rdkit.Chem.BuildFragmentCatalog module — The RDKit 2016.09.1 documentation

# rdkit.Chem.BuildFragmentCatalog module

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

`rdkit.Chem.BuildFragmentCatalog.` `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

  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

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

  calculates info gains by constructing fingerprints DOC

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

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

  calculates info gains from a set of fingerprints

  DOC

`rdkit.Chem.BuildFragmentCatalog.` `OutputGainsData`(outF, gains, cat, nActs=2)

`rdkit.Chem.BuildFragmentCatalog.` `ParseArgs`(details)

`rdkit.Chem.BuildFragmentCatalog.` `ProcessGainsData`(inF, delim=', ', idCol=0, gainCol=1)

  reads a list of ids and info gains out of an input file

class `rdkit.Chem.BuildFragmentCatalog.` `RunDetails`

  Bases: `object`

  `actCol` = -1
  `biasList` = None
  `catalogName` = None
  `dbName` = ''
  `delim` = ','
  `detailsName` = None
  `doBuild` = 0
  `doDetails` = 0
  `doGains` = 0
  `doScore` = 0
  `doSigs` = 0
  `fpName` = None
  `gainsName` = None
  `hasTitle` = 1
  `inFileName` = None
  `maxPath` = 6
  `minPath` = 2
  `nActs` = 2
  `nBits` = -1
  `nameCol` = -1
  `numMols` = -1
  `onBitsName` = None
  `scoresName` = None
  `smiCol` = 1
  `tableName` = None
  `topN` = -1

`rdkit.Chem.BuildFragmentCatalog.` `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. 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)

`rdkit.Chem.BuildFragmentCatalog.` `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. 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

`rdkit.Chem.BuildFragmentCatalog.` `ShowDetails`(catalog, gains, nToDo=-1, outF=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, idCol=0, gainCol=1, outDelim=', ')

  gains should be a sequence of sequences. The idCol entry of each sub-sequence should be a catalog ID. _ProcessGainsData()_ provides suitable input.

`rdkit.Chem.BuildFragmentCatalog.` `SupplierFromDetails`(details)

`rdkit.Chem.BuildFragmentCatalog.` `Usage`()

`rdkit.Chem.BuildFragmentCatalog.` `message`(msg, dest=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)