fragments.sql.in

Create Or Replace Function _OCSCHEMA_.atoms(smi Text, nbrflag Integer)
 Returns SetOf text As $EOPY$
import obchord
import openbabel

#  array for SetOf return
retsmarts = []
oc=obchord.obchord(GD)
mol = oc.parse_smi(smi)
if mol:
 for a in openbabel.OBMolAtomIter(mol):
  if a.GetAtomicNum() == 1: continue
  if nbrflag > 0:
   retsmarts.append(obchord.atom_sym(a,True) + obchord.nbr_smarts(a))
  else:
   retsmarts.append(obchord.atom_sym(a,True))
   if nbrflag == 0:
    retsmarts.append(obchord.atom_sym(a,True) + obchord.nbr_smarts(a))
 return retsmarts
else:
 # bad mol (bad smiles)
 return None
$EOPY$ Language plpythonu Immutable;
Comment on Function _OCSCHEMA_.atoms(Text,Integer)
Is 'return a table of SMARTS of each atom and optionally its nearest neighbors; -1 no neighbors, 0 with neighbors, 1 only neighbors';

Create Or Replace Function _OCSCHEMA_.bonds(smi Text, nbrflag Integer)
 Returns SetOf text As $EOPY$
import obchord
import openbabel

retsmarts = []
oc=obchord.obchord(GD)
mol = oc.parse_smi(smi)
if mol:
 for b in openbabel.OBMolBondIter(mol):
  a1 = b.GetBeginAtom()
  a2 = b.GetEndAtom()
  a1sma = obchord.atom_sym(a1,True)
  a2sma = obchord.atom_sym(a2,True)
  if nbrflag < 0:
   a1nbr = ""
   a2nbr = ""
  else:
   a1nbr = obchord.nbr_smarts(a1,a2)
   a2nbr = obchord.nbr_smarts(a2,a1)

  # use a symbol for every bond type
  if   b.IsSingle():   bnd = "-"
  elif b.IsAromatic(): bnd = ":"
  elif b.IsDouble():   bnd = "="
  elif b.IsTriple():   bnd = "#"
  else: bnd = "~"

  if a1sma+a1nbr < a2sma+a2nbr:
   sma = a1sma + bnd + a2sma
   if nbrflag < 0:
    pass
   else:
    nbrsma = '[$(' + a1sma + a1nbr + ')]' + bnd + '[$(' + a2sma + a2nbr + ')]'
  else:
   sma = a2sma + bnd + a1sma
   if nbrflag < 0:
    pass
   else:
    nbrsma = '[$(' + a2sma + a2nbr + ')]' + bnd + '[$(' + a1sma + a1nbr + ')]'

  if nbrflag > 0:
   retsmarts.append(nbrsma)
  else:
   retsmarts.append(sma)
   if nbrflag == 0:
    retsmarts.append(nbrsma)
 return retsmarts
else:
 return None
$EOPY$ Language plpythonu Immutable;
Comment on Function _OCSCHEMA_.bonds(Text,Integer)
Is 'return a table of SMARTS of atoms in each bond and optionally their nearest neighbors; -1 no neighbors, 0 with neighbors, 1 only neighbors';

Create Or Replace Function _OCSCHEMA_.fragments(smi Text, minpath Integer, maxpath Integer, smarts Boolean)
 Returns SetOf Text As $EOPY$
import obchord
oc = obchord.obchord(GD)
mol = oc.parse_smi(smi)
paths = obchord.make_mol_paths(mol, minpath, maxpath, smarts)
return paths
$EOPY$ Language plpythonu Immutable;
Comment on Function _OCSCHEMA_.fragments(Text,Integer,Integer,Boolean)
Is 'return a table of SMARTS of fragments of length min to max, using atom symbols or smarts with charge and valence';