From ccb50271561cf5a9151e2288f323ab9adb810a55 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 2 Mar 2023 18:58:26 +0100
Subject: [PATCH] feat: SCHWED-5481 validate with fault_tolerant
---
actions/ost-compare-ligand-structures | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index e24258c64..c21537483 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -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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