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Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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Convert input format to YAML and front-end to Python #16

Open sobolevnrm opened 10 years ago

sobolevnrm commented 10 years ago

example

lizutah commented 10 years ago

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.

sobolevnrm commented 4 years ago

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

sobolevnrm commented 3 years ago

Deprecate the current APBS input format and replace with YAML

sobolevnrm commented 3 years ago

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 commented 3 years ago

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