Package rdkit :: Package Chem :: Module MolSurf

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# Module MolSurf

source code

    Exposes functionality for MOE-like approximate molecular surface area
    descriptors.

      The MOE-like VSA descriptors are also calculated here

Functions | [hide private]

_LabuteHelper(mol, includeHs=1, force=0) *Internal Use Only* helper function for LabuteASA calculation returns an array of atomic contributions to the ASA | source code

_pyLabuteHelper(mol, includeHs=1, force=0) *Internal Use Only* helper function for LabuteASA calculation returns an array of atomic contributions to the ASA | source code

pySMR_VSA_(mol, bins=None, force=1) *Internal Use Only*... | source code

pySlogP_VSA_(mol, bins=None, force=1) *Internal Use Only*... | source code

pyPEOE_VSA_(mol, bins=None, force=1) *Internal Use Only*... | source code

_InstallDescriptors() | source code

pyLabuteASA(mol, includeHs=1) calculates Labute's Approximate Surface Area (ASA from MOE) | source code

_pyTPSAContribs(mol, verbose=False) DEPRECATED: this has been reimplmented in C++ calculates atomic contributions to a molecules TPSA | source code

_pyTPSA(mol, verbose=False) DEPRECATED: this has been reimplmented in C++ calculates the polar surface area of a molecule based upon fragments | source code

Variables | [hide private]

| radCol = `5`
| bondScaleFacts = `[.1, 0,.2,.3]`
| mrBins = `[1.29, 1.82, 2.24, 2.45, 2.75, 3.05, 3.63, 3.8, 4.0]`
| SMR_VSA_ = `rdMolDescriptors.SMR_VSA_`
| logpBins = `[-0.4,-0.2, 0, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5,`...``
| SlogP_VSA_ = `rdMolDescriptors.SlogP_VSA_`
| chgBins = `[-.3,-.25,-.20,-.15,-.10,-.05, 0,.05,.10,.15,.20,.25`...``
| PEOE_VSA_ = `rdMolDescriptors.PEOE_VSA_`
| LabuteASA = `lambda* x,** y:`
| TPSA = `lambda* x,** y:`

Imports: Chem, numTable, Crippen, rdPartialCharges, rdMolDescriptors, numpy, bisect

Function Details | [hide private]

### _LabuteHelper(mol, includeHs=1, force=0)

source code

    *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

### _pyLabuteHelper(mol, includeHs=1, force=0)

source code

    *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

### pySMR_VSA_(mol, bins=None, force=1)

source code

    *Internal Use Only*

### pySlogP_VSA_(mol, bins=None, force=1)

source code

    *Internal Use Only*

### pyPEOE_VSA_(mol, bins=None, force=1)

source code

    *Internal Use Only*

### pyLabuteASA(mol, includeHs=1)

source code

    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)

### _pyTPSAContribs(mol, verbose=False)

source code

    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.

### _pyTPSA(mol, verbose=False)

source code

    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

Variables Details | [hide private]

### logpBins

Value:

      [-0.4,-0.2, 0, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5, 0.6]

### chgBins

Value:

      [-.3,-.25,-.20,-.15,-.10,-.05, 0,.05,.10,.15,.20,.25,.30]