How to use Smallworld Java Command Line - Revision history

Frodo: asdf

2024-05-31T23:31:52Z

asdf

← Older revision		Revision as of 23:31, 31 May 2024
Line 166:		Line 166:
	fi		fi
	</source>		</source>


			[[Category:Smallworld]]

Jgutierrez6: /* How to use Smallworld Java Command Line */

2023-02-22T03:48:39Z

How to use Smallworld Java Command Line

← Older revision		Revision as of 03:48, 22 February 2023
Line 76:		Line 76:
	\| integer		\| integer
	\| Max terminal down edits (default: 99)		\| Max terminal down edits (default: 99)
	\|-
	~~\| --tup~~
	~~\| integer~~
	~~\| Max terminal up edits (default: 99)~~
	\|-		\|-
	\| --tup		\| --tup

Jgutierrez6: /* How to use Smallworld Java Command Line */

2023-02-22T03:48:15Z

How to use Smallworld Java Command Line

← Older revision		Revision as of 03:48, 22 February 2023
Line 76:		Line 76:
	\| integer		\| integer
	\| Max terminal down edits (default: 99)		\| Max terminal down edits (default: 99)
			\|-
			\| --tup
			\| integer
			\| Max terminal up edits (default: 99)
	\|-		\|-
	\| --tup		\| --tup
Line 84:		Line 88:
	\|		\|
	\| Sort scored results by distance		\| Sort scored results by distance
	\|-
	~~\| --tup~~
	~~\| integer~~
	~~\| Max terminal up edits (default: 99)~~
	\|}		\|}

Jgutierrez6 at 03:47, 22 February 2023

2023-02-22T03:47:42Z

← Older revision		Revision as of 03:47, 22 February 2023
Line 61:		Line 61:
	\| Max linker down edits (default: 99)		\| Max linker down edits (default: 99)
	\|-		\|-
	\| ~~ldn~~		\| --lup
	\| ~~int~~		\| integer
	\| ~~Topological~~ linker ~~down distance upper bound~~ (default: 10)		\| Max linker up edits (default: 99)
	\|-		\|-
	\| ~~lup~~		\| --rdn
	\| ~~int~~		\| integer
	\| ~~Topological linker up distance upper bound~~ (default: 10)		\| Max ring down edits (default: 99)
	\|-		\|-
	\| ~~scores~~		\| --rup
	\| ~~text~~		\| integer
	\| ~~List of scoring functions~~ (default : ~~none~~) - ~~see /search/config~~		\| 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
			\|-
			\| --tup
			\| integer
			\| Max terminal up edits (default: 99)
	\|}		\|}

Jgutierrez6 at 03:16, 22 February 2023

2023-02-22T03:16:26Z

← Older revision		Revision as of 03:16, 22 February 2023
Line 54:		Line 54:
	\|-		\|-
	\| -n		\| -n
	\| ~~int~~		\| integer
	\| Topological ring down distance upper bound (default: 10)		\| Topological ring down distance upper bound (default: 10)
	\|-		\|-
	\| ~~rup~~		\| --ldn
	\| ~~int~~		\| integer
	\| ~~Topological ring up distance upper bound~~ (default: 10)		\| Max linker down edits (default: 99)
	\|-		\|-
	\| ldn		\| ldn

Jgutierrez6: /* How to use Smallworld Java Command Line */

2023-02-22T02:21:25Z

How to use Smallworld Java Command Line

← Older revision		Revision as of 02:21, 22 February 2023
Line 29:		Line 29:
	:::{\| class="wikitable"		:::{\| class="wikitable"
	\|-		\|-
	! ~~Parameter~~		! Option
	! Type		! Type
	! Description		! Description
	\|-		\|-
	\| ~~smi~~		\| -b
	\| ~~text~~		\| integer
	\| ~~Query SMILES~~		\| Benchmark mode, optionally specify the number of times to repeat: -b=5 (default: 0)
	\|-		\|-
	\| db		\| -d
	\| ~~text~~		\| integer
	\| ~~Reference database~~ (~~see List of available maps~~)		\| Max topological distance (default: 99)
	\|-		\|-
	\| ~~dist~~		\| --db
	\| ~~int~~		\| string
	\| ~~Topological distance upper bound (default: 10)~~		\| Database map file
	\|-		\|-
	\| ~~tdn~~		\| -g
	\| ~~int~~		\| integer
	\| ~~Topological terminal down distance upper bound~~ (default: 10)		\| Max number of generations during query extension (default: 3)
	\|-		\|-
	\| ~~tup~~		\| -k
	\| ~~int~~		\| integer
	\| ~~Topological terminal up distance upper bound~~ (default: 10)		\| Number of top hits to display (default: 0)
	\|-		\|-
	\| ~~rdn~~		\| -n
	\| int		\| int
	\| Topological ring down distance upper bound (default: 10)		\| Topological ring down distance upper bound (default: 10)

Jgutierrez6: /* How to use Smallworld Java Command Line */

2023-02-21T20:17:45Z

How to use Smallworld Java Command Line

@@ Line 27: / Line 27: @@
 </source>
 # Here is a table of the options that could be useful
 == Example Java Command Line Script ==

Jgutierrez6 at 20:06, 21 February 2023

2023-02-21T20:06:00Z

← Older revision		Revision as of 20:06, 21 February 2023
Line 26:		Line 26:
	$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		$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
	</source>		</source>
			# Here is a table of the options that could be useful

	== Example Java Command Line Script ==		== Example Java Command Line Script ==

Jgutierrez6 at 19:42, 21 February 2023

2023-02-21T19:42:13Z

← Older revision		Revision as of 19:42, 21 February 2023
Line 1:		Line 1:
			== Introduction ==
			Here is a brief example on how to use the java command line.

	== How to use Smallworld Java Command Line ==		== How to use Smallworld Java Command Line ==
	# Use bash as your shell		# Use bash as your shell

Jgutierrez6: Created page with "== 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/..."

2023-02-21T19:38:44Z

Created page with "== How to use Smallworld Java Command Line == # Use bash as your shell #* <source>bash //just type in bash and enter</source> # Export these variables #* <source> export SWDIR=/mnt/nfs/db3/public_smallworld_5th_gen export sw='java -jar /nfs/db3/smallworld-5.5/sw.jar' </source> # Run the similarity command and it will display what it can do #* <source> $sw sim </source> # The path of the databases you can search from is here #* /mnt/nfs/db3/public_smallworld_5th_gen/maps/..."

New page

== How to use Smallworld Java Command Line ==
# Use bash as your shell
#* <source>bash //just type in bash and enter</source>
# Export these variables
#* <source>
export SWDIR=/mnt/nfs/db3/public_smallworld_5th_gen
export sw='java -jar /nfs/db3/smallworld-5.5/sw.jar'
</source>
# Run the similarity command and it will display what it can do
#* <source>
$sw sim
</source>
# 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
#* <source>
$sw sim 'c1ccccc1' -db /mnt/nfs/db3/public_smallworld_5th_gen/maps/all-zinc.smi.anon.map
</source>
# Here is an example of an advanced usage
#* <source>
$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
</source>

== 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

<source>
#!/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
</source>