From 90d361f24675d53a880017d8d7ccd0952b3523b5 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 2 Feb 2024 16:12:03 +0100
Subject: [PATCH] fix: clean error message for missing compound lib
Until now, the actions were failing with somewhat cryptic messages
raised from arbitrary locations. This one should be more user-friendly.
---
actions/ost-compare-ligand-structures | 12 ++++++++++++
actions/ost-compare-structures | 11 +++++++++++
2 files changed, 23 insertions(+)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index e8af175af..dd82320f1 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -56,6 +56,7 @@ and "unassigned_reference_ligands".
import argparse
import json
import os
+import sys
import traceback
import ost
@@ -295,6 +296,16 @@ def _ParseArgs():
return parser.parse_args()
+def _CheckCompoundLib():
+ clib = ost.conop.GetDefaultLib()
+ if not clib:
+ ost.LogError("A compound library is required for this action. "
+ "Please refer to the OpenStructure website: "
+ "https://openstructure.org/docs/conop/compoundlib/.")
+ sys.tracebacklimit = 0
+ raise RuntimeError("No compound library found")
+
+
def _GetStructureFormat(structure_path, sformat=None):
"""Get the structure format and return it as "pdb" or "mmcif".
"""
@@ -580,6 +591,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
def _Main():
args = _ParseArgs()
+ _CheckCompoundLib()
ost.PushVerbosityLevel(args.verbosity)
try:
# Load structures
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 56b040fb3..6cb962d52 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -80,6 +80,7 @@ ost compare-structures -m model.pdb -r reference.cif -c A:B B:A
import argparse
import os
import json
+import sys
import traceback
import math
@@ -526,6 +527,15 @@ def _ParseArgs():
return parser.parse_args()
+def _CheckCompoundLib():
+ clib = ost.conop.GetDefaultLib()
+ if not clib:
+ ost.LogError("A compound library is required for this action. "
+ "Please refer to the OpenStructure website: "
+ "https://openstructure.org/docs/conop/compoundlib/.")
+ sys.tracebacklimit = 0
+ raise RuntimeError("No compound library found")
+
def _RoundOrNone(num, decimals = 3):
""" Helper to create valid JSON output
"""
@@ -852,6 +862,7 @@ def _Process(model, reference, args, model_format, reference_format):
def _Main():
args = _ParseArgs()
+ _CheckCompoundLib()
try:
compute_cad = args.cad_score or args.local_cad_score
if compute_cad and not args.residue_number_alignment:
--
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