Package rdkit :: Package Chem :: Package Fingerprints :: Module FingerprintMols
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Module FingerprintMols

source code

utility functionality for fingerprinting sets of molecules
 includes a command line app for working with fingerprints
 and databases


Sample Usage:

  python FingerprintMols.py  -d data.gdb         -t 'raw_dop_data' --smilesName="Structure" --idName="Mol_ID"          --outTable="daylight_sig"

Classes [hide private]
  FingerprinterDetails
class for storing the details of a fingerprinting run,...
Functions [hide private]
 
error(msg) source code
 
message(msg) source code
 
GetRDKFingerprint(mol)
uses default parameters
source code
 
FoldFingerprintToTargetDensity(fp, **fpArgs) source code
 
FingerprintMol(mol, fingerprinter=<Boost.Python.function object at 0x2856ec0>, **fpArgs) source code
 
FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object at 0x2856ec0>, reportFreq=10, maxMols=-1, **fpArgs)
fpArgs are passed as keyword arguments to the fingerprinter
source code
 
FingerprintsFromMols(mols, fingerprinter=<Boost.Python.function object at 0x2856ec0>, reportFreq=10, maxMols=-1, **fpArgs)
fpArgs are passed as keyword arguments to the fingerprinter
source code
 
FingerprintsFromPickles(dataSource, idCol, pklCol, fingerprinter=<Boost.Python.function object at 0x2856ec0>, reportFreq=10, maxMols=-1, **fpArgs)
fpArgs are passed as keyword arguments to the fingerprinter
source code
 
FingerprintsFromDetails(details, reportFreq=10) source code
 
Usage()
prints a usage string and exits
source code
 
ParseArgs(details=None)
parses the command line arguments and returns a _FingerprinterDetails_ instance with the results.
source code
Variables [hide private]
  _cvsVersion = '$Id$'
  idx1 = 0
  idx2 = 3
  __VERSION_STRING = '$Id'
  _usageDoc = '\nUsage: FingerprintMols.py [args] <fName>\n\n I...
  __package__ = 'rdkit.Chem.Fingerprints'

Imports: Chem, MACCSkeys, Murtagh, DataStructs, sys, cPickle


Function Details [hide private]

FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object at 0x2856ec0>, reportFreq=10, maxMols=-1, **fpArgs)

source code 
fpArgs are passed as keyword arguments to the fingerprinter

Returns a list of 2-tuples: (id,fp)

FingerprintsFromMols(mols, fingerprinter=<Boost.Python.function object at 0x2856ec0>, reportFreq=10, maxMols=-1, **fpArgs)

source code 
fpArgs are passed as keyword arguments to the fingerprinter

Returns a list of 2-tuples: (id,fp)

FingerprintsFromPickles(dataSource, idCol, pklCol, fingerprinter=<Boost.Python.function object at 0x2856ec0>, reportFreq=10, maxMols=-1, **fpArgs)

source code 
fpArgs are passed as keyword arguments to the fingerprinter

Returns a list of 2-tuples: (id,fp)

ParseArgs(details=None)

source code 
parses the command line arguments and returns a
_FingerprinterDetails_ instance with the results.

**Note**:

  - If you make modifications here, please update the global
    _usageDoc string so the Usage message is up to date.

  - This routine is used by both the fingerprinter, the clusterer and the
    screener; not all arguments make sense for all applications.


Variables Details [hide private]

_usageDoc

Value:
'''
Usage: FingerprintMols.py [args] <fName>

  If <fName> is provided and no tableName is specified (see below),
  data will be read from the text file <fName>.  Text files delimited
  with either commas (extension .csv) or tabs (extension .txt) are
  supported. 

...