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add sa score
This commit is contained in:
Greg Landrum
9
Contrib/SA_Score/README
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9
Contrib/SA_Score/README
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@@ -0,0 +1,9 @@
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RDKit-based implementation of the method described in:
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Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions
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Peter Ertl and Ansgar Schuffenhauer
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Journal of Cheminformatics 1:8 (2009)
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http://www.jcheminf.com/content/1/1/8
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Contribution from Peter Ertl and Greg Landrum
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34
Contrib/SA_Score/UnitTestSAScore.py
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34
Contrib/SA_Score/UnitTestSAScore.py
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from rdkit import RDConfig
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from rdkit import Chem
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import unittest,os.path
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import sascorer
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print sascorer.__file__
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class TestCase(unittest.TestCase):
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def test1(self):
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testData = [x.strip().split('\t') for x in file('data/zim.100.txt').readlines()]
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testData.pop(0)
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for row in testData:
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smi = row[0]
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m = Chem.MolFromSmiles(smi)
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tgt = float(row[2])
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val = sascorer.calculateScore(m)
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self.failUnlessAlmostEqual(tgt,val,3)
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if __name__ == '__main__':
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import sys,getopt,re
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doLong=0
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if len(sys.argv) >1:
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args,extras=getopt.getopt(sys.argv[1:],'l')
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for arg,val in args:
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if arg=='-l':
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doLong=1
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sys.argv.remove('-l')
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if doLong:
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for methName in dir(TestCase):
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if re.match('_test',methName):
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newName = re.sub('_test','test',methName)
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exec('TestCase.%s = TestCase.%s'%(newName,methName))
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unittest.main()
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101
Contrib/SA_Score/data/zim.100.txt
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101
Contrib/SA_Score/data/zim.100.txt
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@@ -0,0 +1,101 @@
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smiles Name sa_score
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Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 3.166
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Cn1cc(NC=O)cc1C(=O)Nc1cc(C(=O)Nc2cc(C(=O)NCCC(N)=[NH2+])n(C)c2)n(C)c1 ZINC03872327 3.328
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OC(c1ccncc1)c1ccc(OCC[NH+]2CCCC2)cc1 ZINC34421620 3.822
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CC(C(=O)[O-])c1ccc(-c2ccccc2)cc1 ZINC00000361 2.462
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C[NH+](C)CC(O)Cn1c2ccc(Br)cc2c2cc(Br)ccc21 ZINC00626529 3.577
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NC(=[NH2+])NCC1COc2ccccc2O1 ZINC00000357 3.290
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CCC(C)(C)[NH2+]CC(O)COc1ccccc1C#N ZINC04214111 3.698
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C[NH+](C)CC(O)Cn1c2ccc(Br)cc2c2cc(Br)ccc21 ZINC00626528 3.577
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CC12CCC3C(CCC4CC(=O)CCC43C)C1CCC2=O ZINC04081985 3.912
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COc1ccc(OC(=O)N(CC(=O)[O-])Cc2ccc(OCCc3nc(-c4ccccc4)oc3C)cc2)cc1 ZINC03935839 2.644
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COc1ccccc1OC(=O)c1ccccc1 ZINC00000349 1.342
