Package Bio :: Package PDB :: Module StructureBuilder :: Class StructureBuilder
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Class StructureBuilder

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object --+
         |
        StructureBuilder


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

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature
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_is_completely_disordered(self, residue)
Return 1 if all atoms in the residue have a non blank altloc.
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set_header(self, header) source code
 
set_line_counter(self, line_counter)
The line counter keeps track of the line in the PDB file that is being parsed.
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init_structure(self, structure_id)
Initiate a new Structure object with given id.
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init_model(self, model_id, serial_num=None)
Initiate a new Model object with given id.
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init_chain(self, chain_id)
Initiate a new Chain object with given id.
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init_seg(self, segid)
Flag a change in segid.
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init_residue(self, resname, field, resseq, icode)
Initiate a new Residue object.
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init_atom(self, name, coord, b_factor, occupancy, altloc, fullname, serial_number=None, element=None)
Initiate a new Atom object.
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set_anisou(self, anisou_array)
Set anisotropic B factor of current Atom.
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set_siguij(self, siguij_array)
Set standard deviation of anisotropic B factor of current Atom.
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set_sigatm(self, sigatm_array)
Set standard deviation of atom position of current Atom.
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get_structure(self)
Return the structure.
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set_symmetry(self, spacegroup, cell) source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

set_line_counter(self, line_counter)

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The line counter keeps track of the line in the PDB file that
is being parsed.

Arguments:
o line_counter - int

init_structure(self, structure_id)

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Initiate a new Structure object with given id.

Arguments:
o id - string

init_model(self, model_id, serial_num=None)

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Initiate a new Model object with given id.

Arguments:
o id - int
o serial_num - int

init_chain(self, chain_id)

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Initiate a new Chain object with given id.

Arguments:
o chain_id - string

init_seg(self, segid)

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Flag a change in segid.

Arguments:
o segid - string

init_residue(self, resname, field, resseq, icode)

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Initiate a new Residue object.

Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
    hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code

init_atom(self, name, coord, b_factor, occupancy, altloc, fullname, serial_number=None, element=None)

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Initiate a new Atom object.

Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
o element - string, upper case, e.g. "HG" for mercury