compute 2D coordinates during SMILES to MOL conversion

to enable loading SMILES in MarvinJS (related to #83)


Former-commit-id: f3f0006b98d5bb0f5e303c14e1f7fc8c0bf03f9f

ippisite/ippidb/utils.py

@@ -9,6 +9,11 @@ def mol2smi(mol_string):
 
 def smi2mol(smi_string):
     m = pybel.readstring('smi', smi_string)
+    # generate 2D coordinates for MarvinJS layout
+    #NB: the line below should be replaced as soon as the new version of openbabel
+    # is out (>2.4.1), by a call to m.make2D()
+    # (see https://github.com/openbabel/openbabel/blob/06e233e2ca0c6d9f86f74bafe74ffcb75e9d76cd/scripts/python/pybel.py#L577)
+    pybel._operations['gen2D'].Do(m.OBMol)
     return m.write(format='mol')
 
 class FingerPrinter(object):