How to use Smallworld Java Command Line: Difference between revisions
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:::{| class="wikitable" | :::{| class="wikitable" | ||
|- | |- | ||
! | ! Option | ||
! Type | ! Type | ||
! Description | ! 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) | | 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 | |||
|} | |} | ||
Line 154: | Line 166: | ||
fi | fi | ||
</source> | </source> | ||
[[Category:Smallworld]] |
Latest revision as of 23:31, 31 May 2024
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
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