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New biomol fields #400

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New biomol fields #400

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eca24df
added new biomol fields
d-beltran Feb 23, 2022
572a29f
added new biomol sequence fields
d-beltran Feb 23, 2022
173172f
Update optimade.rst
d-beltran Feb 23, 2022
5911d53
Title underlines fit
d-beltran Feb 23, 2022
05a8fed
More explained biomol_chain types
d-beltran Feb 24, 2022
76f690c
Added standard labels for biomol_chain types
d-beltran Feb 25, 2022
1f5650d
Added underscore to new fieldnames
d-beltran Feb 28, 2022
a8781ac
Amend
d-beltran Feb 28, 2022
ac6ed65
New species property: biomol atom name
d-beltran Mar 1, 2022
55f71e2
Restructured biomol sequences
d-beltran Mar 1, 2022
534ec8d
Merge branch 'develop' into iss389_biomol
d-beltran Sep 13, 2022
f865a5a
Laussane discussions update
d-beltran Sep 13, 2022
af3c817
Update optimade.rst
d-beltran Sep 13, 2022
616019c
Update optimade.rst
d-beltran Sep 13, 2022
bd3e9e1
Update optimade.rst
d-beltran Sep 13, 2022
ce93c9d
Update optimade.rst
d-beltran Sep 13, 2022
a875aaf
added a few breaklines with correct indent
d-beltran Sep 13, 2022
a1ddd88
Update optimade.rst
d-beltran Sep 14, 2022
a0ee16a
Update optimade.rst
d-beltran Sep 14, 2022
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Update optimade.rst
d-beltran Sep 14, 2022
af14d72
Update optimade.rst
d-beltran Sep 14, 2022
7610146
insertion_code renamed as icode
d-beltran Sep 14, 2022
c38075c
Merge branch 'develop' into iss389_biomol
rartino Oct 21, 2022
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4 changes: 3 additions & 1 deletion optimade.rst
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Expand Up @@ -2490,7 +2490,9 @@ biomol_chains
- **name**: The chain name/letter.
- **residues**: A list of integers referring to the index of :field:`biomol_residues`, that belong to this chain.
The list SHOULD NOT be empty. The index of the first residue is 0.
- **types**: A list of tags specifying the type of molecules this chain contains.
- **types**: A list of custom tags/labels specifying the type of molecules this chain contains (e.g. 'protein').
This field is useful as an overview of every chain and as a query target for the structure.
Labels in this field are non-standard. Every implementation may use different labels according to its needs.
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I would advise standardizing labels at least for the most common molecule types to benefit the queryability of the field. Implementations could use their own labels, but prefixed with their own database-specific prefixes.

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Good idea. This way we could save a lot of work.

I have been searching for references for our labels in the current mmCIF format (the future PDB standard) and this is the best I have found. They are meant for assemblies and they do not totally suit me, but I will try to resemble them.

So I suggest the standard labels to be the following: 'PROTEIN', 'NUCLEIC ACID', 'CARBOHYDRATES', 'LIPID', 'MEMBRANE', 'LIGAND', 'ION', 'SOLVENT', 'OTHER'.

If you agree I will commit changes soon.

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Yes, it seems like a good idea to define these labels.

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I very much like basing on mmCIF. Maybe there is already a JSON representation for mmCIF data?

So I suggest the standard labels to be the following: 'PROTEIN', 'NUCLEIC ACID', 'CARBOHYDRATES', 'LIPID', 'MEMBRANE', 'LIGAND', 'ION', 'SOLVENT', 'OTHER'.

If you agree I will commit changes soon.

These labels sound very good. I would just render them in lowercase and describe the use of prefixes for custom labels in the form of <prefix>:<label>.

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Maybe there is already a JSON representation for mmCIF data?

In a fast search I found several mmCIF to JSON parsers and one of them seems to be the official one.

I would just render them in lowercase and describe the use of prefixes for custom labels in the form of :

Allright

- **sequences**: A list of residue sequences in current chain.
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If the same sequence occurs twice in a chain. Should the sequence be listed here twice or just once?

- **sequence_types**: A list of tags specifying the type of each sequence in the :property:`sequences` field. The type of a sequence is defined by its components (e.g. 'aminoacids').
- There SHOULD NOT be two or more chains with the same :property:`name`.
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