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Unverified Commit ccb50271 authored by Xavier Robin's avatar Xavier Robin
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feat: SCHWED-5481 validate with fault_tolerant

parent 29b2180b
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......@@ -234,7 +234,7 @@ def _LoadLigand(file):
return ligand_ent.Copy()
def _Validate(structure, ligands, legend):
def _Validate(structure, ligands, legend, fault_tolerant=False):
"""Validate the structure.
If fault_tolerant is True, only warns in case of problems. If False,
......@@ -245,9 +245,12 @@ def _Validate(structure, ligands, legend):
if ligands is not None:
for residue in structure.residues:
if residue.is_ligand:
warnings.warn("Ligand residue %s found in %s polymer structure" %(
residue.qualified_name, legend
), UserWarning)
msg = "Ligand residue %s found in %s polymer structure" %(
residue.qualified_name, legend)
if fault_tolerant:
ost.LogWarning(msg)
else:
raise ValueError(msg)
def _Process(model, model_ligands, reference, reference_ligands, args):
......@@ -328,8 +331,10 @@ def _Main():
reference_ligands = _LoadLigands(args.reference_ligands)
# Validate
_Validate(model, model_ligands, "model")
_Validate(reference, reference_ligands, "reference")
_Validate(model, model_ligands, "model",
fault_tolerant = args.fault_tolerant)
_Validate(reference, reference_ligands, "reference",
fault_tolerant = args.fault_tolerant)
out = _Process(model, model_ligands, reference, reference_ligands, args)
......
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