Package Chem :: Module Crippen

Module Crippen

Atom-based calculation of LogP and MR using Crippen's approach


Reference:
  S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999)

Functions

[hide private]

_ReadPatts(fileName)
*Internal Use Only*...

source code

_GetAtomContribs(...)
returns (as a list of 2-tuples) the contributions of each atom to...

source code

_pyGetAtomContribs(mol, patts=None, order=None, verbose=0, force=0)
*Internal Use Only* calculates atomic contributions to the LogP and MR values if the argument *force* is not set, we'll use the molecules stored _crippenContribs value when possible instead of re-calculating.

source code

_Init()

source code

pyMolLogP(inMol, patts=None, order=None, verbose=0, addHs=1)
Crippen LogP value Definition From JCICS _39_ 868-873 (1999) **Arguments** - inMol: a molecule - patts: (optional) if provided this should be a dictionary of 4 tuples: 1) smarts text 2) SmartsPattern object 3) logp contribution 4) MR contribution - order: (optional) a list with the order in which the keys of the pattern dictionary should be evaluated - verbose: (optional) toggles verbose printing - addHs: (optional) toggles adding of Hs to the molecule for the calculation.

source code

pyMolMR(inMol, patts=None, order=None, verbose=0, addHs=1)
Crippen MR value Definition From JCICS _39_ 868-873 (1999) **Arguments** - inMol: a molecule - patts: (optional) if provided this should be a dictionary of 4 tuples: 1) smarts text 2) SmartsPattern object 3) logp contribution 4) MR contribution - order: (optional) a list with the order in which the keys of the pattern dictionary should be evaluated - verbose: (optional) toggles verbose printing - addHs: (optional) toggles adding of Hs to the molecule for the calculation.

source code

MolLogP(*x, **y)
Wildman-Crippen LogP value Uses an atom-based scheme based on the values in the paper: S.

source code

MolMR(*x, **y)
Wildman-Crippen MR value Uses an atom-based scheme based on the values in the paper: S.

source code

Variables

[hide private]

_smartsPatterns = {}

_patternOrder = []

defaultPatternFileName = '/scratch/RDKitBuild_24_05_08/RDKit/D...

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]

_ReadPatts(fileName)

source code

*Internal Use Only*

parses the pattern list from the data file

_GetAtomContribs(...)

source code

returns (as a list of 2-tuples) the contributions of each atom to
the Wildman-Cripppen logp and mr value
C++ signature:
    _CalcCrippenContribs(RDKit::ROMol mol, bool force=False) -> boost::python::list

_pyGetAtomContribs(mol, patts=None, order=None, verbose=0, force=0)

source code

*Internal Use Only*

  calculates atomic contributions to the LogP and MR values

  if the argument *force* is not set, we'll use the molecules stored
  _crippenContribs value when possible instead of re-calculating.

**Note:** Changes here affect the version numbers of MolLogP and MolMR
  as well as the VSA descriptors in Chem.MolSurf

pyMolLogP(inMol, patts=None, order=None, verbose=0, addHs=1)

source code

Crippen LogP value

Definition From JCICS _39_ 868-873 (1999)

**Arguments**

  - inMol: a molecule

  - patts: (optional)  if provided this should be a dictionary of 4 tuples:

     1)  smarts text

     2)  SmartsPattern object

     3)  logp contribution

     4)  MR contribution
     
  - order: (optional) a list with the order in which the keys of the pattern dictionary
    should be evaluated

  - verbose: (optional) toggles verbose printing

  - addHs: (optional) toggles adding of Hs to the molecule for the calculation.
    If positive, explicit and implicit Hs will be used in the calculation.
    If this negative, then only explicit hydrogens will be taken into account in the
    calculation.  This is available to allow matching of results obtained with the old
    backend code.

pyMolMR(inMol, patts=None, order=None, verbose=0, addHs=1)

source code

Crippen MR value

Definition From JCICS _39_ 868-873 (1999)

**Arguments**

  - inMol: a molecule

  - patts: (optional)  if provided this should be a dictionary of 4 tuples:

     1)  smarts text

     2)  SmartsPattern object

     3)  logp contribution

     4)  MR contribution
     
  - order: (optional) a list with the order in which the keys of the pattern dictionary
    should be evaluated

  - verbose: (optional) toggles verbose printing

  - addHs: (optional) toggles adding of Hs to the molecule for the calculation.
    If positive, explicit and implicit Hs will be used in the calculation.
    If this negative, then only explicit hydrogens will be taken into account in the
    calculation.  This is available to allow matching of results obtained with the old
    backend code.

MolLogP(*x, **y)

source code

Wildman-Crippen LogP value

Uses an atom-based scheme based on the values in the paper:
   S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)

**Arguments**

  - inMol: a molecule

  - addHs: (optional) toggles adding of Hs to the molecule for the calculation.
    If true, hydrogens will be added to the molecule and used in the calculation.

MolMR(*x, **y)

source code

Wildman-Crippen MR value

Uses an atom-based scheme based on the values in the paper:
   S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)

**Arguments**

  - inMol: a molecule

  - addHs: (optional) toggles adding of Hs to the molecule for the calculation.
    If true, hydrogens will be added to the molecule and used in the calculation.

Variables Details

[hide private]

defaultPatternFileName

Value:

'/scratch/RDKitBuild_24_05_08/RDKit/Data/Crippen.txt'