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

Use bash as your shell
- ```
bash //just type in bash and enter
```

Export these variables

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

Run the similarity command and it will display what it can do
- ```
$sw sim
```
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/

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

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

Here is a table of the options that could be useful

Parameter	Type	Description
smi	text	Query SMILES
db	text	Reference database (see List of available maps)
dist	int	Topological distance upper bound (default: 10)
tdn	int	Topological terminal down distance upper bound (default: 10)
tup	int	Topological terminal up distance upper bound (default: 10)
rdn	int	Topological ring down distance upper bound (default: 10)
rup	int	Topological ring up distance upper bound (default: 10)
ldn	int	Topological linker down distance upper bound (default: 10)
lup	int	Topological linker up distance upper bound (default: 10)
scores	text	List of scoring functions (default : none) - see /search/config

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:

-- <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

How to use Smallworld Java Command Line

Introduction

How to use Smallworld Java Command Line

Example Java Command Line Script

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