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support several molecules in input file (for .smi and .sdf) #32

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UnixJunkie
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also, keep molecule names

I don't write Python these days, feel free to rewrite as you wish.
I tested on multi molecules smi and sdf input files.

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corrects #30

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Note that I only corrected 'standardize'.
Please replicate the change if you want to correct 'validate' also.

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