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Only one molecule from the input SMILES file is processed... #30

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UnixJunkie opened this issue Nov 12, 2018 · 7 comments
Open

Only one molecule from the input SMILES file is processed... #30

UnixJunkie opened this issue Nov 12, 2018 · 7 comments
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@UnixJunkie
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Hello,

molvs standardize -i smi input.smi  -o smi -O output.smi

The input file has several molecules, the output a single one.
Is this the expected behavior?
@UnixJunkie
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UnixJunkie commented Nov 12, 2018 •
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I installed via pip.

pip install molvs

@UnixJunkie
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this is probably the file that needs a fix:
https://github.com/mcs07/MolVS/blob/master/molvs/cli.py

@mcs07
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mcs07 commented Feb 5, 2019

Yes that seems to be the case. Also it looks like SDF files will only process the first molecule.

@mcs07 mcs07 added the bug label Feb 5, 2019
@UnixJunkie
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also, output to sdf file is not supported (it creates a mol file instead)

@UnixJunkie
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I'll send a patch for some of these.

@UnixJunkie UnixJunkie mentioned this issue Feb 6, 2019
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@sgujjaABM
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Hi, I am having the same issue with an SDF file. Wondering if there's a fix?
Thanks

@UnixJunkie
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I sent a PR with a fix.
Use the molVS that is inside of rdkit, then you should be good to go.

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@mcs07 @UnixJunkie @sgujjaABM