Hi there RDKitters
RDKit - v2011.09.01 - chokes on massive SDF files when using
Chem.SDMolSupplier(input_file)
Specifically I have an sdf file of 7,210,245,124 bytes - containing
2,711,916 molecules (grep -c '$$$$') and 193,329,781 lines - yes, I buy HDs
by the dozen.
The error message which I get is nonsensical - something like "incorrect
atom count on line". I say nonsensical because if I split the file in half
(roughly) RDKit is happy to read both of them without any errors.
Has anyone else noticed this? Are there any known limitations? (buffer
sizes etc maybe)
Thanks
-
Jean-Paul Ebejer
Early Stage Researcher
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