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Published 20 hours ago • verified publisher icon Electrostatics

Convert input format to YAML and front-end to Python

Open sobolevnrm opened this issue 11 years ago • 5 comments

  • Allow better integration with other codes.
  • Support more robust input file parsing

example

sobolevnrm avatar Feb 21 '14 04:02 sobolevnrm

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.

lizutah avatar Apr 22 '14 22:04 lizutah

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

sobolevnrm avatar Apr 18 '20 22:04 sobolevnrm

Deprecate the current APBS input format and replace with YAML

sobolevnrm avatar Jan 02 '21 23:01 sobolevnrm

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.

sobolevnrm avatar Apr 01 '21 14:04 sobolevnrm

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

sobolevnrm avatar Jun 07 '21 19:06 sobolevnrm