From e79926dde413f6e2d995c298f3974fbba081521d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 1 Mar 2023 12:05:45 +0100
Subject: [PATCH] compare-structures: add fault_tolerant parsing
---
actions/ost-compare-structures-new | 21 ++++++++++++++++-----
1 file changed, 16 insertions(+), 5 deletions(-)
diff --git a/actions/ost-compare-structures-new b/actions/ost-compare-structures-new
index 0f66704b6..1e7460264 100644
--- a/actions/ost-compare-structures-new
+++ b/actions/ost-compare-structures-new
@@ -141,6 +141,14 @@ def _ParseArgs():
help=("Use this suffix to dump structures.\n"
"Defaults to .compare.structures.pdb."))
+ parser.add_argument(
+ "-ft",
+ "--fault-tolerant",
+ dest="fault_tolerant",
+ default=False,
+ action="store_true",
+ help=("Fault tolerant parsing."))
+
parser.add_argument(
"--lddt",
dest="lddt",
@@ -266,7 +274,7 @@ def _ParseArgs():
return parser.parse_args()
-def _LoadStructure(structure_path, sformat=None):
+def _LoadStructure(structure_path, sformat=None, fault_tolerant=False):
"""Read OST entity either from mmCIF or PDB.
The returned structure has structure_path attached as structure name
@@ -289,11 +297,11 @@ def _LoadStructure(structure_path, sformat=None):
ost.PushVerbosityLevel(ost.LogLevel.Error)
# Load the structure
if sformat in ["mmcif", "cif"]:
- entity = io.LoadMMCIF(structure_path)
+ entity = io.LoadMMCIF(structure_path, fault_tolerant = fault_tolerant)
if len(entity.residues) == 0:
raise Exception(f"No residues found in file: {structure_path}")
elif sformat == "pdb":
- entity = io.LoadPDB(structure_path)
+ entity = io.LoadPDB(structure_path, fault_tolerant = fault_tolerant)
if len(entity.residues) == 0:
raise Exception(f"No residues found in file: {structure_path}")
else:
@@ -403,8 +411,11 @@ def _Main():
args = _ParseArgs()
try:
reference = _LoadStructure(args.reference,
- sformat=args.reference_format)
- model = _LoadStructure(args.model, sformat=args.model_format)
+ sformat=args.reference_format,
+ fault_tolerant = args.fault_tolerant)
+ model = _LoadStructure(args.model,
+ sformat=args.model_format,
+ fault_tolerant = args.fault_tolerant)
out = _Process(model, reference, args)
out["status"] = "SUCCESS"
with open(args.output, 'w') as fh:
--
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