Package rdkit :: Package Chem :: Module Lipinski
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Module Lipinski

source code

Calculation of Lipinski parameters for molecules

Functions [hide private]
 
_NumMatches(mol, smarts) source code
 
NumHDonors(x)
Number of Hydrogen Bond Donors
source code
 
_HDonors(x, y=Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;...) source code
 
NumHAcceptors(x)
Number of Hydrogen Bond Acceptors
source code
 
_HAcceptors(x, y=Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]...) source code
 
NumHeteroatoms(x)
Number of Heteroatoms
source code
 
_Heteroatoms(x, y=Chem.MolFromSmarts('[!#6;!#1]')) source code
 
NumRotatableBonds(x)
Number of Rotatable Bonds
source code
 
_RotatableBonds(x, y=Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]')) source code
 
NOCount(x)
Number of Nitrogens and Oxygens
source code
 
NHOHCount(x)
Number of NHs or OHs
source code
 
RingCount(x) source code
 
HeavyAtomCount(mol)
Number of heavy atoms a molecule.
source code
 
FractionCSP3(x, y=<Boost.Python.function object at 0x16510a0>)
CalcFractionCSP3( (Mol)mol) -> float : returns the fraction of C atoms that are SP3 hybridized
source code
 
NumAliphaticCarbocycles(x, y=<Boost.Python.function object at 0x1650f50>)
CalcNumAliphaticCarbocycles( (Mol)mol) -> int : returns the number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule
source code
 
NumAliphaticHeterocycles(x, y=<Boost.Python.function object at 0x1650ee0>)
CalcNumAliphaticHeterocycles( (Mol)mol) -> int : returns the number of aliphatic (containing at least one non-aromatic bond) heterocycles for a molecule
source code
 
NumAliphaticRings(x, y=<Boost.Python.function object at 0x1650e70>)
CalcNumAliphaticRings( (Mol)mol) -> int : returns the number of aliphatic (containing at least one non-aromatic bond) rings for a molecule
source code
 
NumAromaticCarbocycles(x, y=<Boost.Python.function object at 0x1650d20>)
CalcNumAromaticCarbocycles( (Mol)mol) -> int : returns the number of aromatic carbocycles for a molecule
source code
 
NumAromaticHeterocycles(x, y=<Boost.Python.function object at 0x1650cb0>)
CalcNumAromaticHeterocycles( (Mol)mol) -> int : returns the number of aromatic heterocycles for a molecule
source code
 
NumAromaticRings(x, y=<Boost.Python.function object at 0x1650b60>)
CalcNumAromaticRings( (Mol)mol) -> int : returns the number of aromatic rings for a molecule
source code
 
NumSaturatedCarbocycles(x, y=<Boost.Python.function object at 0x1650e00>)
CalcNumSaturatedCarbocycles( (Mol)mol) -> int : returns the number of saturated carbocycles for a molecule
source code
 
NumSaturatedHeterocycles(x, y=<Boost.Python.function object at 0x1650d90>)
CalcNumSaturatedHeterocycles( (Mol)mol) -> int : returns the number of saturated heterocycles for a molecule
source code
 
NumSaturatedRings(x, y=<Boost.Python.function object at 0x1650bd0>)
CalcNumSaturatedRings( (Mol)mol) -> int : returns the number of saturated rings for a molecule
source code
 
_fn(x, y=<Boost.Python.function object at 0x1650f50>)
CalcNumAliphaticCarbocycles( (Mol)mol) -> int : returns the number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule
source code
Variables [hide private]
  HDonorSmarts = Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;...
  HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,...
  HeteroatomSmarts = Chem.MolFromSmarts('[!#6;!#1]')
  RotatableBondSmarts = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$...
  NHOHSmarts = Chem.MolFromSmarts('[#8H1,#7H1,#7H2,#7H3]')
  NOCountSmarts = Chem.MolFromSmarts('[#7,#8]')
  _bulkConvert = ('CalcFractionCSP3', 'CalcNumAromaticRings', 'C...
  __package__ = 'rdkit.Chem'
  nm = 'NumAliphaticCarbocycles'
  txt = 'CalcNumAliphaticCarbocycles'

Imports: Chem, rdMolDescriptors, _cfn


Function Details [hide private]

