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Question: about the error of json input for protein dimer #263

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c00jsw00 opened this issue Jan 15, 2025 · 1 comment
Open

Question: about the error of json input for protein dimer #263

c00jsw00 opened this issue Jan 15, 2025 · 1 comment
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@c00jsw00
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c00jsw00 commented Jan 15, 2025

Dear all,
my json input is shown below. but I alway got the error , such as "json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 3 column 28 (char 62)". How to fixe it ?

my json:

{
    "name": "XXX",
    "modelSeeds": [1, 2],
    "sequences": [
        {
            "protein": {
                "id": ["L"],
                "sequence": "XXX"
            }
        },
        {
            "protein": {
                "id": ["L"],
                "sequence": "XXX"
            }
        }
    ],
    "bondedAtomPairs": [
        [["L", 5, "SG"], ["H", 5, "SG"]],
        [["L", 11, "SG"], ["H", 11, "SG"]],
        [["L", 14, "SG"], ["H", 14, "SG"]]
    ],
    "dialect": "alphafold3",
    "version": 1
}
@Augustin-Zidek
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Augustin-Zidek commented Jan 16, 2025

I am unable to reproduce the error you are seeing, the JSON provided loads fine. Is it possible your name contains the double quote character (")?

One problem I can see though is that both of your proteins have the same id "L". Judging by your bond list, your second protein chain should have ID "H".

@Augustin-Zidek Augustin-Zidek added the question Further information is requested label Jan 16, 2025
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