rdkit.Chem.MolSurf

Package rdkit :: Package Chem :: Module MolSurf |
[hide private]
[frames] | no frames]

# 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
SMR_VSA_(mol, bins=None, force=1) *Internal Use Only*... | source code
SlogP_VSA_(mol, bins=None, force=1) *Internal Use Only*... | source code
PEOE_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
_TPSAContribs(mol, verbose=False) calculates atomic contributions to a molecules TPSA | source code
TPSA(mol, verbose=False) calculates the polar surface area of a molecule based upon fragments | source code
PEOE_VSA1(x, y=0) MOE Chage 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`...``

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

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

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

### PEOE_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)

### _TPSAContribs(mol, verbose=False) | source code
    calculates atomic contributions to a molecules TPSA

    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

### TPSA(mol, verbose=False) | source code
    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,
      ...