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CC(C)CC[NH2+]CC1COc2ccccc2O1 ZINC04214115 3.701
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CN1CCN(C(=O)OC2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1 ZINC19632834 3.196
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CCC1(c2ccccc2)C(=O)N(COC)C(=O)N(COC)C1=O ZINC02986592 2.759
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Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1 ZINC00141883 1.529
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O=C([O-])CCCNC(=O)NC1CCCCC1 ZINC08754389 2.493
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CCC(C)C(C(=O)OC1CC[N+](C)(C)CC1)c1ccccc1 ZINC00000595 3.399
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CCC(C)SSc1ncc[nH]1 ZINC13209429 3.983
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CC[N+](C)(CC)CCOC(=O)C(O)(c1cccs1)C1CCCC1 ZINC01690860 3.471
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CC12CCC3C(CCC4CC(=O)CCC43C)C1CCC2O ZINC03814360 3.994
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CC12CCC3C4CCC(=O)C=C4CCC3C1CCC2O ZINC03814379 4.056
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OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O ZINC04095762 4.282
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CC(C)CC(CC[NH+](C(C)C)C(C)C)(C(N)=O)c1ccccn1 ZINC02016048 4.092
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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
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C=CC[NH+]1CCCC1CNC(=O)c1cc(S(N)(=O)=O)cc(OC)c1OC ZINC00601278 4.286
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CC(=O)OC1C[NH+]2CCC1CC2 ZINC00492792 5.711
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CC12CCC3C(CCC4CC(=O)CCC43C)C1CCC2O ZINC03814418 3.994
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CC1(O)CCC2C3CCC4=CC(=O)CCC4(C)C3CCC21C ZINC03814422 4.022
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CC(=O)OC1(C(C)=O)CCC2C3C=C(Cl)C4=CC(=O)C5CC5C4(C)C3CCC21C ZINC03814423 4.827
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C#CC1(O)CCC2C3CCc4cc(OC)ccc4C3CCC21C ZINC03815424 3.810
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C=CC1(C)CC(OC(=O)CSCC[NH+](CC)CC)C2(C)C3C(=O)CCC3(CCC2C)C(C)C1O ZINC25757051 6.200
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O=C([O-])C(=O)Nc1nc(-c2ccc3c(c2)OCCO3)cs1 ZINC03623428 2.594
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CC[NH+]1CCCC1CNC(=O)C(O)(c1ccccc1)c1ccccc1 ZINC00900569 3.950
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CC(C)(OCc1nn(Cc2ccccc2)c2ccccc12)C(=O)[O-] ZINC00004594 2.573
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Cc1nnc(C(C)C)n1C1CC2CCC(C1)[NH+]2CCC(NC(=O)C1CCC(F)(F)CC1)c1ccccc1 ZINC03817234 5.316
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Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O ZINC03871612 5.290
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O=C([O-])CNC(=O)c1ccccc1 ZINC00097685 2.097
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Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O ZINC03871613 5.290
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Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O ZINC03871614 5.290
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c1ccc(OCc2ccc(CCCN3CCOCC3)cc2)cc1 ZINC19865692 1.702
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CC=CC1=C(C(=O)[O-])N2C(=O)C(NC(=O)C(N)c3ccc(O)cc3)C2SC1 ZINC20444132 4.042
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C[NH+]1CCCC1COc1cccnc1 ZINC03805141 4.510
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O=C([O-])C(O)CC(O)C(O)CO ZINC04803503 4.398
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O=C([O-])C(O)CC(O)C(O)CO ZINC01696607 4.398
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C[NH+]1CCCC1Cc1c[nH]c2ccc(CCS(=O)(=O)c3ccccc3)cc12 ZINC03823475 3.921
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C(=Cc1ccccc1)C[NH+]1CCN(C(c2ccccc2)c2ccccc2)CC1 ZINC19632891 2.973
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Nc1ncnc2c1ncn2C1OC(COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])C(O)C1O ZINC03871615 5.290
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CC(c1ccccc1)N(C)C=O ZINC06932229 2.562
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CC(=O)C1CCC2C3CCC4CC(C)(O)CCC4(C)C3CCC12C ZINC03824281 4.279
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O=C([O-])C(O)CC(O)C(O)CO ZINC04803506 4.398
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COc1cc(O)c(C(=O)c2ccccc2)c(O)c1 ZINC00000187 1.868
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O=C([O-])C(O)CC(O)C(O)CO ZINC04803507 4.398
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COc1c2c(cc3c1C(O)N(C)CC3)OCO2 ZINC00000186 3.183
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CCC(C(=O)[O-])c1ccc(CC(C)C)cc1 ZINC00015537 2.827
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O=C([O-])C1[NH+]=C(c2ccccc2)c2cc(Cl)ccc2NC1(O)O ZINC38611850 4.011
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O=C([O-])C1[NH+]=C(c2ccccc2)c2cc(Cl)ccc2NC1(O)O ZINC38611851 4.011
