Chem.BuildFragmentCatalog

Package Chem :: Module BuildFragmentCatalog |
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# Module BuildFragmentCatalog

source code

    command line utility for working with FragmentCatalogs (CASE-type analysis)

    **Usage**

      BuildFragmentCatalog [optional args] <filename>

     filename, the name of a delimited text file containing InData, is required
     for some modes of operation (see below)

    **Command Line Arguments**

     - -n *maxNumMols*:  specify the maximum number of molecules to be processed

     - -b: build the catalog and OnBitLists
        *requires InData*

     - -s: score compounds
        *requires InData and a Catalog, can use OnBitLists*

     - -g: calculate info gains
        *requires Scores*

     - -d: show details about high-ranking fragments
        *requires a Catalog and Gains*

     - --catalog=*filename*: filename with the pickled catalog.
        If -b is provided, this file will be overwritten.

     - --onbits=*filename*: filename to hold the pickled OnBitLists.
       If -b is provided, this file will be overwritten

     - --scores=*filename*: filename to hold the text score data.
       If -s is provided, this file will be overwritten

     - --gains=*filename*: filename to hold the text gains data.
       If -g is provided, this file will be overwritten

     - --details=*filename*: filename to hold the text details data.
       If -d is provided, this file will be overwritten.

     - --minPath=2: specify the minimum length for a path

     - --maxPath=6: specify the maximum length for a path

     - --smiCol=1: specify which column in the input data file contains
         SMILES

     - --actCol=-1: specify which column in the input data file contains
         activities

     - --nActs=2: specify the number of possible activity values

     - --nBits=-1: specify the maximum number of bits to show details for

Classes | [hide private]
| RunDetails

Functions | [hide private]
message(msg, dest=sys.stdout) | source code
BuildCatalog(suppl, maxPts=-1, groupFileName=None, minPath=2, maxPath=6, reportFreq=10) builds a fragment catalog from a set of molecules in a delimited text block... | source code
ScoreMolecules(suppl, catalog, maxPts=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10) scores the compounds in a supplier using a catalog **Arguments** - suppl: a mol supplier - catalog: the FragmentCatalog - maxPts: (optional) the maximum number of molecules to be considered - actName: (optional) the name of the molecule's activity property. | source code
ScoreFromLists(bitLists, suppl, catalog, maxPts=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10) similar to _ScoreMolecules()_, but uses pre-calculated bit lists for the molecules (this speeds things up a lot) **Arguments** - bitLists: sequence of on bit sequences for the input molecules - suppl: the input supplier (we read activities from here) - catalog: the FragmentCatalog - maxPts: (optional) the maximum number of molecules to be considered - actName: (optional) the name of the molecule's activity property. | source code
CalcGains(suppl, catalog, topN=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10, biasList=None, collectFps=0) calculates info gains by constructing fingerprints... | source code
CalcGainsFromFps(suppl, fps, topN=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10, biasList=None) calculates info gains from a set of fingerprints... | source code
OutputGainsData(outF, gains, cat, nActs=2) | source code
ProcessGainsData(inF, delim=`'``,``'`, idCol=0, gainCol=1) reads a list of ids and info gains out of an input file... | source code
ShowDetails(catalog, gains, nToDo=-1, outF=sys.stdout, idCol=0, gainCol=1, outDelim=`'``,``'`) gains should be a sequence of sequences. | source code
SupplierFromDetails(details) | source code
Usage() | source code
ParseArgs(details) | source code

