Generate database for fast substructure search¶

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

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