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coordinates/PDB.py PDB 3.2 vs. 3.3 consistency #2906

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mieczyslaw opened this issue Aug 12, 2020 · 3 comments
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coordinates/PDB.py PDB 3.2 vs. 3.3 consistency #2906

mieczyslaw opened this issue Aug 12, 2020 · 3 comments
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Component-Docs Format-PDB

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@mieczyslaw
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As suggested by @IAlibay, I am adding here a ticket on consistency issue in package/MDAnalysis/coordinates/PDB.py.

It mentions implementing a subset of 3.2 standard, but CRYST1 link points to 3.3. Is there anything stopping us from moving with all the links to 3.3? Is there anything there which is not compatible with 3.3?

Current version of MDAnalysis

MDAnalysis 1.0.0
@mieczyslaw mieczyslaw mentioned this issue Aug 12, 2020
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@orbeckst
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I don't think that we do anything specific to 3.2 – that's just the slow churn of history. Updates are welcome, especially as 3.3 is the final standard, as far as I understand it.

@mieczyslaw
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done as a part of #2880 (as requested by @IAlibay)

IAlibay pushed a commit that referenced this issue Aug 14, 2020
@mieczyslaw
Write HETATM record types (#2880)
22612de 
Fixes #1753 and #2906 

## Overview of work done in this PR
1) PDBWriter will now write out either `ATOM` or `HETATM` entries based on the contents of the atomgroup `record_types` attribute. If the `record_types` attribute is missing, writing will default to `ATOM` entries.
2) Updates the PDB documentation to refer to PDBv3.3 instead of PDBv3.2.
@mieczyslaw
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@orbeckst, this can be closed as addressed in #2880

PicoCentauri pushed a commit to PicoCentauri/mdanalysis that referenced this issue Mar 30, 2021
@mieczyslaw @PicoCentauri
Write HETATM record types (MDAnalysis#2880)
0f011ac 
Fixes MDAnalysis#1753 and MDAnalysis#2906 

## Overview of work done in this PR
1) PDBWriter will now write out either `ATOM` or `HETATM` entries based on the contents of the atomgroup `record_types` attribute. If the `record_types` attribute is missing, writing will default to `ATOM` entries.
2) Updates the PDB documentation to refer to PDBv3.3 instead of PDBv3.2.
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@orbeckst @mieczyslaw