schrodinger.structure.PDBReader

Class PDBReader

object --+ | _ReaderWriterContextManager --+ | FormatReader --+ | PDBReader

A class for reading structures from a PDB format file.

Instance Methods

__init__(self, filename, index=1, error_handler=None, all_occ=False, allow_obsolete=True, use_strict_resname=False)
Initialize with a filename, an optional starting index (default of 1) and optional error_handler (default of mm.error_handler).

__del__(self)

close(self)
Close the file.

__iter__(self)

next(self)
Return the next Structure object from the file.

getErrorHandler(self)
Returns the error handler by querying the pdb library and if the refcount is > 0 then return the error handler that is in use by pdb.

Inherited from FormatReader: clearReadErrors, getReadErrors, startErrorQueuing, stopErrorQueuing

Inherited from _ReaderWriterContextManager: __enter__, __exit__

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

Properties

[hide private]

Inherited from object: __class__

init(self, filename, index=1, error_handler=None, all_occ=False, allow_obsolete=True, use_strict_resname=False)
(Constructor)

Initialize with a filename, an optional starting index (default of 1) and optional error_handler (default of mm.error_handler).

all_occ - Whether to include alternative positions (default=False)

allow_obsolete - Whether to allow reading obsolete PDB files (default=True).

use_strict_resname - Limit the residue name to 18-20 columns of pdb record.

Overrides: object.__init__

getErrorHandler(self)

Returns the error handler by querying the pdb library and if the refcount is > 0 then return the error handler that is in use by pdb. Otherwise None is returned.

Overrides: FormatReader.getErrorHandler

Class PDBReader

__init__(self, filename, index=1, error_handler=None, all_occ=False, allow_obsolete=True, use_strict_resname=False) (Constructor)

getErrorHandler(self)

init(self, filename, index=1, error_handler=None, all_occ=False, allow_obsolete=True, use_strict_resname=False)
(Constructor)