core::io::AtomInformation Struct Reference

#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

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

inline

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

Member Data Documentation

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_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), and core::io::operator<<().

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::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmtf::create_sfrs_from_mmtf_filename(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::mmtf::make_chain(), core::io::mmtf::ai_cmp::operator()(), core::io::operator<<(), core::io::mmtf::sfrs_to_sd(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

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<<().

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::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), and core::io::mmtf::sfrs_to_sd().

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().

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

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

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

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

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::mmcif::create_sfr_from_cif_file_op(), 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::operator<<(), core::io::mmtf::sfrs_to_sd(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

bool core::io::AtomInformation::isHet

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::mmcif::create_sfr_from_cif_file_op(), 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<<().

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::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_merge_residues_as_necessary(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

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

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), 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().

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::mmcif::create_sfr_from_cif_file_op(), 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::mmtf::make_current_group(), core::io::operator<<(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::ResidueInformation::ResidueInformation().

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::mmcif::create_sfr_from_cif_file_op(), 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::mmtf::ai_cmp::operator()(), core::io::operator<<(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::pose_from_sfr::update_atom_information_based_on_occupancy().

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

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

int core::io::AtomInformation::serial

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::operator<<(), and protocols::electron_density::DockIntoDensityMover::select_points().

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::mmcif::create_sfr_from_cif_file_op(), 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().

int core::io::AtomInformation::terCount

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

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::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::mmtf::sfrs_to_sd().

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::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::mmtf::sfrs_to_sd().

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::mmcif::create_sfr_from_cif_file_op(), core::io::pdb::create_sfr_from_pdb_records(), core::io::mmcif::dump_cif(), core::io::mmtf::make_atom_information(), core::io::operator<<(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::io::pose_from_sfr::randomize_missing_coords(), and core::io::mmtf::sfrs_to_sd().

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

• src/core/io/AtomInformation.hh