diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 12944128409d41b4cc7f3964d8d33f6c34d71e76..b7147b5f3d5859a820fcf5f4250e3908a1d3c875 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -1,6 +1,7 @@
import numpy as np
from ost import mol
+from ost import conop
class SymmetrySettings:
@@ -87,15 +88,17 @@ class lDDTScorer:
:param target: The target
:type target: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param compound_lib: Compound library from which a compound for each residue
- is extracted based on its name. Atoms defined in the
- compound are searched in the residue and build the
- reference for scoring. If the residue has atoms with
- names ["A", "B", "C"] but the corresponding compound
- only has ["A", "B"], "A" and "B" are considered for
- scoring. If the residue has atoms ["A", "B"] but the
- compound has ["A", "B", "C"], "C" is considered missing
- and does not influence scoring, even if present in the
- model.
+ is extracted based on its name. Uses
+ :func:`ost.conop.GetDefaultLib` if not given, raises
+ if this returns no valid compound library. Atoms
+ defined in the compound are searched in the residue and
+ build the reference for scoring. If the residue has
+ atoms with names ["A", "B", "C"] but the corresponding
+ compound only has ["A", "B"], "A" and "B" are
+ considered for scoring. If the residue has atoms
+ ["A", "B"] but the compound has ["A", "B", "C"], "C" is
+ considered missing and does not influence scoring, even
+ if present in the model.
:type compound_lib: :class:`ost.conop.CompoundLib`
:param inclusion_radius: All pairwise distances < *inclusion_radius* are
considered for scoring
@@ -146,7 +149,7 @@ class lDDTScorer:
def __init__(
self,
target,
- compound_lib,
+ compound_lib=None,
inclusion_radius=15,
sequence_separation=0,
symmetry_settings=None,
@@ -157,6 +160,11 @@ class lDDTScorer:
self.target = target
self.inclusion_radius = inclusion_radius
self.sequence_separation = sequence_separation
+ if compound_lib is None:
+ compound_lib = conop.GetDefaultLib()
+ if compound_lib is None:
+ raise RuntimeError("No compound_lib given and conop.GetDefaultLib "
+ "returns no valid compound library")
self.compound_lib = compound_lib
if symmetry_settings is None:
self.symmetry_settings = GetDefaultSymmetrySettings()
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 38727ea1c650d13099097fa7ead8ef9d7d175967..e5ab8d1d76c2a30ac614f81cbead719276ad875d 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -1244,7 +1244,7 @@ class OligoLDDTScorer(object):
raise RuntimeError("OligolDDT computation requires a compound library!")
r = self.settings.radius
seq_sep = self.settings.sequence_separation
- self._lddt_scorer = lddt.lDDTScorer(self.ref, conop.GetDefaultLib(),
+ self._lddt_scorer = lddt.lDDTScorer(self.ref,
inclusion_radius = r,
sequence_separation = seq_sep)
return self._lddt_scorer
diff --git a/modules/mol/alg/tests/test_lddt.py b/modules/mol/alg/tests/test_lddt.py
index 84c274ac7ddca5864dc0bc92875c547828103f40..52598fdc83d8a49c6ba1b7a6bf71af19f13dc83b 100644
--- a/modules/mol/alg/tests/test_lddt.py
+++ b/modules/mol/alg/tests/test_lddt.py
@@ -25,7 +25,7 @@ class TestlDDT(unittest.TestCase):
target = _LoadFile("7SGN_C_target.pdb")
# do awesome implementation
- scorer = lDDTScorer(target, conop.GetDefaultLib())
+ scorer = lDDTScorer(target)
aws_score, aws_per_res_scores = scorer.lDDT(model)
# do reference implementation
@@ -51,7 +51,7 @@ class TestlDDT(unittest.TestCase):
target = _LoadFile("7W1F_B_target.pdb")
# do awesome implementation
- scorer = lDDTScorer(target, conop.GetDefaultLib())
+ scorer = lDDTScorer(target)
aws_score, aws_per_res_scores = scorer.lDDT(model)
# do reference implementation
@@ -80,7 +80,7 @@ class TestlDDT(unittest.TestCase):
target = ent_full.Select('peptide=true and cname=A,B')
# we use functionality from QS-scorer to derive a mapping
qs_scorer = QSscorer(model, target)
- lddt_scorer = lDDTScorer(target, conop.GetDefaultLib())
+ lddt_scorer = lDDTScorer(target)
score, per_res_scores = lddt_scorer.lDDT(model,
chain_mapping=qs_scorer.chain_mapping)
@@ -113,7 +113,7 @@ class TestlDDT(unittest.TestCase):
# we use functionality from QS-scorer to derive a mapping
qs_scorer = QSscorer(model, target)
- lddt_scorer = lDDTScorer(target, conop.GetDefaultLib())
+ lddt_scorer = lDDTScorer(target)
# naively running lDDT will fail, as residue-residue mapping happens
# with resnums. Since we shifted that stuff above we'll get an error
@@ -143,25 +143,20 @@ class TestlDDT(unittest.TestCase):
def test_lDDT_seqsep(self):
target = _LoadFile("7SGN_C_target.pdb")
with self.assertRaises(NotImplementedError):
- scorer = lDDTScorer(target, conop.GetDefaultLib(),
- sequence_separation=42)
- scorer = lDDTScorer(target, conop.GetDefaultLib(),
- sequence_separation=0)
+ scorer = lDDTScorer(target, sequence_separation=42)
+ scorer = lDDTScorer(target, sequence_separation=0)
def test_calpha(self):
model = _LoadFile("7SGN_C_model.pdb")
target = _LoadFile("7SGN_C_target.pdb")
# do scoring and select aname=CA
- scorer = lDDTScorer(target.Select("aname=CA"),
- conop.GetDefaultLib())
+ scorer = lDDTScorer(target.Select("aname=CA"))
score_one, per_res_scores_one = scorer.lDDT(model)
score_two, per_res_scores_two = scorer.lDDT(model.Select("aname=CA"))
# no selection, just setting calpha flag should give the same
- scorer = lDDTScorer(target,
- conop.GetDefaultLib(),
- calpha=True)
+ scorer = lDDTScorer(target, calpha=True)
score_three, per_res_scores_three = scorer.lDDT(model)
# check
@@ -181,8 +176,7 @@ class TestlDDT(unittest.TestCase):
ed.RenameResidue(model.residues[42], "asdf")
# do scoring and select aname=CA
- scorer = lDDTScorer(target.Select("aname=CA"),
- conop.GetDefaultLib())
+ scorer = lDDTScorer(target.Select("aname=CA"))
with self.assertRaises(RuntimeError):
scorer.lDDT(model)