iodata.formats.molekel module

Molekel file format.

This format is used by two programs: Molekel and Orca.

dump_one(f, data)[source]

Dump a single frame into a Molekel file.

Parameters:

  • f (TextIO) – A writeable file object.

  • data (IOData) – An IOData instance which must have the following attributes initialized: atcoords, atnums, mo, obasis. If the following attributes are present, they are also dumped into the file: atcharges.

Notes

load_one(lit, norm_threshold=0.0001)[source]

Load a single frame from a Molekel file.

Parameters:

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

  • norm_threshold (float) – When the normalization of one of the orbitals exceeds norm_threshold, a correction is attempted or an error is raised when no suitable correction can be found.

Return type:

dict

Returns:

result (dict) – A dictionary with IOData attributes. The following attributes are guaranteed to be loaded: atcoords, atnums, mo, obasis. The following may be loaded if present in the file: atcharges.

prepare_dump(data, allow_changes, filename)[source]

Check the compatibility of the IOData object with the Molekel format.

Parameters:

  • data (IOData) – The IOData instance to be checked.

  • allow_changes (bool) – Whether conversion of the IOData object to a compatible form is allowed or not.

  • filename (str) – The file to be written to, only used for error messages.

Return type:

IOData

Returns:

data – The given IOData object or a shallow copy with some new attributes.

Raises: