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Fix amber stdout parsing #56

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merged 7 commits into from
Apr 27, 2023
Merged

Fix amber stdout parsing #56

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1b571d9
Fix electrostatic energy record key.
lohedges Apr 26, 2023
936b32f
Merge branch 'devel' into fix_amber_stdout_parsing
lohedges Apr 26, 2023
90958f6
Handle multiple degrees of freedom when parsing AMBER FEP output.
lohedges Apr 26, 2023
a885339
Store stdout dictionaries in a list to simplify code.
lohedges Apr 27, 2023
1e06b41
Map universal key to original record key and add method to invert.
lohedges Apr 27, 2023
f8eb6b8
Expose missing stdout_key dictionary.
lohedges Apr 27, 2023
485d2c6
Guard against missing keys. [ci skip]
lohedges Apr 27, 2023
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2 changes: 1 addition & 1 deletion python/BioSimSpace/Process/_amber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -895,7 +895,7 @@ def getElectrostaticEnergy(self, time_series=False, block="AUTO"):
energy : :class:`Energy <BioSimSpace.Types.Energy>`
The electrostatic energy.
"""
return self.getRecord("EELECT", time_series, _Units.Energy.kcal_per_mol, block)
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Why is this change?

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Because the key is wrong. All output that I generate for any protocol has EELEC, not EELECT. The commit message explains the reason for the change.

return self.getRecord("EELEC", time_series, _Units.Energy.kcal_per_mol, block)

def getCurrentElectrostaticEnergy(self, time_series=False):
"""
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