Chem.Fingerprints.FingerprintMols

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
GetDaylightFingerprint(mol) uses default parameters | source code
FoldFingerprintToTargetDensity(fp, **fpArgs) | source code
FingerprintMol(mol, fingerprinter=<Boost.Python.function object at 0x8652408>, **fpArgs) | source code
FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object at 0x8652408>, reportFreq=10, maxMols=-1, **fpArgs) fpArgs are passed as keyword arguments to the fingerprinter... | source code
FingerprintsFromMols(mols, fingerprinter=<Boost.Python.function object at 0x8652408>, 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 0x8652408>, 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: FingerprintMols.py 797 2008-08-19 03:13:06``...``
| idx1 = `4`
| idx2 = `58`
| __VERSION_STRING = ``'``FingerprintMols.py 797 2008-08-19 03:13:0``...``
| _usageDoc = ``'``\nUsage: FingerprintMols.py [args] <fName>\n\n I``...``

Function Details | [hide private]

### FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object at 0x8652408>, 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 0x8652408>, 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 0x8652408>, reportFreq=10, maxMols=-1, **fpArgs) | source code
    fpArgs are passed as keyword arguments to the fingerprinter

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

### Usage() | source code
    prints a usage string and exits

### 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]

  ### _cvsVersion Value:
      '$Id: FingerprintMols.py 797 2008-08-19 03:13:06Z glandrum $'

  ### __VERSION_STRING Value:
      ' FingerprintMols.py 797 2008-08-19 03:13:06Z glandrum '

  ### _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.

      ...