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Toolkits--python
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  • Generate database for fast substructure search

Generate database for fast substructure search¶

A program that generates a binary file for fast substructure search. For more explanation, see OECreateSubSearchDatabaseFile function.

../../_images/FastSSGeneration.png

Schematic representation of substructure search database file generation process¶

Code Example

  • Perform SMARTS search on substructure database file example

Command Line Interface¶

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> python makefastss.py --help

will generate the following output:

Simple parameter list
 input/output options
   -in : Input molecule filename
   -out : Output substructure database filename

 other options
   -keep-title : Whether to keep the title of the molecule as unique
                 identifier
   -nrthreads : Number of processors used (zero means all available)
   -screentype : Screen type generated
   -sort : Whether to sort the molecules based on their screen bit counts.

Example¶

prompt> makefastss.py -in dataset.ism -out sss-search-dataset-SMARTS.oeb -stype SMARTS

Code¶

Download code

makefastss.py

See also

  • OECreateSubSearchDatabaseOptions class

  • OESubSearchScreenTypeBase class

  • OEConsoleProgressTracer class

  • OEGetSubSearchScreenType function

  • OECreateSubSearchDatabaseFile function

  • OECreateSubSearchDatabaseOptions function

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© Copyright 2023, OpenEye Scientific Software, Inc. Last updated on Jan 07, 2023.