Dear all,
The svn version of the RDKit now behaves like this:
In [2]: m = Chem.MolFromMolFile('empty.mol')
In [3]: m.GetNumAtoms()
Out[3]: 0
Notice that there are no longer error messages.
There is, however, the following wart:
In [6]: Chem.MolToSmiles(m)
Out[6]: ''
In [7]: m2 = Chem.MolFromSmiles('')
SMILES Parse Error: syntax error for input:
In [8]: m2 is None
Out[8]: True
The SMILES writer happily generates an empty string for the molecule
with no atoms, but the SMILES parser generates an error.
The behavior of the parser is, I believe, consistent with Daylight.
The question is what the writer should do. I see two choices:
1) As is: Writer generates an empty string, but the parser generates an error
2) Change MolToSmiles so that it generates an error if the molecule
has no atoms.
I prefer the status quo (choice 1) because I don't really like the
idea that a valid molecule would lead to an error in the writer.
-greg
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