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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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Represent a single ATOM/HETATM "line" in PDB or mmCIF format. More...
#include <IMP/atom/pdb.h>
Inheritance diagram for IMP::atom::PDBRecord: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 |
| 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