Package Chem :: Module MolSurf

Module MolSurf

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*...

source code

_pyLabuteHelper(mol, includeHs=1, force=0)
*Internal Use Only*...

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) Definition from P.

source code

LabuteASA(*x, **y)

source code

_TPSAContribs(mol, verbose=False)
calculates atomic contributions to a molecules TPSA Algorithm in: P.

source code

TPSA(mol, verbose=False)
calculates the polar surface area of a molecule based upon fragments Algorithm in: P.

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...

Complex0 = 'F'

Complex16 = 'F'

Complex32 = 'F'

Complex64 = 'D'

Complex8 = 'F'

Float0 = 'f'

Float16 = 'f'

Float32 = 'f'

Float64 = 'd'

Float8 = 'f'

Int0 = '1'

Int16 = 's'

Int32 = 'i'

Int8 = '1'

absolute = <ufunc 'absolute'>

add = <ufunc 'add'>

arccos = <ufunc 'arccos'>

arccosh = <ufunc 'arccosh'>

arcsin = <ufunc 'arcsin'>

arcsinh = <ufunc 'arcsinh'>

arctan = <ufunc 'arctan'>

arctan2 = <ufunc 'arctan2'>

arctanh = <ufunc 'arctanh'>

bitwise_and = <ufunc 'bitwise_and'>

bitwise_or = <ufunc 'bitwise_or'>

bitwise_xor = <ufunc 'bitwise_xor'>

ceil = <ufunc 'ceil'>

conjugate = <ufunc 'conjugate'>

cos = <ufunc 'cos'>

cosh = <ufunc 'cosh'>

divide = <ufunc 'divide'>

divide_safe = <ufunc 'divide_safe'>

e = 2.71828182846

equal = <ufunc 'equal'>

exp = <ufunc 'exp'>

fabs = <ufunc 'fabs'>

floor = <ufunc 'floor'>

floor_divide = <ufunc 'floor_divide'>

fmod = <ufunc 'fmod'>

greater = <ufunc 'greater'>

greater_equal = <ufunc 'greater_equal'>

hypot = <ufunc 'hypot'>

invert = <ufunc 'invert'>

left_shift = <ufunc 'left_shift'>

less = <ufunc 'less'>

less_equal = <ufunc 'less_equal'>

log = <ufunc 'log'>

log10 = <ufunc 'log10'>

logical_and = <ufunc 'logical_and'>

logical_not = <ufunc 'logical_not'>

logical_or = <ufunc 'logical_or'>

logical_xor = <ufunc 'logical_xor'>

maximum = <ufunc 'maximum'>

minimum = <ufunc 'minimum'>

multiply = <ufunc 'multiply'>

negative = <ufunc 'negative'>

not_equal = <ufunc 'not_equal'>

pi = 3.14159265359

power = <ufunc 'power'>

remainder = <ufunc 'remainder'>

right_shift = <ufunc 'right_shift'>

sin = <ufunc 'sin'>

sinh = <ufunc 'sinh'>

sqrt = <ufunc 'sqrt'>

subtract = <ufunc 'subtract'>

tan = <ufunc 'tan'>

tanh = <ufunc 'tanh'>

true_divide = <ufunc 'true_divide'>

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,
...