Difference between revisions of "LoadDir"

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m
Line 33: Line 33:
 
from glob import glob
 
from glob import glob
 
from os.path import sep, basename
 
from os.path import sep, basename
from string import split
 
  
 
def loadDir(dirName=".", suff="pdb", group=None):
 
def loadDir(dirName=".", suff="pdb", group=None):
Line 61: Line 60:
 
         """
 
         """
  
        if "." in suff:
+
         g = dirName + sep + "*." + suff.split(".")[-1]
                idx = len(split(suff, "."))-1
 
        else:
 
                idx = 0
 
 
 
         g = dirName + sep + "*." + split(suff, ".")[idx]
 
  
 
         for c in glob( g ):
 
         for c in glob( g ):
Line 72: Line 66:
  
 
                 if ( group != None ):
 
                 if ( group != None ):
                         cmd.group( group, split(basename(c), ".")[0], "add" )
+
                         cmd.group( group, basename(c).split(".")[0], "add" )
  
 
cmd.extend("loadDir", loadDir)
 
cmd.extend("loadDir", loadDir)

Revision as of 03:05, 27 November 2009

Overview

Load all files of the suffix suff from the directory dirName, where suff and dirName are function parameters.

Install

  1. copy the source below to the a file called "loadDir.pml" somewhere on your computer
  2. load the file with "run /your/path/toLoadDir/loadDir.pml"
  3. run loadDir. See examples below.

Examples

# load the script
run ~/loadDir.pml

# load all SD files from /tmp
loadDir /tmp, sdf
loadDir /tmp, .sdf
loadDir /tmp, *.sdf
# even stupid stuff works; hopefully as one would want.
# load all PDBs from /tmp
loadDir /tmp, foo.woo.pdb

# load all the PDBs in all the directories under ./binders/ERK
loadDir ./binders/ERK/*, .pdb

# load the PDBs into groups: now we can load all the files in the tree under
# ./ERK into the group "ERK" and the files from ./SYK into the group "SYK"
loadDir ./binders/ERK/*, .pdb, group=ERKb
loadDir ./binders/SYK/*, .pdb, group=SYKb

The Code

from glob import glob
from os.path import sep, basename

def loadDir(dirName=".", suff="pdb", group=None):
        """
        Loads all files with the suffix suff (the input parameter) from the directory dirName).

        dirName:        directory path
        suff:           file suffix.  Should be simply "pdb" or "sdf" or similar.  Will accept the
                        wildcard and dot in case the user doesn't read this.  So, "*.pdb", ".pdb",
                        and "pdb" should work.  The suffix can be anything valid that PyMOL knows
                        how to natively load.
        group:          groupName to add the files to.

        example:
                # load all the PDBs in the current directory
                loadDir

                # load all SD files from /tmp
                loadDir /tmp, "sdf"

        notes:
                make sure you call this script w/o quotes around your parameters:
                        loadDir ., .pdb
                as opposed to
                        loadDir ".", "*.pdb"
                Use the former.
        """

        g = dirName + sep + "*." + suff.split(".")[-1]

        for c in glob( g ):
                cmd.load(c)

                if ( group != None ):
                        cmd.group( group, basename(c).split(".")[0], "add" )

cmd.extend("loadDir", loadDir)