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Unclarities in specification #6

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padix-key opened this issue Feb 2, 2024 · 3 comments
Open

Unclarities in specification #6

padix-key opened this issue Feb 2, 2024 · 3 comments

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@padix-key
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padix-key commented Feb 2, 2024

While implementing a BinaryCIF file interface and I found some parts of the specification ambiguous:

  • What are the integer values a mask can hold and how do they map to the cif values (. and ?)
  • Is the final offset in a String Arraythe exclusive stop or a start index itself?
  • When encoding using Interval Quantization, are the values assigned to the closest step or to the next lower/higher step?
  • Into which data type does Delta encode?
  • How are the data types mapped to integers?
@epeisach
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epeisach commented Feb 4, 2024

My reading of the code is that
ciftools-python 0 = data, 1 = ., 2 = ?

Molstar/src/mol-data/db/column.ts: 0 = present, 1= ., 2 = ?

Also - lack of mask should be None -- not {}

@padix-key
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Thanks. I my opinion such details should be part of the specification itself.

@dsehnal
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dsehnal commented Oct 14, 2024

Sorry for the late reply. You are right, this should be mentioned in the specification -- I will add it.

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