diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 57d42cce3e00d0a33173191e1d5a49a976f296d5..c1e873f421a1c567607832c499ef97297bb34f24 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -139,11 +139,11 @@ def _ParseArgs():
dest="model_biounit",
required=False,
default=None,
- type=int,
+ type=str,
help=("Only has an effect if model is in mmcif format. By default, "
"the asymmetric unit (AU) is used for scoring. If there are "
"biounits defined in the mmcif file, you can specify the "
- "(0-based) index of the one which should be used."))
+ "ID (as a string) of the one which should be used."))
parser.add_argument(
"-rb",
@@ -151,11 +151,11 @@ def _ParseArgs():
dest="reference_biounit",
required=False,
default=None,
- type=int,
+ type=str,
help=("Only has an effect if reference is in mmcif format. By default, "
"the asymmetric unit (AU) is used for scoring. If there are "
"biounits defined in the mmcif file, you can specify the "
- "(0-based) index of the one which should be used."))
+ "ID (as a string) of the one which should be used."))
parser.add_argument(
"-ft",
@@ -317,7 +317,7 @@ def _GetStructureFormat(structure_path, sformat=None):
f"file {structure_path}.")
-def _LoadStructure(structure_path, sformat, fault_tolerant, bu_idx):
+def _LoadStructure(structure_path, sformat, fault_tolerant, bu_id):
"""Read OST entity either from mmCIF or PDB.
The returned structure has structure_path attached as structure name
@@ -329,24 +329,20 @@ def _LoadStructure(structure_path, sformat, fault_tolerant, bu_idx):
ost.PushVerbosityLevel(ost.LogLevel.Error)
# Load the structure
if sformat == "mmcif":
- if bu_idx is not None:
+ if bu_id is not None:
cif_entity, cif_seqres, cif_info = \
io.LoadMMCIF(structure_path, info=True, seqres=True,
fault_tolerant=fault_tolerant)
- if len(cif_info.biounits) == 0:
- raise RuntimeError(f"No biounit found - requested index"
- f" {bu_idx}.")
- elif bu_idx < 0:
- raise RuntimeError(f"Invalid biounit - requested index {bu_idx}, "
- f"must be a positive integer or 0.")
- elif bu_idx >= len(cif_info.biounits):
- raise RuntimeError(f"Invalid biounit - requested index {bu_idx}, "
- f"must be < {len(cif_info.biounits)}.")
- biounit = cif_info.biounits[bu_idx]
- entity = ost.mol.alg.CreateBU(cif_entity, biounit)
- if not entity.IsValid():
- raise IOError(
- "Provided file does not contain valid entity.")
+ for biounit in cif_info.biounits:
+ if biounit.id == bu_id:
+ entity = ost.mol.alg.CreateBU(cif_entity, biounit)
+ if not entity.IsValid():
+ raise IOError(
+ "Provided file does not contain valid entity.")
+ break
+ else:
+ raise RuntimeError(f"No biounit found with ID '{bu_id}'.")
+
else:
entity = io.LoadMMCIF(structure_path,
fault_tolerant = fault_tolerant)
@@ -594,13 +590,13 @@ def _Main():
sformat=args.reference_format)
reference = _LoadStructure(args.reference,
sformat=reference_format,
- bu_idx=args.reference_biounit,
+ bu_id=args.reference_biounit,
fault_tolerant = args.fault_tolerant)
model_format = _GetStructureFormat(args.model,
sformat=args.model_format)
model = _LoadStructure(args.model,
sformat=model_format,
- bu_idx=args.model_biounit,
+ bu_id=args.model_biounit,
fault_tolerant = args.fault_tolerant)
# Load ligands
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 78aea3eda6086f3f418cb21cc25c50a016ba8b79..900e9c3f778c7a2b93bc15396c22901d50ec3c79 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -141,11 +141,11 @@ def _ParseArgs():
dest="model_biounit",
required=False,
default=None,
- type=int,
+ type=str,
help=("Only has an effect if model is in mmcif format. By default, "
"the asymmetric unit (AU) is used for scoring. If there are "
"biounits defined in the mmcif file, you can specify the "
- "(0-based) index of the one which should be used."))
+ "ID (as a string) of the one which should be used."))
parser.add_argument(
"-rb",
@@ -153,11 +153,11 @@ def _ParseArgs():
dest="reference_biounit",
required=False,
default=None,
- type=int,
+ type=str,
help=("Only has an effect if reference is in mmcif format. By default, "
"the asymmetric unit (AU) is used for scoring. If there are "
"biounits defined in the mmcif file, you can specify the "
- "(0-based) index of the one which should be used."))
+ "ID (as a string) of the one which should be used."))
parser.add_argument(
"-rna",
@@ -563,7 +563,7 @@ def _GetStructureFormat(structure_path, sformat=None):
raise Exception(f"Unknown/unsupported file format found for "
f"file {structure_path}.")
-def _LoadStructure(structure_path, sformat, fault_tolerant, bu_idx):
+def _LoadStructure(structure_path, sformat, fault_tolerant, bu_id):
"""Read OST entity either from mmCIF or PDB.
The returned structure has structure_path attached as structure name
@@ -575,24 +575,19 @@ def _LoadStructure(structure_path, sformat, fault_tolerant, bu_idx):
ost.PushVerbosityLevel(ost.LogLevel.Error)
# Load the structure
if sformat == "mmcif":
- if bu_idx is not None:
+ if bu_id is not None:
cif_entity, cif_seqres, cif_info = \
io.LoadMMCIF(structure_path, info=True, seqres=True,
fault_tolerant=fault_tolerant)
- if len(cif_info.biounits) == 0:
- raise RuntimeError(f"No biounit found - requested index"
- f" {bu_idx}.")
- elif bu_idx < 0:
- raise RuntimeError(f"Invalid biounit - requested index {bu_idx}, "
- f"must be a positive integer or 0.")
- elif bu_idx >= len(cif_info.biounits):
- raise RuntimeError(f"Invalid biounit - requested index {bu_idx}, "
- f"must be < {len(cif_info.biounits)}.")
- biounit = cif_info.biounits[bu_idx]
- entity = ost.mol.alg.CreateBU(cif_entity, biounit)
- if not entity.IsValid():
- raise IOError(
- "Provided file does not contain valid entity.")
+ for biounit in cif_info.biounits:
+ if biounit.id == bu_id:
+ entity = ost.mol.alg.CreateBU(cif_entity, biounit)
+ if not entity.IsValid():
+ raise IOError(
+ "Provided file does not contain valid entity.")
+ break
+ else:
+ raise RuntimeError(f"No biounit found with ID '{bu_id}'.")
else:
entity = io.LoadMMCIF(structure_path,
fault_tolerant = fault_tolerant)
@@ -870,13 +865,13 @@ def _Main():
sformat=args.reference_format)
reference = _LoadStructure(args.reference,
sformat=reference_format,
- bu_idx=args.reference_biounit,
+ bu_id=args.reference_biounit,
fault_tolerant = args.fault_tolerant)
model_format = _GetStructureFormat(args.model,
sformat=args.model_format)
model = _LoadStructure(args.model,
sformat=model_format,
- bu_idx=args.model_biounit,
+ bu_id=args.model_biounit,
fault_tolerant = args.fault_tolerant)
out = _Process(model, reference, args, model_format, reference_format)