From eac0800a04e8ec835111af929bc939f5b45c8b61 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Fri, 23 Apr 2010 08:12:00 +0000
Subject: [PATCH] calpha_only option for ModelRepository and LoadPDB
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2111 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/pymod/__init__.py | 6 ++++--
modules/io/pymod/repository.py | 5 +++--
2 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index e92e93249..344f97129 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -21,7 +21,7 @@ from ost import mol,conop
def LoadPDB(filename, restrict_chains="", no_hetatms=False,
fault_tolerant=False, load_multi=False,
- join_spread_atom_records=False):
+ join_spread_atom_records=False, calpha_only=False):
"""
Load PDB file from disk.
@@ -46,8 +46,10 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
reader=PDBReader(filename)
flags=0
+ if calpha_only:
+ flags|=PDB.CALPHA_ONLY
if fault_tolerant:
- flags=PDB.SKIP_FAULTY_RECORDS
+ flags|=PDB.SKIP_FAULTY_RECORDS
if no_hetatms:
flags|=PDB.NO_HETATMS
if join_spread_atom_records:
diff --git a/modules/io/pymod/repository.py b/modules/io/pymod/repository.py
index ac6c1d1c2..a0ed9cbdd 100644
--- a/modules/io/pymod/repository.py
+++ b/modules/io/pymod/repository.py
@@ -41,9 +41,10 @@ class ModelRepository:
basename=self.file_pattern_ % {'id' : pdb_id, 'chain' :chain, 'dir' : pdb_id[1:3]}
return os.path.join(self.directory_, basename)
- def Load(self, pdb_id, chains=""):
+ def Load(self, pdb_id, chains='', calpha_only=False, fault_tolerant=False):
return io.LoadPDB(self.FilenameForModel(pdb_id, chains),
- chains)
+ chains, calpha_only=calpha_only,
+ fault_tolerant=fault_tolerant)
def LoadMulti(self, pdb_id, chains=""):
return io.LoadMultiPDB(self.FilenameForModel(pdb_id, chains))
--
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