh.

References is_backbone_.

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

Definition at line 133 of file EnzCstTemplateRes.hh.

References param_index_.

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

Definition at line 140 of file EnzCstTemplateRes.hh.

References rb_minimizable_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params ( std::istringstream &  line_stream)

read and set up the general information for one residue of one pair block in a cstfile

Definition at line 145 of file EnzCstTemplateRes.cc.

References core::chemical::aa_from_oneletter_code(), allowed_res_types_, at1_type_, at2_type_, at3_type_, atom1_, atom2_, atom3_, corresponding_res_block_, corresponding_res_num_in_block_, identical_tag_found_, is_backbone_, core::chemical::name_from_aa(), core::chemical::oneletter_code_specifies_aa(), rb_minimizable_, respos_from_external_, and restype_set_.

void protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::remap_resid ( core::id::SequenceMapping const &  smap)

Definition at line 431 of file EnzCstTemplateRes.cc.

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.

Definition at line 576 of file EnzCstTemplateRes.cc.

References core::conformation::Residue::atom(), atom_inds_for_restype_, core::chemical::ResidueType::name(), core::io::serialization::size(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

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

Definition at line 124 of file EnzCstTemplateRes.hh.

References enz_io_param_.

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

Definition at line 424 of file EnzCstTemplateRes.cc.

References respos_from_external_.

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

Definition at line 129 of file EnzCstTemplateRes.hh.

References param_index_.

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

show the contents of a particular instance

Definition at line 235 of file EnzCstTemplateRes.cc.

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

Member Data Documentation

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_
private

Definition at line 206 of file EnzCstTemplateRes.hh.

Referenced by allowed_res_types(), clear_all(), find_in_pose_if_missing_from_header(), get_pose_data(), identical_info_consistency_check(), read_params(), and show_params().

std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at1_type_
private

Definition at line 203 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), determine_atom_inds_for_restype(), read_params(), and show_params().

std::string protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::at2_type_
private

Definition at line 203 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), and read_params().

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

Definition at line 203 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), and read_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom1_
private

Definition at line 202 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), determine_atom_inds_for_restype(), read_params(), and show_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom2_
private

Definition at line 202 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), determine_atom_inds_for_restype(), read_params(), and show_params().

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom3_
private

Definition at line 202 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), determine_atom_inds_for_restype(), read_params(), and show_params().

RestypeToTemplateAtomsMap protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_
mutableprivate

Definition at line 211 of file EnzCstTemplateRes.hh.

Referenced by atom_inds_for_restype(), atom_inds_for_restype_begin(), atom_inds_for_restype_end(), clear_all(), determine_atom_inds_for_restype(), get_pose_data(), and residue_conformations_redundant().

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_block_
private

Definition at line 226 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), corresponding_res_block(), find_in_pose_if_missing_from_header(), identical_info_consistency_check(), and read_params().

core::Size protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_num_in_block_
private

Definition at line 226 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), find_in_pose_if_missing_from_header(), identical_info_consistency_check(), and read_params().

EnzConstraintParametersCAP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::enz_io_param_
private

Definition at line 231 of file EnzCstTemplateRes.hh.

Referenced by find_in_pose_if_missing_from_header(), get_pose_data(), get_template_atoms_at_pos(), identical_info_consistency_check(), and set_enzio_param().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_tag_found_
private

Definition at line 225 of file EnzCstTemplateRes.hh.

Referenced by identical_info_consistency_check(), and read_params().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::is_backbone_
private

Definition at line 220 of file EnzCstTemplateRes.hh.

Referenced by is_backbone(), and read_params().

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

Definition at line 232 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), find_in_pose_if_missing_from_header(), get_pose_data(), get_template_atoms_at_pos(), param_index(), and set_param_index().

bool protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::rb_minimizable_
private

Definition at line 215 of file EnzCstTemplateRes.hh.

Referenced by rb_minimizable(), and read_params().

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

Definition at line 222 of file EnzCstTemplateRes.hh.

Referenced by clear_all(), find_in_pose_if_missing_from_header(), read_params(), remap_resid(), and set_external_position().

core::chemical::ResidueTypeSetCAP protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::restype_set_
private

Definition at line 229 of file EnzCstTemplateRes.hh.

Referenced by read_params().

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