iodata.formats.sdf module¶

SDF file format.

Usually, the different frames in a trajectory describe different geometries of the same molecule, with atoms in the same order. The load_many and dump_many functions below can also handle an SDF file with different molecules, e.g. a molecular database.

The SDF format is somewhat documented on the following page: http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx

This format is one of the chemical table file formats: https://en.wikipedia.org/wiki/Chemical_table_file

dump_many(f, datas)[source]¶

Dump multiple frames into a SDF 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. If the following attributes are present, they are also dumped into the file: title, bonds.

Notes

dump_one(f, data)[source]¶

Dump a single frame into a SDF file.

Parameters:

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

Notes

load_many(lit)[source]¶

Load multiple frames from a SDF 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, bonds, title.
Return type:: Iterator[dict]

load_one(lit)[source]¶

Load a single frame from a SDF 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, bonds, title.