iodata.formats.pdb module¶

PDB file format.

There are different formats of pdb files. The convention used here is the last updated one and is described in this link: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

dump_many(f, datas)[source]¶

Dump multiple frames into a PDB file.

Parameters:

f (TextIO) – A writeable file object.
datas (Iterator[IOData]) – An iterator over IOData instances which must have the following attributes initialized: atcoords, atnums, extra. If the following attributes are present, they are also dumped into the file: atffparams, title.

Notes

dump_one(f, data)[source]¶

Dump a single frame into a PDB file.

Parameters:

f (TextIO) – A writeable file object.
data (IOData) – An IOData instance which must have the following attributes initialized: atcoords, atnums, extra. If the following attributes are present, they are also dumped into the file: atffparams, title, bonds.

Notes

load_many(lit)[source]¶

Load multiple frames from a PDB file.

Parameters:: lit (LineIterator) – The line iterator to read the data from.
Yields:: result (dict) – A dictionary with IOData attributes. The following attribtues are guaranteed to be loaded: atcoords, atnums, atffparams, extra. The following may be loaded if present in the file: title.
Return type:: Iterator[dict]

load_one(lit)[source]¶

Load a single frame from a PDB file.

Parameters:: lit (LineIterator) – The line iterator to read the data from.
Return type:: dict
Returns:: result (dict) – A dictionary with IOData attributes. The following attributes are guaranteed to be loaded: atcoords, atnums, atffparams, extra. The following may be loaded if present in the file: title, bonds.