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OCC(O)COc1ccc(Cl)cc1 ZINC00000135 2.102
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NC(=O)NC(=O)C(Cl)c1ccccc1 ZINC00000134 2.455
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OC(c1ccccc1)(c1ccccc1)C1C[NH+]2CCC1CC2 ZINC01298963 4.530
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C[NH2+]CC(C)c1ccccc1 ZINC04298801 3.471
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Clc1cccc(Cl)c1N=C1NCCO1 ZINC13835972 3.267
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[NH3+]C(Cc1ccccc1)C(=O)CCl ZINC02504633 3.251
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CC(C)Cn1cnc2c1c1ccccc1nc2N ZINC19632912 2.230
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CC(O)CN(C)c1ccc(NN)nn1 ZINC00000624 3.193
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CC1(O)CCC2C3CCC4=CC(=O)CCC4=C3C=CC21C ZINC00001727 4.461
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CCC(C(=O)[O-])c1ccc(-c2ccccc2)cc1 ZINC00000111 2.505
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CC(=O)OCC1OC(n2ncc(=O)[nH]c2=O)C(OC(C)=O)C1OC(C)=O ZINC03830255 3.832
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CC(=O)OCC1OC(n2ncc(=O)[nH]c2=O)C(OC(C)=O)C1OC(C)=O ZINC03830256 3.832
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Cn1cc(C(=O)c2cccc3ccccc32)cc1C(=O)[O-] ZINC00001783 2.456
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CC(=O)OCC1OC(n2ncc(=O)[nH]c2=O)C(OC(C)=O)C1OC(C)=O ZINC03830257 3.832
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Cc1cccc(-c2nc3ccccc3c(Nc3ccc4[nH]ncc4c3)n2)n1 ZINC39279791 2.358
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O=C([O-])C1CC2CCCCC2[NH2+]1 ZINC04899687 5.422
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CC(=O)OCC(=O)C1CCC2C3CC=C4CC(O)CCC4(C)C3CCC12C ZINC00538219 4.187
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O=C([O-])C1CC2CCCCC2[NH2+]1 ZINC04899686 5.422
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O=C(OCc1ccccc1)C(O)c1ccccc1 ZINC00000078 2.038
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CC(=O)OCC(=O)C1(O)CCC2C3CCC4=CC(=O)C=CC4(C)C3C(O)CC21C ZINC00608041 4.394
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Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1 ZINC02570895 2.144
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COCc1cccc(CC(O)C=CC2C(O)CC(=O)C2CCSCCCC(=O)OC)c1 ZINC03940680 3.934
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CCC(=O)N(c1ccccc1)C1CC[NH+](C(C)Cc2ccccc2)CC1 ZINC01664586 3.582
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CCC(=O)N(c1ccccc1)C1CC[NH+](C(C)Cc2ccccc2)CC1 ZINC01664587 3.582
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CCOC(=O)Nc1ccc2c(c1)N(C(=O)CCN1CCOCC1)c1ccccc1S2 ZINC19340795 2.446
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O=C([O-])Cc1cc(=O)[nH]c(=O)[nH]1 ZINC00403617 3.258
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NC(=O)C([NH3+])Cc1c[nH]c2ccccc12 ZINC04899521 3.224
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NC(=O)C([NH3+])Cc1ccc(O)cc1 ZINC04899513 3.280
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O=C(c1cc2ccccc2o1)N1CCN(Cc2ccccc2)CC1 ZINC19632922 1.799
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O=C(CO)C(O)C(O)CO ZINC00902219 3.473
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CC(Cc1ccccc1)NC(=O)C([NH3+])CCCC[NH3+] ZINC11680943 3.967
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C[NH+]1CCC(c2c(O)cc(=O)c3c(O)cc(-c4ccccc4Cl)oc2-3)C(O)C1 ZINC05966679 4.616
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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
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Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CC(O)C(O)C(O)CO)c2cc1C ZINC03650334 3.791
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C[NH+]1C2CCC1CC(OC(=O)c1c[nH]c3ccccc13)C2 ZINC18130447 4.892
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Cc1ccccc1NC(=O)C(C)[NH+]1CCCC1 ZINC00000051 3.809
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O=S(=O)([O-])CCN1CCOCC1 ZINC19419111 2.776
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C[NH+]1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1 ZINC19632927 3.379
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CCCCCC=CCC=CCCCCCCCC(=O)[O-] ZINC03802188 2.805
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CC(CC([NH3+])C(=O)[O-])C(=O)[O-] ZINC01747048 5.690
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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
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Cc1cc2nc3nc([O-])[nH]c(=O)c3nc2cc1C ZINC12446789 3.079
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CC1=CC(C)C2(CO)COC(c3ccc(O)cc3)C1C2C ZINC38190856 4.749
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CC[NH+]1CCC(=C2c3ccccc3CCc3ccccc32)C1C ZINC02020004 3.925
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BIN
Contrib/SA_Score/fpscores.pkl.gz
Normal file
BIN
Contrib/SA_Score/fpscores.pkl.gz
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Binary file not shown.
