fixed modifcation parsing #389
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csbrasnett
commented
Oct 8, 2024
csbrasnett
commented
- -mods flag now only read once for all modifications
- patch all molecule termini as proteins, so any modification in addition to these ones are also applied.
- add more modifications from vermouth to martini3 forcefield
- change logging level and fix tests as per change in record level #385
- -mods flag now only read once for all modifications - patch all molecule termini as proteins, so any modification in addition to these ones are also applied. - add more modifications from vermouth to martini3 forcefield - change logging level and fix tests as per marrink-lab#385
- -mods flag now only read once for all modifications - patch all molecule termini as proteins, so any modification in addition to these ones are also applied. - add more modifications from vermouth to martini3 forcefield - change logging level and fix tests as per marrink-lab#385
# Conflicts: # polyply/src/apply_modifications.py
fgrunewald
requested changes
Oct 8, 2024
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| ;[ edges ] | ||
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are these commented out on purpose?
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yes. For some reason modifications.ff can't be read if they're included, and excluding them doesn't seem to affect them being applied correctly 🤷♂️
polyply/src/apply_modifications.py
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| LOGGER.warning("meta_molecule has come from itp. Will not attempt to modify.") | ||
| LOGGER.info("meta_molecule has come from itp. Will not attempt to modify.") |
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having a test for this one would be ideal
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Re: the ignoring if coming from an itp test, two quick questions:
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- input -seq HIS:5 - with two modifications, HIS1:HIS-HD HIS1:NH2-ter, so the first residue is modified twice, both in its terminal type, and in its histidine variant.
- input -seq HIS:5 - with two modifications, HIS1:HIS-HD HIS1:NH2-ter, so the first residue is modified twice, both in its terminal type, and in its histidine variant.
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