Perform SMARTS search on substructure database file¶

A program that searches substructure search database using a SMARTS pattern. For more explanation, see OESubSearchDatabase class.

Schematic representation of using substructure search database¶

Code Example

Generate database for fast substructure search example

Command Line Interface¶

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

prompt> python searchfastss.py --help

will generate the following output:

Simple parameter list
 input/output options
   -database : Input substructure search database filename
   -smarts : SMARTS pattern, quote for safety

 other options
   -maxmatches : The maximum number of matches returned in case of parameters
                 (-titles) and (-out)
   -nrthreads : Number of processors used (zero means all available)

 search types
   -count : Output count of number matched
   -out : Output molecule filename of matches
   -titles : Output title of matches

Example¶

prompt> searchfastss.py -db ss-search-dataset-SMARTS.oeb -s "C1CC[O,N]CC1" -out matches.ism
prompt> searchfastss.py -db ss-search-dataset-SMARTS.oeb -s "C1CC[O,N]CC1" -count
prompt> searchfastss.py -dbss-search-dataset-SMARTS.oeb -s "C1CC[O,N]CC1"  -titles

Code¶

Download code

searchfastss.py