diff CADDSuite-1.6/galaxyconfigs/molFiles.py @ 10:eda78e0f5df6 draft default tip

Deleted selected files

--- a/CADDSuite-1.6/galaxyconfigs/molFiles.py	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import data
-import logging
-from galaxy.datatypes.sniff import *
-import commands
-
-log = logging.getLogger(__name__)
-
-class GenericMolFile( data.Text ):
-	file_ext = "mol2/sdf/drf"
-	def check_filetype( self,filename ):
-		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			self.file_ext="sdf"
-			return True
-		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			self.file_ext="mol2"
-			return True
-		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			self.file_ext="drf"
-			return True
-		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			self.file_ext="pdb"
-			return True
-		return False
-
-	def set_peek( self, dataset, is_multi_byte=False ):
-		if not dataset.dataset.purged:
-			if(self.check_filetype(dataset.file_name)) :
-				if (self.no_mols[1] == '1'):
-					dataset.blurb = "1 molecule"
-				else:
-					dataset.blurb = "%s molecules"%self.no_mols[1]
-			dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-		else:
-			dataset.peek = 'file does not exist'
-			dataset.blurb = 'file purged from disk'
-
-	def get_mime(self):
-		return 'text/plain'
-
-
-class GenericMultiMolFile( GenericMolFile ):
-	def set_peek( self, dataset, is_multi_byte=False ):
-		if not dataset.dataset.purged:
-			self.sniff(dataset.file_name)
-			if (self.no_mols[1] == '1'):
-				dataset.blurb = "1 molecule"
-			else:
-				dataset.blurb = "%s molecules"%self.no_mols[1]
-			dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-		else:
-			dataset.peek = 'file does not exist'
-			dataset.blurb = 'file purged from disk'
-
-class SDF( GenericMultiMolFile ):
-	file_ext = "sdf"
-	def sniff( self, filename ):
-		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			return True
-		else:
-			return False
-
-class MOL2( GenericMultiMolFile ):
-	file_ext = "mol2"
-	def sniff( self, filename ):
-		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			return True
-		else:
-			return False
-
-class DRF( GenericMultiMolFile ):
-	file_ext = "drf"
-	def sniff( self, filename ):
-		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			return True
-		else:
-			return False
-
-class PDB( GenericMolFile ):
-	file_ext = "pdb"
-	def sniff( self, filename ):
-		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
-		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
-			return True
-		else:
-			return False
-	def set_peek( self, dataset, is_multi_byte=False ):
-	#def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
-		if not dataset.dataset.purged:
-			res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
-			dataset.peek = res[1]
-			self.sniff(dataset.file_name)
-			if (self.no_mols[1] == '1'):
-				dataset.blurb = "1 protein structure"
-			else:
-				dataset.blurb = "%s protein structures"%self.no_mols[1]
-		else:
-			dataset.peek = 'file does not exist'
-			dataset.blurb = 'file purged from disk'
-
-class grd ( data.Text ) :
-	file_ext = "grd"
-	def set_peek( self, dataset, is_multi_byte=False ):
-		if not dataset.dataset.purged:
-			#dataset.peek = ""
-			dataset.blurb = "score-grids for docking"
-		else:
-			dataset.peek = 'file does not exist'
-			dataset.blurb = 'file purged from disk'
-
-class grdtgz ( data.Text ) :
-	file_ext = "grd.tgz"
-	def set_peek( self, dataset, is_multi_byte=False ):
-		if not dataset.dataset.purged:
-			#dataset.peek = ""
-			dataset.blurb = "compressed score-grids for docking"
-		else:
-			dataset.peek = 'file does not exist'
-			dataset.blurb = 'file purged from disk'
-