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]

Notes

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.

Notes