rdkit.Chem.Crippen

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

# Module Crippen

source code

    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(...) _CalcCrippenContribs( (Mol)mol [, (bool)force=False]) -> list : returns (as a list of 2-tuples) the contributions of each atom to the Wildman-Cripppen logp and mr value | source code
_pyGetAtomContribs(mol, patts=None, order=None, verbose=0, force=0) *Internal Use Only* | source code
_Init() | source code
pyMolLogP(inMol, patts=None, order=None, verbose=0, addHs=1) Crippen LogP value | source code
pyMolMR(inMol, patts=None, order=None, verbose=0, addHs=1) Crippen MR value | source code
MolLogP(*x, **y) Wildman-Crippen LogP value | source code
MolMR(*x, **y) Wildman-Crippen MR value | source code

Variables | [hide private]
| _smartsPatterns = ``{``}``
| _patternOrder = ``[``]``
| defaultPatternFileName = ``'``/scratch/RDKit_trunk/Data/Crippen.txt``'``

Imports: os, RDConfig, Chem, rdMolDescriptors, numpy

Function Details | [hide private]

### _ReadPatts(fileName) | source code
    *Internal Use Only*

    parses the pattern list from the data file

### _GetAtomContribs(...) | source code
    _CalcCrippenContribs( (Mol)mol [, (bool)force=False]) -> list :
        returns (as a list of 2-tuples) the contributions of each atom to
        the Wildman-Cripppen logp and mr value

        C++ signature :
            boost::python::list _CalcCrippenContribs(RDKit::ROMol [,bool=False])

### _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.