From 0a25424d90ede5dc08e7bda8720c0105e85a811b Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 5 Sep 2012 17:19:17 +0200
Subject: [PATCH] Fixed loop indentation in the PDBize function for bio units,
leading to exponential running time/ memory consumption. This problem only
affected a fraction of PDB entries.
---
CHANGELOG.txt | 5 +++++
modules/io/pymod/__init__.py | 33 ++++++++++++++++++++-------------
2 files changed, 25 insertions(+), 13 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 4151f7269..af0072594 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,8 @@
+Changes in Release 1.2.2
+
+ * Fixed loop indentation in the PDBize function for bio units, leading to
+ exponential running time/ memory consumption. This problem only affected a
+ fraction of PDB entries.
Changes in Release 1.2.1
--------------------------------------------------------------------------------
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 0d6d0e142..71ea2ec6c 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -387,19 +387,19 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
tr = geom.Mat4()
tr = trans * rot
trans_matrices.append(tr)
- for op_n in range(1, len(operations)):
- tmp_ops = list()
- for o in operations[op_n]:
- rot = geom.Mat4()
- rot.PasteRotation(o.rotation)
- trans = geom.Mat4()
- trans.PasteTranslation(o.translation)
- tr = geom.Mat4()
- tr = trans * rot
- for t_o in trans_matrices:
- tp = t_o * tr
- tmp_ops.append(tp)
- trans_matrices = tmp_ops
+ for op_n in range(1, len(operations)):
+ tmp_ops = list()
+ for o in operations[op_n]:
+ rot = geom.Mat4()
+ rot.PasteRotation(o.rotation)
+ trans = geom.Mat4()
+ trans.PasteTranslation(o.translation)
+ tr = geom.Mat4()
+ tr = trans * rot
+ for t_o in trans_matrices:
+ tp = t_o * tr
+ tmp_ops.append(tp)
+ trans_matrices = tmp_ops
# select chains into a view as basis for each transformation
assu = asu.Select('cname=' + ','.join(biounit.GetChainList()))
# use each transformation on the view, store as entity and transform, PDBize
@@ -425,6 +425,9 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
edi.SetChainDescription(new_chain, chain.description)
edi.SetChainType(new_chain, chain.type)
new_chain.SetStringProp('original_name', chain.name)
+ if chain.HasProp("pdb_auth_chain_name"):
+ new_chain.SetStringProp("pdb_auth_chain_name",
+ chain.GetStringProp("pdb_auth_chain_name"))
for res in chain.residues:
new_res = edi.AppendResidue(new_chain, res.name, res.number)
_CopyAtoms(res, new_res, edi, tr)
@@ -455,6 +458,10 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
mol.ResNum(last_rnum+1, ins_code))
new_res.SetStringProp('description', chain.description)
new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ new_res.SetStringProp("original_name", chain.name)
+ if chain.HasProp("pdb_auth_chain_name"):
+ new_res.SetStringProp("pdb_auth_chain_name",
+ chain.GetStringProp("pdb_auth_chain_name"))
ins_code = chr(ord(ins_code)+1)
_CopyAtoms(res, new_res, edi, tr)
conop.ConnectAll(pdb_bu)
--
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