biopython

v1.71.0

biopython v1.71.0 Bio.PDB.StructureBuilder.StructureBuilder

Deals with contructing the Structure object.

The StructureBuilder class is used by the PDBParser classes to translate a file to a Structure object.

Link to this section Summary

Functions

__init__()

Initialize the class

_is_completely_disordered()

Return 1 if all atoms in the residue have a non blank altloc

get_structure()

Return the structure

init_atom()

Initiate a new Atom object

init_chain()

Initiate a new Chain object with given id

init_model()

Initiate a new Model object with given id

init_residue()

Initiate a new Residue object

init_seg()

Flag a change in segid

init_structure()

Initiate a new Structure object with given id

set_anisou()

Set anisotropic B factor of current Atom

set_line_counter()

Tracks line in the PDB file that is being parsed

set_sigatm()

Set standard deviation of atom position of current Atom

set_siguij()

Set standard deviation of anisotropic B factor of current Atom

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function _is_completely_disordered()

Return 1 if all atoms in the residue have a non blank altloc.

Link to this function get_structure()

Return the structure.

Link to this function init_atom()

Initiate a new Atom object.

Arguments:

  • name - string, atom name, e.g. CA, spaces should be stripped
  • coord - Numeric array (Float0, size 3), atomic coordinates
  • b_factor - float, B factor
  • occupancy - float
  • altloc - string, alternative location specifier
  • fullname - string, atom name including spaces, e.g. “ CA “
  • element - string, upper case, e.g. “HG” for mercury
Link to this function init_chain()

Initiate a new Chain object with given id.

Arguments:

  • chain_id - string
Link to this function init_model()

Initiate a new Model object with given id.

Arguments:

  • id - int
  • serial_num - int
Link to this function init_residue()

Initiate a new Residue object.

Arguments:

  • resname - string, e.g. “ASN”
  • field - hetero flag, “W” for waters, “H” for hetero residues, otherwise blank.
  • resseq - int, sequence identifier
  • icode - string, insertion code
Link to this function init_seg()

Flag a change in segid.

Arguments:

  • segid - string
Link to this function init_structure()

Initiate a new Structure object with given id.

Arguments:

  • id - string
Link to this function set_anisou()

Set anisotropic B factor of current Atom.

Link to this function set_line_counter()

Tracks line in the PDB file that is being parsed.

Arguments:

  • line_counter - int
Link to this function set_sigatm()

Set standard deviation of atom position of current Atom.

Link to this function set_siguij()

Set standard deviation of anisotropic B factor of current Atom.