Questions tagged [rdkit]

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3 votes
1 answer
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Parsing pre-2007 SMILES string

How would one parse the SMILES string BrC[2]:C[3]:C(:CH:CH:CH:@2):CH:CH:CH:CH:@3 I rely on tools like rdkit and ...
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2 votes
1 answer
40 views

Is it possible to correct bond order and conectivity problems in an sdf file according to mol2 files?

I was doing a Virtual Screening Search using Pharmer software. The .sdf output file contains a column in mol format and another column with Root Mean Square Deviations. I can see some bond order and ...
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1 vote
1 answer
629 views

How to convert a SDF molecular structure file to a pandas dataframe with Python?

What is the best python tool to convert a SDF file to a structured data frame (pandas.DataFrame). Similar to Molconvert from ChemAxon? SDF can have different datafields for each compound which I would ...
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