diff --git a/Contrib/SA_Score/README b/Contrib/SA_Score/README
new file mode 100644
index 000000000..cdd442f8b
--- /dev/null
+++ b/Contrib/SA_Score/README
@@ -0,0 +1,9 @@
+RDKit-based implementation of the method described in:
+
+Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions
+Peter Ertl and Ansgar Schuffenhauer
+Journal of Cheminformatics 1:8 (2009)
+http://www.jcheminf.com/content/1/1/8
+
+Contribution from Peter Ertl and Greg Landrum
+
diff --git a/Contrib/SA_Score/UnitTestSAScore.py b/Contrib/SA_Score/UnitTestSAScore.py
new file mode 100644
index 000000000..59d8bed3b
--- /dev/null
+++ b/Contrib/SA_Score/UnitTestSAScore.py
@@ -0,0 +1,34 @@
+from rdkit import RDConfig
+from rdkit import Chem
+import unittest,os.path
+import sascorer
+print sascorer.__file__
+
+class TestCase(unittest.TestCase):
+  def test1(self):
+   testData = [x.strip().split('\t') for x in file('data/zim.100.txt').readlines()]
+   testData.pop(0)
+   for row in testData:
+     smi = row[0]
+     m = Chem.MolFromSmiles(smi)
+     tgt = float(row[2])
+     val = sascorer.calculateScore(m)
+     self.failUnlessAlmostEqual(tgt,val,3)
+
+if __name__ == '__main__':
+  import sys,getopt,re
+  doLong=0
+  if len(sys.argv) >1:
+    args,extras=getopt.getopt(sys.argv[1:],'l')
+    for arg,val in args:
+      if arg=='-l':
+        doLong=1
+      sys.argv.remove('-l')
+  if doLong:
+    for methName in dir(TestCase):
+      if re.match('_test',methName):
+        newName = re.sub('_test','test',methName)
+        exec('TestCase.%s = TestCase.%s'%(newName,methName))
+        
+  unittest.main()
+
diff --git a/Contrib/SA_Score/data/zim.100.txt b/Contrib/SA_Score/data/zim.100.txt
new file mode 100644
index 000000000..f8eb6f413
--- /dev/null
+++ b/Contrib/SA_Score/data/zim.100.txt
@@ -0,0 +1,101 @@
+smiles	Name	sa_score
+Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]	ZINC21984717	3.166
+Cn1cc(NC=O)cc1C(=O)Nc1cc(C(=O)Nc2cc(C(=O)NCCC(N)=[NH2+])n(C)c2)n(C)c1	ZINC03872327	3.328
+OC(c1ccncc1)c1ccc(OCC[NH+]2CCCC2)cc1	ZINC34421620	3.822
+CC(C(=O)[O-])c1ccc(-c2ccccc2)cc1	ZINC00000361	2.462
+C[NH+](C)CC(O)Cn1c2ccc(Br)cc2c2cc(Br)ccc21	ZINC00626529	3.577
+NC(=[NH2+])NCC1COc2ccccc2O1	ZINC00000357	3.290
+CCC(C)(C)[NH2+]CC(O)COc1ccccc1C#N	ZINC04214111	3.698
+C[NH+](C)CC(O)Cn1c2ccc(Br)cc2c2cc(Br)ccc21	ZINC00626528	3.577
+CC12CCC3C(CCC4CC(=O)CCC43C)C1CCC2=O	ZINC04081985	3.912
+COc1ccc(OC(=O)N(CC(=O)[O-])Cc2ccc(OCCc3nc(-c4ccccc4)oc3C)cc2)cc1	ZINC03935839	2.644
+COc1ccccc1OC(=O)c1ccccc1	ZINC00000349	1.342
+CC(C)CC[NH2+]CC1COc2ccccc2O1	ZINC04214115	3.701
+CN1CCN(C(=O)OC2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1	ZINC19632834	3.196
