From 38e0537e439b168d0f41e9f5557bb6535e4e8f0b Mon Sep 17 00:00:00 2001
From: juergen <juergen@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 22 Apr 2010 18:58:29 +0000
Subject: [PATCH] adding missing implementation for pdb writer flags
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2108 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/pymod/__init__.py | 48 ++++++++++++++++++++----------------
1 file changed, 27 insertions(+), 21 deletions(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 996ff1ffc..e92e93249 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -20,27 +20,27 @@ from _io import *
from ost import mol,conop
def LoadPDB(filename, restrict_chains="", no_hetatms=False,
- fault_tolerant=False, load_multi=False,
+ fault_tolerant=False, load_multi=False,
join_spread_atom_records=False):
"""
Load PDB file from disk.
-
+
If restrict_chains is not an empty string, only chains listed in the
- string will be imported.
-
+ string will be imported.
+
If fault_tolerant is set to true, the import will succeed, even if the
PDB contains faulty records. The faulty records will be ignored in that
case.
-
+
If not_hetatms is set to True, HETATM records will be ignored
-
+
If load_multi is set to true, a list of entities will be returned instead
of only the first.
-
- If join_spread_atom_records is set to true, atom records belonging to the
+
+ If join_spread_atom_records is set to true, atom records belonging to the
same residue are joined, even if they do not appear sequentially in the PDB
file.
- """
+ """
conop_inst=conop.Conopology.Instance()
builder=conop_inst.GetBuilder("DEFAULT")
reader=PDBReader(filename)
@@ -64,7 +64,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
PDB.PopFlags()
return ent_list
else:
- ent=mol.CreateEntity()
+ ent=mol.CreateEntity()
if reader.HasNext():
reader.Import(ent, restrict_chains)
conop_inst.ConnectAll(builder, ent, 0)
@@ -81,18 +81,24 @@ def SavePDB(models, filename):
if not getattr(models, '__len__', None):
models=[models]
writer=PDBWriter(filename)
- if len(models)>1:
- writer.SetFlags(PDB.WRITE_MULTIPLE_MODELS)
- for model in models:
- writer.Write(model)
-
+ try:
+ if len(models)>1:
+ PDB.PushFlags(PDB.Flags() |PDB.WRITE_MULTIPLE_MODELS)
+ else:
+ PDB.PushFlags(0)
+ for model in models:
+ writer.Write(model)
+ PDB.PopFlags()
+ except:
+ PDB.PopFlags()
+ raise
try:
from ost import img
LoadMap = LoadImage
- SaveMap = SaveImage
+ SaveMap = SaveImage
except ImportError:
pass
-
+
## loads several images and puts them in an ImageList
# \sa \ref fft_li.py "View Fourier Transform Example"
def LoadImageList (files):
@@ -100,14 +106,14 @@ def LoadImageList (files):
for file in files:
image=LoadImage(file)
image_list.append(image)
- return image_list
-
+ return image_list
+
LoadMapList=LoadImageList
## \example fft_li.py
#
-# This scripts loads one or more images and shows their Fourier Transforms on the screen. A viewer
-# is opened for each loaded image. The Fourier Transform honors the origin of the reference system,
+# This scripts loads one or more images and shows their Fourier Transforms on the screen. A viewer
+# is opened for each loaded image. The Fourier Transform honors the origin of the reference system,
# which is assumed to be at the center of the image.
#
# Usage:
--
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