How to use Smallworld Java Command Line

Introduction

Here is a brief example on how to use the java command line.

How to use Smallworld Java Command Line

1. Use bash as your shell

   • bash //just type in bash and enter

2. Export these variables

   • export SWDIR=/mnt/nfs/db3/public_smallworld_5th_gen
     export sw='java -jar /nfs/db3/smallworld-5.5/sw.jar'

3. Run the similarity command and it will display what it can do

   • $sw sim

4. The path of the databases you can search from is here
   • /mnt/nfs/db3/public_smallworld_5th_gen/maps/
   • /mnt/nfs/db3/private_smallworld_5th_gen/maps/
   • /mnt/nfs/db3/super_private_smallworld_5th_gen/maps/
5. Here is an example of a basic usage

   • $sw sim 'c1ccccc1' -db /mnt/nfs/db3/public_smallworld_5th_gen/maps/all-zinc.smi.anon.map

6. Here is an example of an advanced usage

   • $sw sim 'c1ccccc1' --tdn 0 --rdn 0 --ldn 0 -db /mnt/nfs/db3/public_smallworld_5th_gen/maps/all-zinc.smi.anon.map -n 0 -d 2

7. Here is a table of the options that could be useful

Option	Type	Description
-b	integer	Benchmark mode, optionally specify the number of times to repeat: -b=5 (default: 0)
-d	integer	Max topological distance (default: 99)
--db	string	Database map file
-g	integer	Max number of generations during query extension (default: 3)
-k	integer	Number of top hits to display (default: 0)
-n	integer	Topological ring down distance upper bound (default: 10)
--ldn	integer	Max linker down edits (default: 99)
--lup	integer	Max linker up edits (default: 99)
--rdn	integer	Max ring down edits (default: 99)
--rup	integer	Max ring up edits (default: 99)
--tdn	integer	Max terminal down edits (default: 99)
--tup	integer	Max terminal up edits (default: 99)
--sort		Sort scored results by distance

Example Java Command Line Script

This script performs a similarity search on all databases in the public or private smallworld.

Usage: bash cmd_sim.sh <smiles text file> <library> <max_hits> <distance>

-- <smiles text file> | a text file of smiles in this format:

<smiles> <name of molecule>

-- <library> | public or private

-- <max_hits> | needs an integer, putting 0 means show all results

-- <distance> | needs an integer"

Example: bash cmd_sim.sh smiles.txt public 0 2

#!/bin/bash

smi_file=$1
library=$2
max_hits=$3
distance=$4

version="5.5"

sw_dir=/mnt/nfs/db3
sw='java -jar /nfs/db3/smallworld-'$version'/sw.jar'
public_dir=${sw_dir}/public_smallworld_5th_gen/
private_dir=${sw_dir}/private_smallworld_5th_gen/

public_maps=${public_dir}maps/*.anon.map
private_maps=${private_dir}maps/*.anon.map

if [ "$smi_file" = "-h" ] || [ "$smi_file" = "--help" ]
then
        printf '%*s\n' "${COLUMNS:-$(tput cols)}" '' | tr ' ' -
        echo "This script performs a similarity search on all databases in the public or private smallworld."
        printf '%*s\n' "${COLUMNS:-$(tput cols)}" '' | tr ' ' -
        echo "Usage: bash cmd_sim.sh <smiles text file> <library> <max_hits>  <distance>
        -- <smiles text file> | a text file of smiles in this format:
                <smiles> <name of molecule>
        -- <library> | public or private
        -- <max_hits> | needs an integer, putting 0 means show all results
        -- <distance> | needs an integer"
        printf '%*s\n' "${COLUMNS:-$(tput cols)}" '' | tr ' ' -
        echo "Example:
        bash cmd_sim.sh smiles.txt public 0 2"
        printf '%*s\n' "${COLUMNS:-$(tput cols)}" '' | tr ' ' -
else
while IFS= read -r line
do
        smiles=$(echo $line | awk '{print $1}')
        name=$(echo $line | awk '{print $2}')
        echo $name $smiles
        if [ $library == "public" ]
                then
                        export SWDIR=$public_dir
                        for maps in $public_maps
                                do
                                        echo $maps
                                        $sw sim -db $maps -v -n$max_hits -d$distance -score AtomAlignment:SMILES $smiles
                                done
        elif [ $library == "private" ]
                then
                        export SWDIR=$private_dir
                        for maps in $private_maps
                                do
                                        echo $maps
                                        $sw sim -db $maps -v -n$max_hits -d$distance -score AtomAlignment:SMILES $smiles
                                done
        else
                echo "Invalid Options"
        fi

done < $smi_file
fi