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Raise an issue if a link is not applied correctly #325

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Raise an issue if a link is not applied correctly #325

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6 changes: 6 additions & 0 deletions polyply/src/gen_itp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,12 @@ def gen_params(name="polymer", outpath=Path("polymer.itp"), inpath=[], lib=None,
LOGGER.info("applying links between residues", type="step")
meta_molecule = ApplyLinks().run_molecule(meta_molecule)

#Check missing edges and raise issues if links between amino acids are not applied.
#Bug if the backbone is correct links between amino acids in a chain are not applied correctly
for missing in find_missing_edges(meta_molecule, meta_molecule.molecule):
msg = "Link between residue {idxA} {resA} and residue {idxB} {resB} was not applied."
LOGGER.warning(msg, **missing)
Comment on lines +105 to +109
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Instead of just adding this line we should check if there are missing edges and then raise a general error message like the "disconnected molecule warning" and then proceed to list the edges. The connected molecule check becomes then redundant and can be removed.


# Raise warning if molecule is disconnected
if not nx.is_connected(meta_molecule.molecule):
LOGGER.warning("Your molecule consists of disjoint parts."
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