Improving parameterized inferrence #1162
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swails
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Mar 29, 2021
parmed/structure.py
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| # everything else... we don't want __repr__ to be super expensive | ||
| if len(self.bonds) > 0 and self.bonds[0].type is not None: | ||
| retstr.append('; parametrized>') | ||
| if self.atoms[0].type: |
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Suggested change
| if self.atoms[0].type: | |
| if self.atoms[0].atom_type is not UnassignedAtomType and self.atoms[0]._epsilon is None: |
This is probably a better heuristic to use. It's possible to provide parameters without defining an explicit type string, but you really can't provide parameters and have the atoms have an UnassignedAtomType and the nonbonded L-J terms be not set.
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Even better, but shouldn't the condition be the following?
if self.atoms[0].atom_type is not UnassignedAtomType and self.atoms[0]._epsilon is not None: 
Co-authored-by: Jason Swails <[email protected]>
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|
I went with the most logical criterion based on your suggestion: if self.atoms[0].atom_type is UnassignedAtomType and self.atoms[0]._epsilon is None:
retstr.append('; NOT parameterized>')
else:
retstr.append('; parameterized>') |
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In parmed.structure.Structure._ repr _, parameterization is inferred from bonds/bond types. However, for a system of non-bonded parameterized atoms, Structure appears unparameterized. An improvement is suggested here based on atom types.