--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes/molFiles.py	Tue Dec 25 05:16:25 2012 -0500
@@ -0,0 +1,242 @@
+# -*- coding: utf-8 -*-
+
+from galaxy.datatypes import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+import pybel
+import openbabel
+openbabel.obErrorLog.StopLogging()
+
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes import metadata
+
+log = logging.getLogger(__name__)
+
+class GenericMolFile( data.Text ):
+
+    MetadataElement( name="molecules", default=0, desc="Number of molecules", readonly=True, visible=False, optional=True, no_value=0 )
+
+    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 FPS( GenericMultiMolFile ):
+    file_ext = "fps"
+    def sniff( self, filename ):
+        self.no_mols = commands.getstatusoutput("grep -c -v '^#' "+filename)
+        with open(filename) as in_handle:
+            for line_counter, line in enumerate(in_handle):
+                line = line.strip()
+                if line.startswith('#FPS1'):
+                    return True
+                if line_counter > 10:
+                    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 PHAR( GenericMultiMolFile ):
+    MetadataElement( name="base_name", desc="base name", default='Phar',
+    readonly=True, set_in_upload=True)
+    file_ext = "phar"
+    def sniff( self, filename ):
+        self.no_mols = commands.getstatusoutput("grep -c -v '^#' "+filename)
+        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'
+
+
+class InChI( GenericMultiMolFile ):
+    file_ext = "inchi"
+    def sniff( self, filename ):
+        self.no_mols = commands.getstatusoutput("grep -c '^InChI=' "+filename)
+        word_count = commands.getoutput("wc -w "+filename).split()[0]
+        
+        if self.no_mols[1] != word_count:
+            return False
+        
+        if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+            return True
+        else:
+            return False
+
+    def set_meta( self, dataset, **kwd ):
+        """
+        Set the number of sequences and the number of data lines
+        in dataset.
+        """
+        if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
+            dataset.metadata.data_lines = None
+            dataset.metadata.sequences = None
+            return
+        #word_count = commands.getoutput("wc -w "+filename).split()[0]
+        # word_count are the lines of the file, if word_count and molecule count
+        # are the same, that must hold to be an InChI File, then that should be
+        # the same number as all non-empty lines
+        #dataset.metadata.data_lines = word_count
+        #int(commands.getoutput("grep -cve '^\s*$' "+filename))
+        #dataset.metadata.molecules = word_count
+
+
+class SMILES( GenericMultiMolFile ):
+    file_ext = "smi"
+    def sniff( self, filename ):
+        """
+        Its hard or impossible to sniff a SMILES File. All what i know is the
+        word_count must be the same as the non-empty line count. And that i can
+        try to import the first SMILES and check if it is a molecule.
+        """
+        
+        # that corresponds to non-empty line count
+        self.no_mols = commands.getstatusoutput("grep -cve '^\s*$' "+filename)
+        word_count = int(commands.getoutput("wc -w "+filename).split()[0])
+        
+        if int(self.no_mols[1]) != word_count:
+            return False
+        
+        if (self.no_mols[0] == 0) & (int(self.no_mols[1]) > 0):
+            for line in open(filename):
+                line = line.strip()
+                if line:
+                    # if we have atoms, we have a molecule
+                    try:
+                        if len(pybel.readstring('smi', line).atoms) > 0:
+                            return True
+                        else:
+                            return False
+                    except:
+                        # if convert fails its not a smiles string
+                        return False
+            return True
+        else:
+            return False
+
+    def set_meta( self, dataset, **kwd ):
+        """
+        Set the number of sequences and the number of data lines
+        in dataset.
+        """
+        if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
+            dataset.metadata.data_lines = None
+            dataset.metadata.sequences = None
+            return
+
+        #word_count = int(commands.getoutput("wc -w "+filename).split()[0])
+        # word_count are the lines of the file, if word_count and molecule count
+        # are the same, that must hold to be an InChI File, then that should be
+        # the same number as all non-empty lines
+        #dataset.metadata.data_lines = word_count
+        #dataset.metadata.molecules = word_count
+
+