Package Chem :: Package Fingerprints :: Module FingerprintMols

Module FingerprintMols

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

FingerprintMol(mol, fingerprinter=<Boost.Python.function object at 0x8344080>, **fpArgs)

source code

FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object at 0x8344080>, 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 0x8344080>, reportFreq=10, maxMols=-1, **fpArgs)
fpArgs are passed as keyword arguments to the fingerprinter...

source code

FingerprintsFromDetails(details)

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 346 2007-09-27 05:27:16...

idx1 = 4

idx2 = 58

__VERSION_STRING = ' FingerprintMols.py 346 2007-09-27 05:27:1...

_usageDoc = '\nUsage: FingerprintMols.py [args] <fName>\n\n I...

Function Details

[hide private]

FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object at 0x8344080>, 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 0x8344080>, 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 346 2007-09-27 05:27:16Z glandrum $'

__VERSION_STRING

Value:

' FingerprintMols.py 346 2007-09-27 05:27:16Z 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. 

...