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Adds numbers to equal atom names in HETATM entries #71
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I'd be in favor of doing two changes related to this issue:
Also comes to mind that our names are maybe not super intuitive. For instance |
Add a check to pdb_validate to throw a warning on duplicate atom names in the same residue. Or maybe add a new tool?
Add a new tool that fixes this by renaming atoms with their original name + a number - and throw and error if the name grows beyond 4 characters: pdb_rename?
Probably need a new tool for this. pdf_rename could work.
Also comes to mind that our names are maybe not super intuitive. For instance pdb_reres should maybe be pdb_numres or pdb_reatom should be pdb_reserial. What do you think?
Less intuitive to me I would keep the old names. pdb_reres -> renumber residues and it is consistent with pdf_reatom. They do the same on atoms or residues.
And now that we are the server up let’s try to keep the names rather constant.
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So, the new |
Good question. I would assume that for standard proteins/nucleic acids the naming is correct.
So probably only doing it on HETATM should be fine (and simpler)
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I'd leave it more generic because anyway, ATOM names should be unique but, just in case... A new tool it is then: |
welcome back 😉 👍 |
A user requested:
Developers, do you feel is there a tool already to accommodate this, or should we go for:
pdb_numhetatoms
?@JoaoRodrigues @amjjbonvin @brianjimenez @mtrellet
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