IMP logo
IMP Reference Guide  develop.7cb8855c60,2024/10/04
The Integrative Modeling Platform
IMP::atom::PDBRecord Class Reference

Represent a single ATOM/HETATM "line" in PDB or mmCIF format. More...

#include <IMP/atom/pdb.h>

+ Inheritance diagram for IMP::atom::PDBRecord:

Detailed Description

Represent a single ATOM/HETATM "line" in PDB or mmCIF format.

Definition at line 34 of file pdb.h.

Public Member Functions

std::string get_alt_loc_indicator () const
 Returns the alternative location indicator. More...
 
std::string get_chain_id () const
 Returns the chain ID. More...
 
std::string get_element () const
 Returns the element as a string. More...
 
bool get_is_atom () const
 Returns true if the record is an ATOM record. More...
 
std::string get_padded_atom_name () const
 Returns the atom type in a PDB-style padded string. More...
 
std::string get_residue_name () const
 Returns the residue type. More...
 
std::string get_trimmed_atom_name () const
 Returns the atom type as a string with no leading or trailing whitespace. More...
 
void set_keywords (internal::CifKeyword &group, internal::CifKeyword &element, internal::CifKeyword &atom_name, internal::CifKeyword &alt_loc_id, internal::CifKeyword &residue_name, internal::CifKeyword &auth_chain, internal::CifKeyword &chain, internal::CifKeyword &auth_seq_id)
 Point the record to a single atom_site loop row from an mmCIF file. More...
 
void set_line (const std::string &line)
 Point the record to a line of text from a PDB file. More...
 
void show (std::ostream &out=std::cout) const
 

Member Function Documentation

std::string IMP::atom::PDBRecord::get_alt_loc_indicator ( ) const

Returns the alternative location indicator.

This is a single character in PDB, but can be longer in mmCIF.

std::string IMP::atom::PDBRecord::get_chain_id ( ) const

Returns the chain ID.

This is a single character in PDB format, but can be longer in mmCIF. In mmCIF, the author-provided chain ID is provided if available; otherwise, the mmCIF asym_id is returned.

std::string IMP::atom::PDBRecord::get_element ( ) const

Returns the element as a string.

bool IMP::atom::PDBRecord::get_is_atom ( ) const

Returns true if the record is an ATOM record.

std::string IMP::atom::PDBRecord::get_padded_atom_name ( ) const

Returns the atom type in a PDB-style padded string.

The atom type is at least a 4 character long field. The first character is space in many cases, but not always.

std::string IMP::atom::PDBRecord::get_residue_name ( ) const

Returns the residue type.

std::string IMP::atom::PDBRecord::get_trimmed_atom_name ( ) const

Returns the atom type as a string with no leading or trailing whitespace.

void IMP::atom::PDBRecord::set_keywords ( internal::CifKeyword &  group,
internal::CifKeyword &  element,
internal::CifKeyword &  atom_name,
internal::CifKeyword &  alt_loc_id,
internal::CifKeyword &  residue_name,
internal::CifKeyword &  auth_chain,
internal::CifKeyword &  chain,
internal::CifKeyword &  auth_seq_id 
)

Point the record to a single atom_site loop row from an mmCIF file.

This uses pointers to the CIF keywords, so should not be used after the keywords are freed.

void IMP::atom::PDBRecord::set_line ( const std::string &  line)

Point the record to a line of text from a PDB file.

This uses a pointer to line so should not be used after line is freed


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