From ac71ab58cc4050ccb3e51538e8e53cf9beac7135 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 26 Oct 2021 11:32:41 +0200
Subject: [PATCH] Consider file suffix when loading structures in
compare-structures action
If fault_tolerant is enabled, it might happily read a cif file as PDB file.
As a consequence, there are no residues in the returned entity.
---
actions/ost-compare-structures | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 0ae1dad2d..7aaaf6914 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -568,17 +568,26 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False,
entities = list()
if not os.path.isfile(path):
raise IOError("%s is not a file" % path)
- try:
+
+ # Determine file format from suffix.
+ ext = path.split(".")
+ if ext[-1] == "gz":
+ ext = ext[:-1]
+ if len(ext) <= 1:
+ raise RuntimeError(f"Could not determine format of file {path}.")
+ sformat = ext[-1].lower()
+
+ if sformat in ["pdb"]:
entity = LoadPDB(
path,
fault_tolerant=fault_tolerant,
calpha_only=c_alpha_only)
- if not entity.IsValid():
+ if not entity.IsValid() or len(entity.residues) == 0:
raise IOError("Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
entity = _Select(entity)
entities.append(entity)
- except Exception:
+ elif sformat in ["cif", "mmcif"]:
try:
tmp_entity, cif_info = LoadMMCIF(
path,
@@ -623,6 +632,9 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False,
except Exception:
raise
+ else:
+ raise RuntimeError(f"Unsupported file extension found for file {path}.")
+
return entities
--
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