Package Chem :: Module BuildFragmentCatalog

Module BuildFragmentCatalog

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.

Module BuildFragmentCatalog

BuildCatalog(suppl, maxPts=-1, groupFileName=None, minPath=2, maxPath=6, reportFreq=10)

ScoreMolecules(suppl, catalog, maxPts=-1, actName='', acts=None, nActs=2, reportFreq=10)

ScoreFromLists(bitLists, suppl, catalog, maxPts=-1, actName='', acts=None, nActs=2, reportFreq=10)

CalcGains(suppl, catalog, topN=-1, actName='', acts=None, nActs=2, reportFreq=10, biasList=None, collectFps=0)

CalcGainsFromFps(suppl, fps, topN=-1, actName='', acts=None, nActs=2, reportFreq=10, biasList=None)

ProcessGainsData(inF, delim=',', idCol=0, gainCol=1)

ShowDetails(catalog, gains, nToDo=-1, outF=sys.stdout, idCol=0, gainCol=1, outDelim=',')

ScoreMolecules(suppl, catalog, maxPts=-1, actName=`''`, acts=None, nActs=2, reportFreq=10)

ScoreFromLists(bitLists, suppl, catalog, maxPts=-1, actName=`''`, acts=None, nActs=2, reportFreq=10)

CalcGains(suppl, catalog, topN=-1, actName=`''`, acts=None, nActs=2, reportFreq=10, biasList=None, collectFps=0)

CalcGainsFromFps(suppl, fps, topN=-1, actName=`''`, acts=None, nActs=2, reportFreq=10, biasList=None)

ProcessGainsData(inF, delim=`','`, idCol=0, gainCol=1)

ShowDetails(catalog, gains, nToDo=-1, outF=sys.stdout, idCol=0, gainCol=1, outDelim=`','`)