183
Contrib/SA_Score/sascorer.py
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183
Contrib/SA_Score/sascorer.py
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@@ -0,0 +1,183 @@
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#
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# calculation of synthetic accessibility score as described in:
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#
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# Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions
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# Peter Ertl and Ansgar Schuffenhauer
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# Journal of Cheminformatics 1:8 (2009)
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# http://www.jcheminf.com/content/1/1/8
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#
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# several small modifications to the original paper are included
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# particularly slightly different formula for marocyclic penalty
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# and taking into account also molecule symmetry (fingerprint density)
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#
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# for a set of 10k diverse molecules the agreement between the original method
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# as implemented in PipelinePilot and this implementation is r2 = 0.97
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#
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# peter ertl & greg landrum, september 2013
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#
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from rdkit import Chem
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from rdkit.Chem import rdMolDescriptors
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import math
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from collections import defaultdict
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_fscores = None
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def readFragmentScores(name='fpscores'):
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import cPickle,gzip
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global _fscores
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_fscores = cPickle.load(gzip.open('%s.pkl.gz'%name))
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def numBridgeheadsAndSpiro(mol,ri=None):
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if ri is None:
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ri=mol.GetRingInfo()
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arings = [set(x) for x in ri.AtomRings()]
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spiros=set()
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for i,ari in enumerate(arings):
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for j in range(i+1,len(arings)):
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shared=ariås[j]
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if len(shared)==1:
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spiros.update(shared)
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nSpiro=len(spiros)
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# find bonds that are shared between rings that share at least 2 bonds:
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nBridge=0
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brings = [set(x) for x in ri.BondRings()]
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bridges=set()
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for i,bri in enumerate(brings):
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for j in range(i+1,len(brings)):
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shared=bri&brings[j]
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if len(shared)>1:
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atomCounts=defaultdict(int)
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for bi in shared:
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bond = mol.GetBondWithIdx(bi)
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atomCounts[bond.GetBeginAtomIdx()]+=1
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atomCounts[bond.GetEndAtomIdx()]+=1
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tmp=0
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for ai,cnt in atomCounts.items():
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if cnt==1:
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tmp+=1
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bridges.add(ai)
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#if tmp!=2: # no need to stress the users
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#print 'huh:',tmp
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return len(bridges),nSpiro
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def calculateScore(m):
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if _fscores is None: readFragmentScores()
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# fragment score
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fp = rdMolDescriptors.GetMorganFingerprint(m,2) #<- 2 is the *radius* of the circular fingerprint
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fps = fp.GetNonzeroElements()
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score1 = 0.
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nf = 0
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for bitId,v in fps.iteritems():
|
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nf += v
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sfp = bitId
|
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score1 += _fscores.get(sfp,-4)*v
|
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score1 /= nf
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# features score
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nAtoms = m.GetNumAtoms()
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nChiralCenters = len(Chem.FindMolChiralCenters(m,includeUnassigned=True))
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ri = m.GetRingInfo()
|
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nBridgeheads,nSpiro=numBridgeheadsAndSpiro(m,ri)
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nMacrocycles=0
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for x in ri.AtomRings():
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if len(x)>8: nMacrocycles+=1
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sizePenalty = nAtoms**1.005 - nAtoms
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stereoPenalty = math.log10(nChiralCenters+1)
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spiroPenalty = math.log10(nSpiro+1)
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bridgePenalty = math.log10(nBridgeheads+1)
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macrocyclePenalty = 0.
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# ---------------------------------------
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# This differs from the paper, which defines:
|
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# macrocyclePenalty = math.log10(nMacrocycles+1)
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# This form generates better results when 2 or more macrocycles are present
|
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if nMacrocycles > 0: macrocyclePenalty = math.log10(2)
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|
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score2 = 0. -sizePenalty -stereoPenalty -spiroPenalty -bridgePenalty -macrocyclePenalty
|
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|
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# correction for the fingerprint density
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# not in the original publication, added in version 1.1
|
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# to make highly symmetrical molecules easier to synthetise
|
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score3 = 0.
|
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if nAtoms > len(fps):
|
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score3 = math.log(float(nAtoms) / len(fps)) * .5
|
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|
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sascore = score1 + score2 + score3
|
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|
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# need to transform "raw" value into scale between 1 and 10
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min = -4.0
|
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max = 2.5
|
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sascore = 11. - (sascore - min + 1) / (max - min) * 9.
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# smooth the 10-end
|
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if sascore > 8.: sascore = 8. + math.log(sascore+1.-9.)
|
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if sascore > 10.: sascore = 10.0
|
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elif sascore < 1.: sascore = 1.0
|
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|
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return sascore
|
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|
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|
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def processMols(mols,outf):
|
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|
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print 'smiles\tName\tsa_score'
|
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count = {}
|
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for i,m in enumerate(mols):
|
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if m is None:
|
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continue
|
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|
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s = calculateScore(m)
|
||||
|
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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.
|
||||
#
|
||||
Reference in New Issue
Block a user