+CCC1(c2ccccc2)C(=O)N(COC)C(=O)N(COC)C1=O	ZINC02986592	2.759
+Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1	ZINC00141883	1.529
+O=C([O-])CCCNC(=O)NC1CCCCC1	ZINC08754389	2.493
+CCC(C)C(C(=O)OC1CC[N+](C)(C)CC1)c1ccccc1	ZINC00000595	3.399
+CCC(C)SSc1ncc[nH]1	ZINC13209429	3.983
+CC[N+](C)(CC)CCOC(=O)C(O)(c1cccs1)C1CCCC1	ZINC01690860	3.471
+CC12CCC3C(CCC4CC(=O)CCC43C)C1CCC2O	ZINC03814360	3.994
+CC12CCC3C4CCC(=O)C=C4CCC3C1CCC2O	ZINC03814379	4.056
+OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O	ZINC04095762	4.282
+CC(C)CC(CC[NH+](C(C)C)C(C)C)(C(N)=O)c1ccccn1	ZINC02016048	4.092
+C=CC1(C)CC(=O)C2(O)C(C)(O1)C(OC(C)=O)C(OC(=O)CC[NH+](C)C)C1C(C)(C)CCC(O)C12C	ZINC38595287	5.519
+C=CC[NH+]1CCCC1CNC(=O)c1cc(S(N)(=O)=O)cc(OC)c1OC	ZINC00601278	4.286
+CC(=O)OC1C[NH+]2CCC1CC2	ZINC00492792	5.711
+CC12CCC3C(CCC4CC(=O)CCC43C)C1CCC2O	ZINC03814418	3.994
+CC1(O)CCC2C3CCC4=CC(=O)CCC4(C)C3CCC21C	ZINC03814422	4.022
+CC(=O)OC1(C(C)=O)CCC2C3C=C(Cl)C4=CC(=O)C5CC5C4(C)C3CCC21C	ZINC03814423	4.827
+C#CC1(O)CCC2C3CCc4cc(OC)ccc4C3CCC21C	ZINC03815424	3.810
+C=CC1(C)CC(OC(=O)CSCC[NH+](CC)CC)C2(C)C3C(=O)CCC3(CCC2C)C(C)C1O	ZINC25757051	6.200
+O=C([O-])C(=O)Nc1nc(-c2ccc3c(c2)OCCO3)cs1	ZINC03623428	2.594
+CC[NH+]1CCCC1CNC(=O)C(O)(c1ccccc1)c1ccccc1	ZINC00900569	3.950
+CC(C)(OCc1nn(Cc2ccccc2)c2ccccc12)C(=O)[O-]	ZINC00004594	2.573
+Cc1nnc(C(C)C)n1C1CC2CCC(C1)[NH+]2CCC(NC(=O)C1CCC(F)(F)CC1)c1ccccc1	ZINC03817234	5.316
+Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O	ZINC03871612	5.290
+O=C([O-])CNC(=O)c1ccccc1	ZINC00097685	2.097
+Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O	ZINC03871613	5.290
+Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O	ZINC03871614	5.290
+c1ccc(OCc2ccc(CCCN3CCOCC3)cc2)cc1	ZINC19865692	1.702
+CC=CC1=C(C(=O)[O-])N2C(=O)C(NC(=O)C(N)c3ccc(O)cc3)C2SC1	ZINC20444132	4.042
+C[NH+]1CCCC1COc1cccnc1	ZINC03805141	4.510
+O=C([O-])C(O)CC(O)C(O)CO	ZINC04803503	4.398
+O=C([O-])C(O)CC(O)C(O)CO	ZINC01696607	4.398
+C[NH+]1CCCC1Cc1c[nH]c2ccc(CCS(=O)(=O)c3ccccc3)cc12	ZINC03823475	3.921
+C(=Cc1ccccc1)C[NH+]1CCN(C(c2ccccc2)c2ccccc2)CC1	ZINC19632891	2.973
+Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O	ZINC03871615	5.290
+CC(c1ccccc1)N(C)C=O	ZINC06932229	2.562
+CC(=O)C1CCC2C3CCC4CC(C)(O)CCC4(C)C3CCC12C	ZINC03824281	4.279
+O=C([O-])C(O)CC(O)C(O)CO	ZINC04803506	4.398
+COc1cc(O)c(C(=O)c2ccccc2)c(O)c1	ZINC00000187	1.868
+O=C([O-])C(O)CC(O)C(O)CO	ZINC04803507	4.398
+COc1c2c(cc3c1C(O)N(C)CC3)OCO2	ZINC00000186	3.183
+CCC(C(=O)[O-])c1ccc(CC(C)C)cc1	ZINC00015537	2.827
+O=C([O-])C1[NH+]=C(c2ccccc2)c2cc(Cl)ccc2NC1(O)O	ZINC38611850	4.011
+O=C([O-])C1[NH+]=C(c2ccccc2)c2cc(Cl)ccc2NC1(O)O	ZINC38611851	4.011
