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Fix PolyConf dihedral_solver() bug and quiet irrelevant warnings #73

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Merged
lunamorrow merged 2 commits into from
Feb 18, 2025
Merged

Fix PolyConf dihedral_solver() bug and quiet irrelevant warnings #73

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334842c
Ignore MDAnalysis PDB writer UserWarnings about missing formalcharge …
lunamorrow Feb 18, 2025
8f4e691
Add bandaid fix to make sure that dihedral_solver() fails gracefully …
lunamorrow Feb 18, 2025
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6 changes: 5 additions & 1 deletion polyconf/polyconf/PDB.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#!/usr/bin/env python

import warnings
import MDAnalysis as mda

class PDB:
Expand Down Expand Up @@ -53,6 +53,10 @@ def save(self, dummies="X*", fname="polymer", selectionString = None, gmx = Fals
defaults to False
:type gmx: bool, optional
"""
# ignore MDAnalysis "UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'"
warnings.simplefilter('ignore', category=UserWarning, lineno=1154)
# ignore MDAnalysis "UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'"
warnings.simplefilter('ignore', category=UserWarning, lineno=1201)
if selectionString:
if gmx:
self.select_atoms(f"{selectionString} and not name {dummies}").atoms._write(f"{fname}.gro")
Expand Down
1 change: 1 addition & 0 deletions polyconf/polyconf/Polymer.py
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Expand Up @@ -446,6 +446,7 @@ def dihedral_solver(self,pairlist,dummies='X*',cutoff=0.7,backwards_only=True):
if i==0: # yes, and this is the first monomer
failed=True
done=True
i=-1 # force exit from while loops upon failure
else: # yes, and this is not the first monomer
#print(i,tries[i])
retry=True
Expand Down