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)

Dump multiple frames into a PDB file.

Parameters

• f (Textio) – A writeable file object.

• data – 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.

None

dump_one(f, data)

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.

Notes

None

load_many(lit)

Load a single frame from a PDB file.

Parameters

lit (LineIterator) – The line iterator to read the data from.

Returns

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.

Return type

data

Notes

load_one(lit)

Load a single frame from a PDB file.

Parameters

lit (LineIterator) – The line iterator to read the data from.

Returns

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.

Return type

data

Notes