diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index c2d16bc044e4d8933d3b32e061b4794bff25c1a2..9455000f7d4f4e17155ea7c3ec1abceb376739d3 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -116,25 +116,19 @@ class ReprResult:
:func:`ChainMapper.GetRepr` whether this is backbone only or
full atom lDDT.
:type lDDT: :class:`float`
- :param ref_residues: Qualified names of ref structure, i.e. return values
- of :func:`ost.mol.ResidueHandle.GetQualifiedName`
- :type ref_residues: :class:`list` of :class:`str`
- :param mdl_residues: Same for mdl residues
- :type mdl_residues: :class:`list` of :class:`str`
- :param ref_bb_pos: Representative backbone positions for reference residues.
- Thats CA positions for peptides and C3' positions for
- Nucleotides.
- :type ref_bb_pos: :class:`geom.Vec3List`
+ :param ref_residues: The reference residues
+ :type ref_residues: :class:`list` of :class:`mol.alg.ResidueView`
+ :param mdl_residues: The model residues
+ :type mdl_residues: :class:`list` of :class:`mol.alg.ResidueView`
"""
- def __init__(self, lDDT, ref_residues, mdl_residues, ref_bb_pos,
- mdl_bb_pos):
+ def __init__(self, lDDT, ref_residues, mdl_residues):
self._lDDT = lDDT
self._ref_residues = ref_residues
self._mdl_residues = mdl_residues
- self._ref_bb_pos = ref_bb_pos
- self._mdl_bb_pos = mdl_bb_pos
# lazily evaluated attributes
+ self._ref_bb_pos = None
+ self._mdl_bb_pos = None
self._transform = None
self._superposed_mdl_bb_pos = None
self._bb_rmsd = None
@@ -157,21 +151,17 @@ class ReprResult:
@property
def ref_residues(self):
- """ Qualified names of ref structure residues
+ """ The reference residues
- The return values of :func:`ost.mol.ResidueHandle.GetQualifiedName`
-
- :type: :class:`list` of :class:`str`
+ :type: :class:`list` of :class:`mol.alg.ResidueView`
"""
return self._ref_residues
@property
def mdl_residues(self):
- """ Qualified names of mdl structure residues
-
- The return values of :func:`ost.mol.ResidueHandle.GetQualifiedName`
+ """ The model residues
- :type: :class:`list` of :class:`str`
+ :type: :class:`list` of :class:`mol.alg.ResidueView`
"""
return self._mdl_residues
@@ -183,6 +173,15 @@ class ReprResult:
:type: :class:`geom.Vec3List`
"""
+ if self._ref_bb_pos is None:
+ self._ref_bb_pos = geom.Vec3List()
+ for r in self.ref_residues:
+ at = r.FindAtom("CA")
+ if not at.IsValid():
+ at = r.FindAtom("C3'")
+ if not at.IsValid():
+ raise RuntimeError("Something terrible happened... RUN...")
+ self._ref_bb_pos.append(at.GetPos())
return self._ref_bb_pos
@property
@@ -193,6 +192,15 @@ class ReprResult:
:type: :class:`geom.Vec3List`
"""
+ if self._mdl_bb_pos is None:
+ self._mdl_bb_pos = geom.Vec3List()
+ for r in self.mdl_residues:
+ at = r.FindAtom("CA")
+ if not at.IsValid():
+ at = r.FindAtom("C3'")
+ if not at.IsValid():
+ raise RuntimeError("Something terrible happened... RUN...")
+ self._mdl_bb_pos.append(at.GetPos())
return self._mdl_bb_pos
@property
@@ -281,8 +289,8 @@ class ReprResult:
if self._ost_query is None:
chain_rnums = dict()
for r in self.mdl_residues:
- chname = r.split('.')[0]
- rnum = r.split('.')[1][3:]
+ chname = r.GetChain().GetName()
+ rnum = r.GetNumber().GetNum()
if chname not in chain_rnums:
chain_rnums[chname] = list()
chain_rnums[chname].append(rnum)
@@ -297,8 +305,10 @@ class ReprResult:
"""
json_dict = dict()
json_dict["lDDT"] = self.lDDT
- json_dict["ref_residues"] = self.ref_residues
- json_dict["mdl_residues"] = self.mdl_residues
+ json_dict["ref_residues"] = [r.GetQualifiedName() for r in \
+ self.ref_residues]
+ json_dict["mdl_residues"] = [r.GetQualifiedName() for r in \
+ self.mdl_residues]
json_dict["transform"] = list(self.transform.data)
json_dict["bb_rmsd"] = self.bb_rmsd
json_dict["gdt_8"] = self.gdt_8
@@ -1140,9 +1150,6 @@ class ChainMapper:
for scored_mapping in scored_mappings:
ref_residues = list()
mdl_residues = list()
- ref_bb_pos = geom.Vec3List()
- mdl_bb_pos = geom.Vec3List()
-
for ref_ch_group, mdl_ch_group in zip(substructure_chem_groups,
scored_mapping[1]):
for ref_ch, mdl_ch in zip(ref_ch_group, mdl_ch_group):
@@ -1150,21 +1157,11 @@ class ChainMapper:
aln = substructure_ref_mdl_alns[(ref_ch, mdl_ch)]
for col in aln:
if col[0] != '-' and col[1] != '-':
- ref_r = col.GetResidue(0)
- mdl_r = col.GetResidue(1)
- ref_residues.append(ref_r.GetQualifiedName())
- mdl_residues.append(mdl_r.GetQualifiedName())
- ref_at = ref_r.FindAtom("CA")
- if ref_at is None:
- ref_at = ref_r.FindAtom("C3'")
- mdl_at = mdl_r.FindAtom("CA")
- if mdl_at is None:
- mdl_at = mdl_r.FindAtom("C3'")
- ref_bb_pos.append(ref_at.GetPos())
- mdl_bb_pos.append(mdl_at.GetPos())
+ ref_residues.append(col.GetResidue(0))
+ mdl_residues.append(col.GetResidue(1))
results.append(ReprResult(scored_mapping[0], ref_residues,
- mdl_residues, ref_bb_pos, mdl_bb_pos))
+ mdl_residues))
return results
def GetNMappings(self, model):
diff --git a/modules/mol/alg/tests/test_lddt.py b/modules/mol/alg/tests/test_lddt.py
index f429b60ebaf57c5a63af0aa812ba99d970d6744b..cb8f1d28ad8c910d44954e05758d11c769503607 100644
--- a/modules/mol/alg/tests/test_lddt.py
+++ b/modules/mol/alg/tests/test_lddt.py
@@ -237,7 +237,8 @@ class TestlDDTBS(unittest.TestCase):
ref_bs = ref.Select("grasdf:0=1")
ref_bs = ref_bs.Select("peptide=true")
ref_bs_names = [r.GetQualifiedName() for r in ref_bs.residues]
- self.assertEqual(sorted(ref_bs_names), sorted(bs_repr.ref_residues))
+ repr_bs_names = [r.GetQualifiedName() for r in bs_repr.ref_residues]
+ self.assertEqual(sorted(ref_bs_names), sorted(repr_bs_names))
# everything below basically computes lDDTBS manually and