FractionCSP3(x, y=<Boost.Python.function object at 0x16510a0>)

source code 

CalcFractionCSP3( (Mol)mol) -> float :
    returns the fraction of C atoms that are SP3 hybridized

    C++ signature :
        double CalcFractionCSP3(RDKit::ROMol)

NumAliphaticCarbocycles(x, y=<Boost.Python.function object at 0x1650f50>)

source code 

CalcNumAliphaticCarbocycles( (Mol)mol) -> int :
    returns the number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule

    C++ signature :
        unsigned int CalcNumAliphaticCarbocycles(RDKit::ROMol)

NumAliphaticHeterocycles(x, y=<Boost.Python.function object at 0x1650ee0>)

source code 

CalcNumAliphaticHeterocycles( (Mol)mol) -> int :
    returns the number of aliphatic (containing at least one non-aromatic bond) heterocycles for a molecule

    C++ signature :
        unsigned int CalcNumAliphaticHeterocycles(RDKit::ROMol)

NumAliphaticRings(x, y=<Boost.Python.function object at 0x1650e70>)

source code 

CalcNumAliphaticRings( (Mol)mol) -> int :
    returns the number of aliphatic (containing at least one non-aromatic bond) rings for a molecule

    C++ signature :
        unsigned int CalcNumAliphaticRings(RDKit::ROMol)

NumAromaticCarbocycles(x, y=<Boost.Python.function object at 0x1650d20>)

source code 

CalcNumAromaticCarbocycles( (Mol)mol) -> int :
    returns the number of aromatic carbocycles for a molecule

    C++ signature :
        unsigned int CalcNumAromaticCarbocycles(RDKit::ROMol)

NumAromaticHeterocycles(x, y=<Boost.Python.function object at 0x1650cb0>)

source code 

CalcNumAromaticHeterocycles( (Mol)mol) -> int :
    returns the number of aromatic heterocycles for a molecule

    C++ signature :
        unsigned int CalcNumAromaticHeterocycles(RDKit::ROMol)

NumAromaticRings(x, y=<Boost.Python.function object at 0x1650b60>)

source code 

CalcNumAromaticRings( (Mol)mol) -> int :
    returns the number of aromatic rings for a molecule

    C++ signature :
        unsigned int CalcNumAromaticRings(RDKit::ROMol)

NumSaturatedCarbocycles(x, y=<Boost.Python.function object at 0x1650e00>)

source code 

CalcNumSaturatedCarbocycles( (Mol)mol) -> int :
    returns the number of saturated carbocycles for a molecule

    C++ signature :
        unsigned int CalcNumSaturatedCarbocycles(RDKit::ROMol)

NumSaturatedHeterocycles(x, y=<Boost.Python.function object at 0x1650d90>)

source code 

CalcNumSaturatedHeterocycles( (Mol)mol) -> int :
    returns the number of saturated heterocycles for a molecule

    C++ signature :
        unsigned int CalcNumSaturatedHeterocycles(RDKit::ROMol)

NumSaturatedRings(x, y=<Boost.Python.function object at 0x1650bd0>)

source code 

CalcNumSaturatedRings( (Mol)mol) -> int :
    returns the number of saturated rings for a molecule

    C++ signature :
        unsigned int CalcNumSaturatedRings(RDKit::ROMol)

_fn(x, y=<Boost.Python.function object at 0x1650f50>)

source code 

CalcNumAliphaticCarbocycles( (Mol)mol) -> int :
    returns the number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule

    C++ signature :
        unsigned int CalcNumAliphaticCarbocycles(RDKit::ROMol)


Variables Details [hide private]

HDonorSmarts

Value:
Chem.MolFromSmarts('[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([\
n;H1;+0])]')

HAcceptorSmarts

Value:
Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),\
$([O,S;H0;v2]),$([O,S;-]),\
$([N;v3;!$(N-*=!@[O,N,P,S])]),\
$([nH0,o,s;+0])\
]')

RotatableBondSmarts

Value:
Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]')

_bulkConvert

Value:
('CalcFractionCSP3',
 'CalcNumAromaticRings',
 'CalcNumSaturatedRings',
 'CalcNumAromaticHeterocycles',
 'CalcNumAromaticCarbocycles',
 'CalcNumSaturatedHeterocycles',
 'CalcNumSaturatedCarbocycles',
 'CalcNumAliphaticRings',
...