Variables | [hide private]
| _cvsVersion = ``'``$Revision: 2 $``'``
| idx1 = `10`
| idx2 = `13`
| __VERSION_STRING = ``'``2` `'``
| Complex0 = ``'``F``'``
| Complex16 = ``'``F``'``
| Complex32 = ``'``F``'``
| Complex64 = ``'``D``'``
| Complex8 = ``'``F``'``
| Float0 = ``'``f``'``
| Float16 = ``'``f``'``
| Float32 = ``'``f``'``
| Float64 = ``'``d``'``
| Float8 = ``'``f``'``
| Int0 = ``'``1``'``
| Int16 = ``'``s``'``
| Int32 = ``'``i``'``
| Int8 = ``'``1``'``
| absolute = `<ufunc 'absolute'>`
| add = `<ufunc 'add'>`
| arccos = `<ufunc 'arccos'>`
| arccosh = `<ufunc 'arccosh'>`
| arcsin = `<ufunc 'arcsin'>`
| arcsinh = `<ufunc 'arcsinh'>`
| arctan = `<ufunc 'arctan'>`
| arctan2 = `<ufunc 'arctan2'>`
| arctanh = `<ufunc 'arctanh'>`
| bitwise_and = `<ufunc 'bitwise_and'>`
| bitwise_or = `<ufunc 'bitwise_or'>`
| bitwise_xor = `<ufunc 'bitwise_xor'>`
| ceil = `<ufunc 'ceil'>`
| conjugate = `<ufunc 'conjugate'>`
| cos = `<ufunc 'cos'>`
| cosh = `<ufunc 'cosh'>`
| divide = `<ufunc 'divide'>`
| divide_safe = `<ufunc 'divide_safe'>`
| e = `2.71828182846`
| equal = `<ufunc 'equal'>`
| exp = `<ufunc 'exp'>`
| fabs = `<ufunc 'fabs'>`
| floor = `<ufunc 'floor'>`
| floor_divide = `<ufunc 'floor_divide'>`
| fmod = `<ufunc 'fmod'>`
| greater = `<ufunc 'greater'>`
| greater_equal = `<ufunc 'greater_equal'>`
| hypot = `<ufunc 'hypot'>`
| invert = `<ufunc 'invert'>`
| left_shift = `<ufunc 'left_shift'>`
| less = `<ufunc 'less'>`
| less_equal = `<ufunc 'less_equal'>`
| log = `<ufunc 'log'>`
| log10 = `<ufunc 'log10'>`
| logical_and = `<ufunc 'logical_and'>`
| logical_not = `<ufunc 'logical_not'>`
| logical_or = `<ufunc 'logical_or'>`
| logical_xor = `<ufunc 'logical_xor'>`
| maximum = `<ufunc 'maximum'>`
| minimum = `<ufunc 'minimum'>`
| multiply = `<ufunc 'multiply'>`
| negative = `<ufunc 'negative'>`
| not_equal = `<ufunc 'not_equal'>`
| pi = `3.14159265359`
| power = `<ufunc 'power'>`
| remainder = `<ufunc 'remainder'>`
| right_shift = `<ufunc 'right_shift'>`
| sin = `<ufunc 'sin'>`
| sinh = `<ufunc 'sinh'>`
| sqrt = `<ufunc 'sqrt'>`
| subtract = `<ufunc 'subtract'>`
| tan = `<ufunc 'tan'>`
| tanh = `<ufunc 'tanh'>`
| true_divide = `<ufunc 'true_divide'>`

Function Details | [hide private]

### BuildCatalog(suppl, maxPts=-1, groupFileName=None, minPath=2, maxPath=6, reportFreq=10) | source code
    builds a fragment catalog from a set of molecules in a delimited text block

    **Arguments**

      - suppl: a mol supplier

      - maxPts: (optional) if provided, this will set an upper bound on the
        number of points to be considered

      - groupFileName: (optional) name of the file containing functional group
        information

      - minPath, maxPath: (optional) names of the minimum and maximum path lengths
        to be considered

      - reportFreq: (optional) how often to display status information

    **Returns**

      a FragmentCatalog

### ScoreMolecules(suppl, catalog, maxPts=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10) | source code
    scores the compounds in a supplier using a catalog

    **Arguments**

      - suppl: a mol supplier

      - catalog: the FragmentCatalog

      - maxPts: (optional) the maximum number of molecules to be
        considered

      - actName: (optional) the name of the molecule's activity property.
        If this is not provided, the molecule's last property will be used.

      - acts: (optional) a sequence of activity values (integers).
        If not provided, the activities will be read from the molecules.

      - nActs: (optional) number of possible activity values

      - reportFreq: (optional) how often to display status information

    **Returns**

      a 2-tuple:

        1) the results table (a 3D array of ints nBits x 2 x nActs)

        2) a list containing the on bit lists for each molecule

### ScoreFromLists(bitLists, suppl, catalog, maxPts=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10) | source code
    similar to _ScoreMolecules()_, but uses pre-calculated bit lists
    for the molecules (this speeds things up a lot)

    **Arguments**

      - bitLists: sequence of on bit sequences for the input molecules

      - suppl: the input supplier (we read activities from here)

      - catalog: the FragmentCatalog

      - maxPts: (optional) the maximum number of molecules to be
        considered

      - actName: (optional) the name of the molecule's activity property.
        If this is not provided, the molecule's last property will be used.

      - nActs: (optional) number of possible activity values

      - reportFreq: (optional) how often to display status information

    **Returns**

       the results table (a 3D array of ints nBits x 2 x nActs)

### CalcGains(suppl, catalog, topN=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10, biasList=None, collectFps=0) | source code
    calculates info gains by constructing fingerprints
    *DOC*

    Returns a 2-tuple:
       1) gains matrix
       2) list of fingerprints

### CalcGainsFromFps(suppl, fps, topN=-1, actName=`'````'`, acts=None, nActs=2, reportFreq=10, biasList=None) | source code
    calculates info gains from a set of fingerprints

    *DOC*

### ProcessGainsData(inF, delim=`'``,``'`, idCol=0, gainCol=1) | source code
    reads a list of ids and info gains out of an input file

### ShowDetails(catalog, gains, nToDo=-1, outF=sys.stdout, idCol=0, gainCol=1, outDelim=`'``,``'`) | source code
    gains should be a sequence of sequences.  The idCol entry of each
    sub-sequence should be a catalog ID.  _ProcessGainsData()_ provides
    suitable input.