Mercurial > repos > marcel > caddsuite_linux_x86_64
view CADDSuite-1.5/galaxyconfigs/molFiles.py @ 16:1a24aef40d01 draft
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author | marcel |
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date | Tue, 24 Jul 2012 11:10:07 -0400 |
parents | ac342506cd4e |
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# -*- 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'