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]