rdkit.Chem.MolSurf

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
LabuteASA(*x, **y) | 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
TPSA(*x, **y) | source code
PEOE_VSA1(x, y=0) MOE Charge VSA Descriptor 1 (-inf < x < -0.30) | source code
PEOE_VSA10(x, y=9) MOE Charge VSA Descriptor 10 ( 0.10 <= x < 0.15) | source code
PEOE_VSA11(x, y=10) MOE Charge VSA Descriptor 11 ( 0.15 <= x < 0.20) | source code
PEOE_VSA12(x, y=11) MOE Charge VSA Descriptor 12 ( 0.20 <= x < 0.25) | source code
PEOE_VSA13(x, y=12) MOE Charge VSA Descriptor 13 ( 0.25 <= x < 0.30) | source code
PEOE_VSA14(x, y=13) MOE Charge VSA Descriptor 14 ( 0.30 <= x < inf) | source code
PEOE_VSA2(x, y=1) MOE Charge VSA Descriptor 2 (-0.30 <= x < -0.25) | source code
PEOE_VSA3(x, y=2) MOE Charge VSA Descriptor 3 (-0.25 <= x < -0.20) | source code
PEOE_VSA4(x, y=3) MOE Charge VSA Descriptor 4 (-0.20 <= x < -0.15) | source code
PEOE_VSA5(x, y=4) MOE Charge VSA Descriptor 5 (-0.15 <= x < -0.10) | source code
PEOE_VSA6(x, y=5) MOE Charge VSA Descriptor 6 (-0.10 <= x < -0.05) | source code
PEOE_VSA7(x, y=6) MOE Charge VSA Descriptor 7 (-0.05 <= x < 0.00) | source code
PEOE_VSA8(x, y=7) MOE Charge VSA Descriptor 8 ( 0.00 <= x < 0.05) | source code
PEOE_VSA9(x, y=8) MOE Charge VSA Descriptor 9 ( 0.05 <= x < 0.10) | source code
SMR_VSA1(x, y=0) MOE MR VSA Descriptor 1 (-inf < x < 1.29) | source code
SMR_VSA10(x, y=9) MOE MR VSA Descriptor 10 ( 4.00 <= x < inf) | source code
SMR_VSA2(x, y=1) MOE MR VSA Descriptor 2 ( 1.29 <= x < 1.82) | source code
SMR_VSA3(x, y=2) MOE MR VSA Descriptor 3 ( 1.82 <= x < 2.24) | source code
SMR_VSA4(x, y=3) MOE MR VSA Descriptor 4 ( 2.24 <= x < 2.45) | source code
SMR_VSA5(x, y=4) MOE MR VSA Descriptor 5 ( 2.45 <= x < 2.75) | source code
SMR_VSA6(x, y=5) MOE MR VSA Descriptor 6 ( 2.75 <= x < 3.05) | source code
SMR_VSA7(x, y=6) MOE MR VSA Descriptor 7 ( 3.05 <= x < 3.63) | source code
SMR_VSA8(x, y=7) MOE MR VSA Descriptor 8 ( 3.63 <= x < 3.80) | source code
SMR_VSA9(x, y=8) MOE MR VSA Descriptor 9 ( 3.80 <= x < 4.00) | source code
SlogP_VSA1(x, y=0) MOE logP VSA Descriptor 1 (-inf < x < -0.40) | source code
SlogP_VSA10(x, y=9) MOE logP VSA Descriptor 10 ( 0.40 <= x < 0.50) | source code
SlogP_VSA11(x, y=10) MOE logP VSA Descriptor 11 ( 0.50 <= x < 0.60) | source code
SlogP_VSA12(x, y=11) MOE logP VSA Descriptor 12 ( 0.60 <= x < inf) | source code
SlogP_VSA2(x, y=1) MOE logP VSA Descriptor 2 (-0.40 <= x < -0.20) | source code
SlogP_VSA3(x, y=2) MOE logP VSA Descriptor 3 (-0.20 <= x < 0.00) | source code
SlogP_VSA4(x, y=3) MOE logP VSA Descriptor 4 ( 0.00 <= x < 0.10) | source code
SlogP_VSA5(x, y=4) MOE logP VSA Descriptor 5 ( 0.10 <= x < 0.15) | source code
SlogP_VSA6(x, y=5) MOE logP VSA Descriptor 6 ( 0.15 <= x < 0.20) | source code
SlogP_VSA7(x, y=6) MOE logP VSA Descriptor 7 ( 0.20 <= x < 0.25) | source code
SlogP_VSA8(x, y=7) MOE logP VSA Descriptor 8 ( 0.25 <= x < 0.30) | source code
SlogP_VSA9(x, y=8) MOE logP VSA Descriptor 9 ( 0.30 <= x < 0.40) | source code

Variables | [hide private]
| radCol = `5`
| bondScaleFacts = ``[`0.1`,` 0`,` 0.2`,` 0.3`]``
| mrBins = ``[`1.29`,` 1.82`,` 2.24`,` 2.45`,` 2.75`,` 3.05`,` 3.63`,` 3.8`,` 4.0`]``
| logpBins = ``[`-0.4`,` -0.2`,` 0`,` 0.1`,` 0.15`,` 0.2`,` 0.25`,` 0.3`,` 0.4`,` 0.5`...``
| chgBins = ``[`-0.3`,` -0.25`,` -0.2`,` -0.15`,` -0.1`,` -0.05`,` 0`,` 0.05`,` 0.1`...``
| __package__ = ``'``rdkit.Chem``'``

Imports: Chem, numTable, Crippen, rdPartialCharges, rdMolDescriptors, numpy, bisect, SMR_VSA_, SlogP_VSA_, PEOE_VSA_

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:
      [-0.3,
       -0.25,
       -0.2,
       -0.15,
       -0.1,
       -0.05,
       0,
       0.05,
      ...