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I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex.

Is there a way to do that with BioPython or similar tools? Taking this PDB entry as an example, the tools should return 7FM.

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  • $\begingroup$ Can you please edit your question and include some examples and the output you would want from them? That way, we can test our solutions using your examples and we can be sure to give you the output you need. $\endgroup$
    – terdon
    May 4, 2019 at 16:22
  • $\begingroup$ The PDB entry states that the ligand is 7FM. $\endgroup$
    – wrong_path
    May 4, 2019 at 17:35
  • $\begingroup$ Anyway use the MMCIF2Dict tool to extract the information from the header via the PDB module of BioPython. If it's not in the header you can't do it because XML is not supported (not currently supported). Goodluck $\endgroup$
    – M__
    May 4, 2019 at 17:43

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I found out that the package PyPDB has the function get_ligands that does exactly what I'm looking for.

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  • $\begingroup$ Thanks, for the feedback. Apologies for not spotting this. $\endgroup$
    – M__
    May 7, 2019 at 9:44
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    $\begingroup$ No problem! Strange I was not able to find this tool before... $\endgroup$
    – wrong_path
    May 7, 2019 at 11:52

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