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QED stands for quantitative estimation of drug-likeness and the concept was for the first time introduced by Richard Bickerton and coworkers [1]. The empirical rationale of the QED measure reflects the underlying distribution of molecular properties including molecular weight, logP, topological polar surface area, number of hydrogen bond donors and acceptors, the number of aromatic rings and rotatable bonds, and the presence of unwanted chemical functionalities. The QED results as generated by the RDKit-based implementation of Biscu-it(tm) are not completely identical to those from the original publication [1]. These differences are a consequence of differences within the underlying calculated property calculators used in both methods. For example, discrepancies can be noted in the results from the logP calculations, nevertheless despite the fact that both approaches (Pipeline Pilot in the original publication and RDKit in our Biscu-it(tm) implementation) mention to use the Wildmann and Crippen methodology for the calculation of their logP-values [2]. However, the differences in the resulting QED-values are very small and are not compromising the usefulness of using Qed in your daily research. [1] Bickerton, G.R.; Paolini, G.V.; Besnard, J.; Muresan, S.; Hopkins, A.L. (2012) 'Quantifying the chemical beauty of drugs', Nature Chemistry, 4, 90-98 [http://dx.doi.org/10.1038/nchem.1243] History: 2012-04 Adapted to internal RDkit implementation 2013-05 moved to rdkit.Chem.QED
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QEDproperties = namedtuple('QEDproperties', 'MW,ALOGP,HBA,HBD,
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ADSparameter = namedtuple('ADSparameter', 'A,B,C,D,E,F,DMAX')
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WEIGHT_MAX = QEDproperties(0.50, 0.25, 0.00, 0.50, 0.00, 0.50,
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WEIGHT_MEAN = QEDproperties(0.66, 0.46, 0.05, 0.61, 0.06, 0.65
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WEIGHT_NONE = QEDproperties(1.00, 1.00, 1.00, 1.00, 1.00, 1.00
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AliphaticRings = Chem.MolFromSmarts('[$([A;R][!a])]')
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AcceptorSmarts = ['[oH0;X2]', '[OH1;X2;v2]', '[OH0;X2;v2]', '[
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Acceptors = [Chem.MolFromSmarts(hba) for hba in AcceptorSmarts]
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StructuralAlertSmarts = ['*1[O,S,N]*1', '[S,C](=[O,S])[F,Br,Cl
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StructuralAlerts = [Chem.MolFromSmarts(smarts) for smarts in S
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adsParameters = {'MW': ADSparameter(A= 2.817065973, B= 392.575
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Imports: namedtuple, math, Chem, MolSurf, Crippen, rdmd, setDescriptorVersion
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Calculate the weighted sum of ADS mapped properties some examples from the QED paper, reference values from Peter G's original implementation >>> m = Chem.MolFromSmiles('N=C(CCSCc1csc(N=C(N)N)n1)NS(N)(=O)=O') >>> qed(m) 0.253... >>> m = Chem.MolFromSmiles('CNC(=NCCSCc1nc[nH]c1C)NC#N') >>> qed(m) 0.234... >>> m = Chem.MolFromSmiles('CCCCCNC(=N)NN=Cc1c[nH]c2ccc(CO)cc12') >>> qed(m) 0.234...
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QEDproperties
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WEIGHT_MAX
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WEIGHT_MEAN
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WEIGHT_NONE
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AcceptorSmarts
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StructuralAlertSmarts
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StructuralAlerts
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adsParameters
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