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Exposes functionality for MOE-like approximate molecular surface area descriptors. The MOE-like VSA descriptors are also calculated here
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radCol = 5
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bondScaleFacts = [.1, 0,.2,.3]
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mrBins = [1.29, 1.82, 2.24, 2.45, 2.75, 3.05, 3.63, 3.8, 4.0]
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SMR_VSA_ = rdMolDescriptors.SMR_VSA_
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logpBins = [-0.4,-0.2, 0, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5,
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SlogP_VSA_ = rdMolDescriptors.SlogP_VSA_
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chgBins = [-.3,-.25,-.20,-.15,-.10,-.05, 0,.05,.10,.15,.20,.25
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PEOE_VSA_ = rdMolDescriptors.PEOE_VSA_
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LabuteASA = lambda* x,** y:
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TPSA = lambda* x,** y:
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Imports: Chem, numTable, Crippen, rdPartialCharges, rdMolDescriptors, numpy, bisect
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*Internal Use Only* helper function for LabuteASA calculation returns an array of atomic contributions to the ASA **Note:** Changes here affect the version numbers of all ASA descriptors |
*Internal Use Only* helper function for LabuteASA calculation returns an array of atomic contributions to the ASA **Note:** Changes here affect the version numbers of all ASA descriptors |
*Internal Use Only* |
*Internal Use Only* |
*Internal Use Only* |
calculates Labute's Approximate Surface Area (ASA from MOE) Definition from P. Labute's article in the Journal of the Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477 (2000) |
DEPRECATED: this has been reimplmented in C++ calculates atomic contributions to a molecules TPSA Algorithm described in: P. Ertl, B. Rohde, P. Selzer Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based Contributions and Its Application to the Prediction of Drug Transport Properties, J.Med.Chem. 43, 3714-3717, 2000 Implementation based on the Daylight contrib program tpsa.c NOTE: The JMC paper describing the TPSA algorithm includes contributions from sulfur and phosphorus, however according to Peter Ertl (personal communication, 2010) the correlation of TPSA with various ADME properties is better if only contributions from oxygen and nitrogen are used. This matches the daylight contrib implementation. |
DEPRECATED: this has been reimplmented in C++ calculates the polar surface area of a molecule based upon fragments Algorithm in: P. Ertl, B. Rohde, P. Selzer Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based Contributions and Its Application to the Prediction of Drug Transport Properties, J.Med.Chem. 43, 3714-3717, 2000 Implementation based on the Daylight contrib program tpsa.c |
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logpBins
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chgBins
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