+OCC(O)COc1ccc(Cl)cc1	ZINC00000135	2.102
+NC(=O)NC(=O)C(Cl)c1ccccc1	ZINC00000134	2.455
+OC(c1ccccc1)(c1ccccc1)C1C[NH+]2CCC1CC2	ZINC01298963	4.530
+C[NH2+]CC(C)c1ccccc1	ZINC04298801	3.471
+Clc1cccc(Cl)c1N=C1NCCO1	ZINC13835972	3.267
+[NH3+]C(Cc1ccccc1)C(=O)CCl	ZINC02504633	3.251
+CC(C)Cn1cnc2c1c1ccccc1nc2N	ZINC19632912	2.230
+CC(O)CN(C)c1ccc(NN)nn1	ZINC00000624	3.193
+CC1(O)CCC2C3CCC4=CC(=O)CCC4=C3C=CC21C	ZINC00001727	4.461
+CCC(C(=O)[O-])c1ccc(-c2ccccc2)cc1	ZINC00000111	2.505
+CC(=O)OCC1OC(n2ncc(=O)[nH]c2=O)C(OC(C)=O)C1OC(C)=O	ZINC03830255	3.832
+CC(=O)OCC1OC(n2ncc(=O)[nH]c2=O)C(OC(C)=O)C1OC(C)=O	ZINC03830256	3.832
+Cn1cc(C(=O)c2cccc3ccccc32)cc1C(=O)[O-]	ZINC00001783	2.456
+CC(=O)OCC1OC(n2ncc(=O)[nH]c2=O)C(OC(C)=O)C1OC(C)=O	ZINC03830257	3.832
+Cc1cccc(-c2nc3ccccc3c(Nc3ccc4[nH]ncc4c3)n2)n1	ZINC39279791	2.358
+O=C([O-])C1CC2CCCCC2[NH2+]1	ZINC04899687	5.422
+CC(=O)OCC(=O)C1CCC2C3CC=C4CC(O)CCC4(C)C3CCC12C	ZINC00538219	4.187
+O=C([O-])C1CC2CCCCC2[NH2+]1	ZINC04899686	5.422
+O=C(OCc1ccccc1)C(O)c1ccccc1	ZINC00000078	2.038
+CC(=O)OCC(=O)C1(O)CCC2C3CCC4=CC(=O)C=CC4(C)C3C(O)CC21C	ZINC00608041	4.394
+Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1	ZINC02570895	2.144
+COCc1cccc(CC(O)C=CC2C(O)CC(=O)C2CCSCCCC(=O)OC)c1	ZINC03940680	3.934
+CCC(=O)N(c1ccccc1)C1CC[NH+](C(C)Cc2ccccc2)CC1	ZINC01664586	3.582
+CCC(=O)N(c1ccccc1)C1CC[NH+](C(C)Cc2ccccc2)CC1	ZINC01664587	3.582
+CCOC(=O)Nc1ccc2c(c1)N(C(=O)CCN1CCOCC1)c1ccccc1S2	ZINC19340795	2.446
+O=C([O-])Cc1cc(=O)[nH]c(=O)[nH]1	ZINC00403617	3.258
+NC(=O)C([NH3+])Cc1c[nH]c2ccccc12	ZINC04899521	3.224
+NC(=O)C([NH3+])Cc1ccc(O)cc1	ZINC04899513	3.280
+O=C(c1cc2ccccc2o1)N1CCN(Cc2ccccc2)CC1	ZINC19632922	1.799
+O=C(CO)C(O)C(O)CO	ZINC00902219	3.473
+CC(Cc1ccccc1)NC(=O)C([NH3+])CCCC[NH3+]	ZINC11680943	3.967
+C[NH+]1CCC(c2c(O)cc(=O)c3c(O)cc(-c4ccccc4Cl)oc2-3)C(O)C1	ZINC05966679	4.616
+CN(C)c1ccc(O)c2c1CC1CC3C([NH+](C)C)C(=O)C(C(N)=O)=C(O)C3(O)C(=O)C1=C2O	ZINC04019704	4.713
+Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CC(O)C(O)C(O)CO)c2cc1C	ZINC03650334	3.791
+C[NH+]1C2CCC1CC(OC(=O)c1c[nH]c3ccccc13)C2	ZINC18130447	4.892
+Cc1ccccc1NC(=O)C(C)[NH+]1CCCC1	ZINC00000051	3.809
+O=S(=O)([O-])CCN1CCOCC1	ZINC19419111	2.776
+C[NH+]1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1	ZINC19632927	3.379
+CCCCCC=CCC=CCCCCCCCC(=O)[O-]	ZINC03802188	2.805
+CC(CC([NH3+])C(=O)[O-])C(=O)[O-]	ZINC01747048	5.690
+CC1c2cccc(O)c2C(=O)C2=C(O)C3(O)C(O)=C(C(N)=O)C(=O)C([NH+](C)C)C3C(O)C21	ZINC04019706	5.069
+Cc1cc2nc3nc([O-])[nH]c(=O)c3nc2cc1C	ZINC12446789	3.079
+CC1=CC(C)C2(CO)COC(c3ccc(O)cc3)C1C2C	ZINC38190856	4.749
+CC[NH+]1CCC(=C2c3ccccc3CCc3ccccc32)C1C	ZINC02020004	3.925
