@app.route("/chemblws/compounds/<chembl_id>")
def compound_by_ChEMBLID(chembl_id):
    compound = chembldb.query(Molecule).filter_by(chembl_id=chembl_id).one()
    result = {...}
    return jsonify(result)

{
    "compound": {
        "acdLogd": 7.67, 
        "acdLogp": 7.67, 
        "alogp": 3.63, 
        "chemblId": "CHEMBL1", 
        "knownDrug": "No", 
        "medChemFriendly": "Yes", 
        "molecularFormula": "C32H32O8", 
        "molecularWeight": 544.59, 
        "numRo5Violations": 1, 
        "passesRuleOfThree": "No", 
        "rotatableBonds": 2, 
        "smiles": "COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56", 
        "stdInChiKey": "GHBOEFUAGSHXPO-XZOTUCIWSA-N"
    }
}

{
    "compound": {
        "acdBasicPka": 6.52, 
        "acdLogd": 2.09, 
        "acdLogp": 2.14, 
        "alogp": 2.11, 
        "chemblId": "CHEMBL2", 
        "knownDrug": "Yes", 
        "medChemFriendly": "Yes", 
        "molecularFormula": "C19H21N5O4", 
        "molecularWeight": 383.4, 
        "numRo5Violations": 0, 
        "passesRuleOfThree": "No", 
        "preferredCompoundName": "PRAZOSIN", 
        "rotatableBonds": 4, 
        "smiles": "COc1cc2nc(nc(N)c2cc1OC)N3CCN(CC3)C(=O)c4occc4", 
        "species": "NEUTRAL", 
        "stdInChiKey": "IENZQIKPVFGBNW-UHFFFAOYSA-N", 
        "synonyms": "CP-12299,Minipress,Minizide,PRAZOSIN,Prazosin"
    }
}

from pptx import Presentation
from pptx.util import Inches
from pychembldb import *

prs = Presentation()
title_only_slidelayout = prs.slidelayouts[5]
slide = prs.slides.add_slide(title_only_slidelayout)
shapes = slide.shapes

shapes.title.text = "10.1016/S0960-894X(01)80693-4"

rows = 6
cols = 6
left = Inches(0.5)
top = Inches(1.5)
width = Inches(8.0)
height = Inches(0.8)

tbl = shapes.add_table(rows, cols, left, top, width, height)

tbl.columns[0].width = Inches(2.0)

tbl.cell(0, 0).text = 'inchi_key'
tbl.cell(0, 1).text = 'activity'
tbl.cell(0, 2).text = 'HBD'
tbl.cell(0, 3).text = 'HBA'
tbl.cell(0, 4).text = 'PSA'
tbl.cell(0, 5).text = 'MWT'

for journal in chembldb.query(Doc).filter_by(doi="10.1016/S0960-894X(01)80693-4"):
    for assay in journal.assays[:1]:
        for i, activity in enumerate(assay.activities[:5], 1):
            tbl.cell(i, 0).text = activity.compound.molecule.structure.standard_inchi_key
            tbl.cell(i, 1).text = str(activity.published_value)
            tbl.cell(i, 2).text = str(activity.compound.molecule.property.hbd)
            tbl.cell(i, 3).text = str(activity.compound.molecule.property.hba)
            tbl.cell(i, 4).text = str(activity.compound.molecule.property.psa)
            tbl.cell(i, 5).text = str(activity.compound.molecule.property.mw_freebase)

prs.save('test.pptx')

from pychembldb import *
for target in chembldb.query(Target).filter_by(pref_name="Tyrosine-protein kinase ABL"):
    for assay in target.assays:
        for activity in assay.activities:
            print activity.published_value, activity.molecule.structure.standard_inchi_key

from pychembldb import *
for journal in chembldb.query(Doc).filter_by(doi="10.1016/S0960-894X(01)80693-4"):
    for assay in journal.assays:
        for activity in assay.activities:
            print activity.published_value, activity.molecule.structure.standard_inchi_key

File "sdf2gsp", line 17, in convert
  for i,atom in enumerate(ob.OBMolAtomIter(mol)): 
File "/usr/local/Cellar/python/2.7.3/lib/python2.7/site-packages/openbabel.py", line 4499, in __init__
  if not self.iter.__bool__():
AttributeError: '_OBMolAtomIter' object has no attribute '__bool__'

#!/usr/bin/env python
import sys
import pybel
import openbabel as ob

def convert(sdf):
    mols = pybel.readfile('sdf',sdf)
    for n, mol in enumerate(mols, 1):
        print "t # %d" % n
        for i in range(mol.OBMol.NumAtoms()):
            print "v %d %d " % (i+1, mol.OBMol.GetAtom(i+1).GetAtomicNum())
        for j in range(mol.OBMol.NumBonds()):
            b = mol.OBMol.GetBond(j)
            print "e %d %d %d" % (b.GetBeginAtomIdx(),
                                  b.GetEndAtomIdx(),
                                  b.GetBondOrder())

if __name__ == "__main__":
    sdffile = sys.argv[1]
    convert(sdffile)

./gwt-build -iteration 2 chembl_14.gsp chembl14

$ ./gwt-search -kthreshold 0.8 chembl14 query.gsp
reading index file:chembl14
end reading
start building rank dictionary
end building rank dictionary
start transferring labels
end transferring labels
id:0 1080597:0.809449 712949:0.838758 413038:0.847826 \
394513:0.826087 391369:0.819028 179393:0.815124 \
175534:0.899647 48523:0.804348 47164:1.000000 16405:0.802727 
cpu time (sec):0.712119
mean cpu time (sec):0.712119

cmake -L

cmake ../openbabel-2.3.1 -DPYTHON_BINDINGS=ON \
-DPYTHON_LIBRARY=/usr/local/lib/libpython2.7.dylib\
-DPYTHON_EXECUTABLE=/usr/local/bin/python \
-DEIGEN2_INCLUDE_DIR=/Users/kzfm/openbabel/eigen-eigen-2.0.17 \
-DRUN_SWIG=ON \
-DSWIG_EXECUTABLE=/usr/loca/bin/swig