Adding CA ions to parsing list - proteincomponent.py #265
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I found this missing Ion reccently . We should add it,, as it is frequently used.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #265 +/- ##
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- Coverage 99.20% 98.74% -0.47%
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Files 36 36
Lines 1898 1992 +94
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+ Hits 1883 1967 +84
- Misses 15 25 +10 ☔ View full report in Codecov by Sentry. |
gufe/components/proteincomponent.py
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| negative_ions = ["F", "CL", "Br", "I"] | ||
| positive_ions = ["NA", "MG", "ZN"] | ||
| negative_ions = ["F", "CL", "BR", "I"] | ||
| positive_ions = ["NA", "MG", "CA", "ZN"] |
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Would it make sense to just add every mono and divalent ions that are defined in the AMBER ffxml?
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We're probably replacing this entirely soon, so a small fix is ok for now. I'd be more interested in a test to encode the fix/behaviour
RiesBen
changed the title
was previously looking at the enum values rather than the bond order values
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I checked this new version of the ProteinComponent against the old one and both give the same formal charges for the atoms and same bond order for the bonds. |
make ion name not case sensitive, Cl == CL ignore trailing numbers on ion names, allows CL1 for CL
gufe/components/proteincomponent.py
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| if atom_name in positive_ions: | ||
| if atom_name.upper() in positive_ions: | ||
| fc = default_valence # e.g. Sodium ions | ||
| elif atom_name in negative_ions: | ||
| elif atom_name.upper() in negative_ions: | ||
| fc = - default_valence # e.g. Chlorine ions | ||
| elif atom_name.strip(string.digits).upper() in positive_ions: | ||
| # catches cases like 'CL1' as name | ||
| fc = default_valence | ||
| elif atom_name.strip(string.digits).upper() in negative_ions: | ||
| fc = - default_valence |
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this could be simplified, right?
if atom_name.strip(string.digits).upper() in positive_ions:
# catches cases like 'CL1' as name
fc = default_valence
elif atom_name.strip(string.digits).upper() in negative_ions:
fc = - default_valence
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hmm yeah you're right here
I found this missing Ion reccently . We should add it,, as it is frequently used.