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Add function to parse secondary structure elements from PDBx #534

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padix-key opened this issue Feb 16, 2024 · 3 comments
Open

Add function to parse secondary structure elements from PDBx #534

padix-key opened this issue Feb 16, 2024 · 3 comments

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@padix-key
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As MMTF is now deprecated (#525) another method is desired to parse the secondary structure from PDB. PDBx files contain annotations of helices and sheets in the struct_conf and struct_sheet_range categories respectively.

Hence, a pdbx.get_sse() function could be implemented.

@ceziegler
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ceziegler commented Aug 21, 2024

Is there a preferred format for the output?

@padix-key
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padix-key commented Aug 23, 2024

I think a dictionary mapping the chain ID to the secondary structure elements (SSE) would be good. I think the SSE should be an ndarray

Residues without defined secondary structure could get a c or some COIL value from the enum value assigned

@padix-key
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Thanks by the way for tackling this feature! I assigned the issue to you.

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