diff --git a/Contrib/SA_Score/fpscores.pkl.gz b/Contrib/SA_Score/fpscores.pkl.gz
new file mode 100644
index 000000000..0f0abe2a9
Binary files /dev/null and b/Contrib/SA_Score/fpscores.pkl.gz differ
diff --git a/Contrib/SA_Score/sascorer.py b/Contrib/SA_Score/sascorer.py
new file mode 100644
index 000000000..9bf71150b
--- /dev/null
+++ b/Contrib/SA_Score/sascorer.py
@@ -0,0 +1,183 @@
+#
+# calculation of synthetic accessibility score as described in:
+#
+# Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions
+# Peter Ertl and Ansgar Schuffenhauer
+# Journal of Cheminformatics 1:8 (2009)
+# http://www.jcheminf.com/content/1/1/8
+#
+# several small modifications to the original paper are included
+# particularly slightly different formula for marocyclic penalty
+# and taking into account also molecule symmetry (fingerprint density)
+#
+# for a set of 10k diverse molecules the agreement between the original method
+# as implemented in PipelinePilot and this implementation is r2 = 0.97
+#
+# peter ertl & greg landrum, september 2013
+#
+
+from rdkit import Chem
+from rdkit.Chem import rdMolDescriptors
+
+import math
+from collections import defaultdict
+
+_fscores = None
+
+def readFragmentScores(name='fpscores'):
+  import cPickle,gzip
+  global _fscores
+  _fscores = cPickle.load(gzip.open('%s.pkl.gz'%name))
+
+def numBridgeheadsAndSpiro(mol,ri=None):
+  if ri is None:
+    ri=mol.GetRingInfo()
+  arings = [set(x) for x in ri.AtomRings()]
+  spiros=set()
+  for i,ari in enumerate(arings):
+    for j in range(i+1,len(arings)):
+      shared=ari&arings[j]
+      if len(shared)==1:
+        spiros.update(shared)
+  nSpiro=len(spiros)
+
+  # find bonds that are shared between rings that share at least 2 bonds:
+  nBridge=0
+  brings = [set(x) for x in ri.BondRings()]
+  bridges=set()
+  for i,bri in enumerate(brings):
+    for j in range(i+1,len(brings)):
+      shared=bri&brings[j]
+      if len(shared)>1:
+        atomCounts=defaultdict(int)
+        for bi in shared:
+          bond = mol.GetBondWithIdx(bi)
+          atomCounts[bond.GetBeginAtomIdx()]+=1
+          atomCounts[bond.GetEndAtomIdx()]+=1
+        tmp=0
+        for ai,cnt in atomCounts.items():
+          if cnt==1:
+            tmp+=1
+            bridges.add(ai)
+        #if tmp!=2: # no need to stress the users
+          #print 'huh:',tmp
+  return len(bridges),nSpiro
+
+def calculateScore(m):
+  if _fscores is None: readFragmentScores()
+
+  # fragment score
+  fp = rdMolDescriptors.GetMorganFingerprint(m,2)  #<- 2 is the *radius* of the circular fingerprint
+  fps = fp.GetNonzeroElements()
+  score1 = 0.
