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=Chem.RDKFingerprint, **fpArgs) | source code

FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=Chem.RDKFingerprint, reportFreq=10, maxMols=-1, **fpArgs) fpArgs are passed as keyword arguments to the fingerprinter | source code

FingerprintsFromMols(mols, fingerprinter=Chem.RDKFingerprint, reportFreq=10, maxMols=-1, **fpArgs) fpArgs are passed as keyword arguments to the fingerprinter | source code

FingerprintsFromPickles(dataSource, idCol, pklCol, fingerprinter=Chem.RDKFingerprint, 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 = `_cvsVersion.find(':')+ 1`
| idx2 = `_cvsVersion.rfind('$')`
| __VERSION_STRING = `"%s" %(_cvsVersion [idx1: idx2])`
| _usageDoc = ``...``

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

Function Details | [hide private]

### FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=Chem.RDKFingerprint, 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=Chem.RDKFingerprint, 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=Chem.RDKFingerprint, 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.

      ...