Rosetta: core::io::AtomInformation Struct Reference

Rosetta

#include <AtomInformation.hh>

Public Member Functions
	AtomInformation ()
	default constructor to initialize all values (except the connected indices) More...

Public Attributes
bool	isHet

int	serial

std::string	name

char	altLoc

std::string	resName

char	chainID

int	resSeq

char	iCode

core::Real	x

core::Real	y

core::Real	z

core::Real	occupancy

core::Real	temperature

std::string	segmentID

std::string	element

signed short int	formalcharge

int	terCount

std::string	chem_comp_type
	our best mapping to mmcif chem_comp.type More...

utility::vector1< core::Size >	connected_indices
	List of lower-numbered atoms that this atom is connected to. More...

utility::vector1< core::chemical::BondName >	connected_orders
	bond order list that matches connected_indices More...

Detailed Description

Only fields that are present in the PDB file will be initialized; others will have the default value.
This class basically reflects the structure of 'ATOM' lines in PDB file format.

Constructor & Destructor Documentation

◆ AtomInformation()

core::io::AtomInformation::AtomInformation ( )

inline

default constructor to initialize all values (except the connected indices)

Member Data Documentation

◆ altLoc

char core::io::AtomInformation::altLoc

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), and core::io::operator<<().

◆ chainID

char core::io::AtomInformation::chainID

Referenced by core::io::mmtf::add_link_and_ss_information(), core::io::mmtf::add_xbond_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmtf::create_sfrs_from_mmtf_filename(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::mmtf::make_chain(), core::io::ResidueInformation::matches(), core::io::operator<<(), protocols::chromophore::ReadResidueCoordinatesFromPDB::read_coordinates(), core::io::mmtf::sfrs_to_sd(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

◆ chem_comp_type

std::string core::io::AtomInformation::chem_comp_type

our best mapping to mmcif chem_comp.type

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::mmtf::make_atom_information(), core::io::mmtf::make_current_group(), and core::io::operator<<().

◆ connected_indices

utility::vector1< core::Size > core::io::AtomInformation::connected_indices

List of lower-numbered atoms that this atom is connected to.

Referenced by core::io::mmtf::add_bond_information(), core::io::mmtf::add_bonds_to_sd(), core::io::pdb::create_records_from_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), and core::io::mmtf::sfrs_to_sd().

◆ connected_orders

utility::vector1< core::chemical::BondName > core::io::AtomInformation::connected_orders

bond order list that matches connected_indices

Referenced by core::io::mmtf::add_bond_information(), core::io::mmtf::add_bonds_to_sd(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom().

◆ element

std::string core::io::AtomInformation::element

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::operator<<(), and protocols::ligand_docking::StartFrom::parse_pdb_file().

◆ formalcharge

signed short int core::io::AtomInformation::formalcharge

Referenced by core::io::operator<<().

◆ iCode

char core::io::AtomInformation::iCode

Referenced by core::io::mmtf::add_xbond_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::mmtf::make_chain(), core::io::ResidueInformation::matches(), core::io::operator<<(), core::io::mmtf::sfrs_to_sd(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

◆ isHet

bool core::io::AtomInformation::isHet

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), and core::io::operator<<().

◆ name

std::string core::io::AtomInformation::name

Referenced by core::io::mmtf::add_link_and_ss_information(), core::io::mmtf::add_xbond_information(), core::io::ResidueInformation::append_atom(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::ResidueInformation::append_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::pose_from_sfr::create_working_data(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::randomize_missing_coords(), protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

◆ occupancy

core::Real core::io::AtomInformation::occupancy

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::operator<<(), core::io::pose_from_sfr::randomize_missing_coords(), core::io::mmtf::sfrs_to_sd(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

◆ resName

std::string core::io::AtomInformation::resName

Referenced by core::io::mmtf::add_xbond_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::ResidueInformation::append_atoms(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::pose_from_sfr::create_working_data(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::mmtf::make_chain(), core::io::mmtf::make_current_group(), core::io::ResidueInformation::matches(), core::io::operator<<(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::ResidueInformation::ResidueInformation().

◆ resSeq

int core::io::AtomInformation::resSeq

Referenced by core::io::mmtf::add_link_and_ss_information(), core::io::mmtf::add_xbond_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::mmtf::make_chain(), core::io::ResidueInformation::matches(), core::io::operator<<(), core::io::pose_from_sfr::randomize_missing_coords(), protocols::chromophore::ReadResidueCoordinatesFromPDB::read_coordinates(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

◆ segmentID

std::string core::io::AtomInformation::segmentID

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmtf::make_atom_information(), and core::io::operator<<().

◆ serial

int core::io::AtomInformation::serial

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), and core::io::operator<<().

◆ temperature

core::Real core::io::AtomInformation::temperature

Referenced by core::io::ResidueInformation::append_atom(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::ResidueInformation::append_atoms(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::operator<<(), and core::io::mmtf::sfrs_to_sd().

◆ terCount

int core::io::AtomInformation::terCount

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmtf::make_atom_information(), core::io::ResidueInformation::matches(), and core::io::operator<<().

◆ x

core::Real core::io::AtomInformation::x

Referenced by core::io::mmtf::add_xbond_information(), core::io::ResidueInformation::append_atom(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::ResidueInformation::append_atoms(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::randomize_missing_coords(), protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates(), and core::io::mmtf::sfrs_to_sd().

◆ y

core::Real core::io::AtomInformation::y

Referenced by core::io::mmtf::add_xbond_information(), core::io::ResidueInformation::append_atom(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::ResidueInformation::append_atoms(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::randomize_missing_coords(), protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates(), and core::io::mmtf::sfrs_to_sd().

◆ z

core::Real core::io::AtomInformation::z

Referenced by core::io::mmtf::add_xbond_information(), core::io::ResidueInformation::append_atom(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::ResidueInformation::append_atoms(), core::io::pdb::create_records_from_sfr(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::randomize_missing_coords(), protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates(), and core::io::mmtf::sfrs_to_sd().

The documentation for this struct was generated from the following file:

src/core/io/AtomInformation.hh