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Comments (5)

lizutah avatar lizutah commented on July 19, 2024

Adding Nathan's comment to this issue:
Run apbs from the pdb2pqr command line.
Examine/rethink/re-implement pdb2pka/apbs.py, apbslib.py and _apbslib.so
Create command line interface for inputs to apbs.

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sobolevnrm avatar sobolevnrm commented on July 19, 2024

I'd still like to see this happen but it's not a very high priority.

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sobolevnrm avatar sobolevnrm commented on July 19, 2024

Deprecate the current APBS input format and replace with YAML

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sobolevnrm avatar sobolevnrm commented on July 19, 2024

Here's my plan for this:

  1. Develop a schema. YAML supports JSON-format schemas which can be registered online for others to use.
  2. Implement in standalone Python code that @intendo or someone can integrate later.
  3. Replace existing documentation with documentation of YAML-format input

Please let me know if you have any concerns.

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sobolevnrm avatar sobolevnrm commented on July 19, 2024

Oops -- PR didn't fully resolve this issue.

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