From 85f84516e614842a056ca23d184deb44f3bacdb3 Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 13 Jul 2010 09:39:45 +0000
Subject: [PATCH] added load pdb from pdb.org: io.LoadPDB(<ID>,remote=True)
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2557 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/pymod/__init__.py | 38 +++++++++++++++++++++++++++++++++++-
1 file changed, 37 insertions(+), 1 deletion(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 095cacb89..5455ceb9e 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -16,12 +16,38 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
+import os, tempfile, ftplib, httplib
+
from _io import *
from ost import mol, conop
+def __GetModelFromPDB(model_id, output_dir, file_pattern='pdb%s.ent.gz'):
+ file_name = file_pattern % model_id
+ file_path = os.path.join(output_dir,file_name)
+ try:
+ server="ftp.wwpdb.org"
+ ftp=ftplib.FTP(server,"anonymous","user@")
+ ftp.cwd("pub/pdb/data/structures/all/pdb")
+ ftp_retrfile=open(file_path,"wb")
+ ftp.retrbinary("RETR "+file_name,ftp_retrfile.write)
+ ftp_retrfile.close()
+ except:
+ conn=httplib.HTTPConnection('www.pdb.org')
+ conn.request('GET', '/pdb/files/%s.pdb.gz' % model_id )
+ response=conn.getresponse()
+ if response.status==200:
+ data=response.read()
+ f=open(os.path.join(output_dir, file_pattern % model_id), 'w+')
+ f.write(data)
+ f.close()
+ else:
+ conn.close()
+ return False
+ return os.path.getsize(file_path) > 0
+
def LoadPDB(filename, restrict_chains="", no_hetatms=False,
fault_tolerant=False, load_multi=False,
- join_spread_atom_records=False, calpha_only=False):
+ join_spread_atom_records=False, calpha_only=False, remote=False):
"""
Load PDB file from disk and returns one or more entities. Several options
allow to customize the exact behaviour of the PDB import.
@@ -41,12 +67,22 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
:param join_spread_atom_records: If set to true, atom records belonging to the
same residue are joined, even if they do not appear sequentially in the PDB
file.
+
+ :param remote: If set to true, the method tries to load the pdb from the remote
+ pdb repository www.pdb.org.
:rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is
True.
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or
inexistent file
"""
+ if remote:
+ output_dir = tempfile.gettempdir()
+ if __GetModelFromPDB(filename, output_dir):
+ filename = os.path.join(output_dir, 'pdb%s.ent.gz' % filename)
+ else:
+ raise IOError('Can not load PDB %s from www.pdb.org'%filename)
+
conop_inst=conop.Conopology.Instance()
builder=conop_inst.GetBuilder("DEFAULT")
reader=PDBReader(filename)
--
GitLab