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,
...