Secondary Structure Information about biostructures.jl

[emrekuecuek]

Thank you for your very fast response. I will think about using mmCIF files, maybe I can parse string from PDB files as well, I haven't decided on that yet. Maybe after my graduation, I would like to make some contributions in my free time to this great project. Perhaps even this issue maybe? 😅

[jgreener64]

You are right, it would be useful. On the todo list is wrapping DSSP to calculate secondary structure from the structure itself, rather than reading it from the PDB/mmCIF header. This approach fits the philosophy of BioStructures better than reading the header, since it would work on custom PDB files without a header too.

No promises about that being implemented soon though, sorry. In the meantime you could write the mmCIF header parsing functions you need using the mmCIF dictionary, for example for helices:

using BioStructures
downloadpdb("1AKE", format=MMCIF)
d = MMCIFDict("1AKE.cif")
hs, he = d["_struct_conf.beg_auth_seq_id"], d["_struct_conf.end_auth_seq_id"]
helices = [(parse(Int, s), parse(Int, e)) for (s, e) in zip(hs, he)]

Note chain IDs etc. are neglected for simplicity in this example.