+  nf = 0
+  for bitId,v in fps.iteritems():
+    nf += v
+    sfp = bitId
+    score1 += _fscores.get(sfp,-4)*v
+  score1 /= nf
+
+  # features score
+  nAtoms = m.GetNumAtoms()
+  nChiralCenters = len(Chem.FindMolChiralCenters(m,includeUnassigned=True))
+  ri = m.GetRingInfo()
+  nBridgeheads,nSpiro=numBridgeheadsAndSpiro(m,ri)
+  nMacrocycles=0
+  for x in ri.AtomRings():
+    if len(x)>8: nMacrocycles+=1
+
+  sizePenalty = nAtoms**1.005 - nAtoms
+  stereoPenalty = math.log10(nChiralCenters+1)
+  spiroPenalty = math.log10(nSpiro+1)
+  bridgePenalty = math.log10(nBridgeheads+1)
+  macrocyclePenalty = 0.
+  # ---------------------------------------
+  # This differs from the paper, which defines:
+  #  macrocyclePenalty = math.log10(nMacrocycles+1)
+  # This form generates better results when 2 or more macrocycles are present
+  if nMacrocycles > 0: macrocyclePenalty = math.log10(2)
+
+  score2 = 0. -sizePenalty -stereoPenalty -spiroPenalty -bridgePenalty -macrocyclePenalty
+
+  # correction for the fingerprint density
+  # not in the original publication, added in version 1.1
+  # to make highly symmetrical molecules easier to synthetise
+  score3 = 0.
+  if nAtoms > len(fps):
+    score3 = math.log(float(nAtoms) / len(fps)) * .5
+
+  sascore = score1 + score2 + score3
+
+  # need to transform "raw" value into scale between 1 and 10
+  min = -4.0
+  max = 2.5
+  sascore = 11. - (sascore - min + 1) / (max - min) * 9.
+  # smooth the 10-end
+  if sascore > 8.: sascore = 8. + math.log(sascore+1.-9.)
+  if sascore > 10.: sascore = 10.0
+  elif sascore < 1.: sascore = 1.0 
+
+  return sascore
+    
+
+def processMols(mols,outf):
+  
+  print 'smiles\tName\tsa_score'
+  count = {}
+  for i,m in enumerate(mols):
+    if m is None:
+      continue
+ 
+    s = calculateScore(m)
+
+    smiles = Chem.MolToSmiles(m)
+    print smiles+"\t"+m.GetProp('_Name') + "\t%3f"%s
+
+
+if __name__=='__main__':
+  import sys,gzip,time
+
+  outf = None
+
+  t1=time.time()
+  readFragmentScores("fpscores")
+  t2=time.time()
+
+  suppl = Chem.SmilesMolSupplier(sys.argv[1])
+  t3=time.time()
+  processMols(suppl,outf)
+  t4=time.time()
+
+  print >>sys.stderr,'Reading took %.2f seconds. Calculating took %.2f seconds'%((t2-t1),(t4-t3))
+
+  
+#
+#  Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
+#  All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met: 
+#
+#     * Redistributions of source code must retain the above copyright 
+#       notice, this list of conditions and the following disclaimer.
+#     * Redistributions in binary form must reproduce the above
+#       copyright notice, this list of conditions and the following 
+#       disclaimer in the documentation and/or other materials provided 
+#       with the distribution.
+#     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
+#       nor the names of its contributors may be used to endorse or promote 
+#       products derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#