FetchLocal - Revision history

Cchem: 3 revisions

2016-10-17T00:06:59Z

3 revisions

Hongbo zhu: add async to cmd.fetch. It was in the API of fetchlocal but not passed to fetch.

2016-10-06T07:27:26Z

add async to cmd.fetch. It was in the API of fetchlocal but not passed to fetch.

Pyadmin: 1 revision

2014-03-28T02:16:24Z

1 revision

Hongbo zhu: /* See Also */ add reference to Psico

2012-10-16T13:20:45Z

Hongbo zhu: /* The Code */ load(object=name)

2012-09-21T14:19:06Z

The Code: load(object=name)

Hongbo zhu: create a new page FetchLocal for script fetchlocal

2012-09-21T11:46:06Z

create a new page FetchLocal for script fetchlocal

New page

== Overview ==
Try fetching local copy of PDB files before going on internet to fetch a remote copy.

Sometimes you have a local copy of the PDB structure files, or [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html biological unit] files. They are, however, usually organized into sub-directories (for a good reason). Setting [[Fetch_Path]] to the top directory will not make PyMOL to use local files before go on internet to fetch a remote copy. This script extends the functionality of the PyMOL command [[Fetch]] by searching local sub-directories for target files first.

The search order of the script: 1. local copy of PDB; 2. [[Fetch_Path]]; 3. remote repository ([[Fetch_Host]]).

== Note ==
The script only copes with <tt>.pdb</tt> and <tt>.pdb1</tt> (or <tt>.pdb2</tt>, <tt>.pdb3</tt>, ...) file types.

== Syntax ==
See [[Fetch]]

== The Code ==
<source lang="python">

""" 2012_09_18, Hongbo Zhu <hongbo.zhu.cn gmail>
DESCRIPTION: Look for pdb* on local disk before fetching remotely.
"""
import os
import cmd

#####################
# user configuration
localpdbdir = '/your/dir/to/PDB/divided'
localbudir = '/your/dir/to/PDB_BU/divided' # set to '' (empty string) if N/A

def fetchlocal(code, name='', state=0, finish=1, discrete=-1,
multiplex=-2, zoom=-1, type='pdb', async=-1, path=None,
file=None, quiet=1):
""" Default parameters are the same as in function definition for fetch()
in file ./modules/pymol/importing.py
"""
if type.startswith('pdb'): # pdb files, or biological unit files .pdb1 .pdb2 etc.
if type == 'pdb': # pdb files
localdir = localpdbdir
else:
localdir = localbudir
for c in string.split(str(code)):
subdir = c.lower()[1:3]
if type == 'pdb':
if os.path.isfile('%s/%s/pdb%s.ent.gz' % (localdir,subdir,c.lower())):
localfn = '%s/%s/pdb%s.ent.gz' % (localdir,subdir,c.lower())
elif os.path.isfile('%s/%s/pdb%s.ent' % (localdir,subdir,c.lower())):
localfn = '%s/%s/pdb%s.ent.gz' % (localdir,subdir,c.lower())
else:
localfn = None
else:
if os.path.isfile('%s/%s/%s.%s.gz' % (localdir,subdir,c.lower(),type)):
localfn = '%s/%s/%s.%s.gz' % (localdir,subdir,c.lower(),type)
elif os.path.isfile('%s/%s/%s.%s' % (localdir,subdir,c.lower(),type)):
localfn = '%s/%s/%s.%s' % (localdir,subdir,c.lower(),type)
else:
localfn = None

if localfn is not None:
print 'Load local file instead of fetching from internet: ', localfn
cmd.load(filename=localfn, object='', format='pdb', state=state,
finish=finish, discrete=discrete, multiplex=multiplex,
zoom=zoom, quiet=quiet)
else: # otherwise hand it over to pymol fetch function
cmd.fetch(c,name,state,finish,discrete,multiplex,zoom,type,path,file,quiet)
else:
cmd.fetch(code,name,state,finish,discrete,multiplex,zoom,type,path,file,quiet)

cmd.extend('fetchlocal', fetchlocal)

</source>

= See Also =
[[Fetch]], [[Fetch_Path]], [[Fetch_Host]]

[[Category:Script_Library]]
[[Category:System_Scripts]]

← Older revision	Revision as of 00:06, 17 October 2016
(No difference)

@@ Line 60: / Line 60: @@
                           zoom=zoom, quiet=quiet)
              else:  # otherwise hand it over to pymol fetch function
-                 cmd.fetch(c,name,state,finish,discrete,multiplex,zoom,type,path,file,quiet)
+                 cmd.fetch(c,name,state,finish,discrete,multiplex,zoom,type,async,path,file,quiet)
      else:
-         cmd.fetch(code,name,state,finish,discrete,multiplex,zoom,type,path,file,quiet)
+         cmd.fetch(code,name,state,finish,discrete,multiplex,zoom,type,async,path,file,quiet)

← Older revision	Revision as of 02:16, 28 March 2014
(No difference)

@@ Line 71: / Line 71: @@
 = See Also =
-[[Fetch]], [[Fetch_Path]], [[Fetch_Host]]
+[[Fetch]], [[Fetch_Path]], [[Fetch_Host]], [[Psico]]
 [[Category:Script_Library]]
 [[Category:System_Scripts]]

@@ Line 56: / Line 56: @@
              if localfn is not None:
                  print 'Load local file instead of fetching from internet: ', localfn
-                 cmd.load(filename=localfn, object='', format='pdb', state=state,
+                 cmd.load(filename=localfn, object=name, format='pdb', state=state,
                           finish=finish, discrete=discrete, multiplex=multiplex,
                           zoom=zoom, quiet=quiet)