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mapping maltiple reactions #7
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@iwatobipen Did you ever find out how to do this? I have the same problem
Reacted by TakaI wrote shell script to do it. But I took long time to process many reactions. I'm not good at Java so it has room for improvement.
Thanks.Thanks, scripting is a way to go.
We are exploring an inbuilt routine.Reacted by TakaBelow is the shell script which can be used in BASH environment on UNIX/LINUX.
a) Store this in a file.. maybe
run_recoder.sh
b) change the jar file name in JAR variable
c) RXN_FILE_DIR is the path to RXN files directory
d) run it in a shell promptsh run_recoder.sh RXN_FILE_DIR#!/bin/bash rxn_dir=$1 job_DIR="OUTPUT" mkdir $job_DIR for i in rxn_dir/*.rxn do echo "Preparing job for $i" rxn_file = $i xbase=${rxn_file##*/} xpref=${xbase%.*} job_id=xpref JAR="ReactionDecoder.jar" echo "Processing JobID=$job_id rxn_file=$rxn_file" JOB="java -Xmx4G -jar $JAR -c -g -x -f BOTH -j AAM -p $job_id -Q RXN -q $rxn_file" echo "Running command $JOB" $JOB >> job.log done echo "===DONE=="Hi,
Here's a way to process many SMILES reactions in parallel.parallel --joblog results/runtask.log --colsep ',' -j 10 'java -jar ReactionDecoder.jar -Q SMI -q "{=2 uq() =}" -g-c -j AAM -p results/{1} -f TEXT' :::: rxn_list.csv
rxn_list.csvis comma separated file, first column is reaction name or id, second column is the reaction smiles- outputs and log are put under
resultsfolder, so create it before running the command - requires newer version of
parallel, (>2019) - I chose number of jobs as 10 but due to Java's inability to configure cpu affinity, still uses all cpus
Reacted by Taka, Gopal Narayan Srivastava and Syed Asad Rahmanthere should be a -i option: reaction SMILES input file.
And a -o option: reaction SMILES (mapped) output file@iwatobipen you should try this updated version https://github.com/Laboratoire-de-Chemoinformatique/RDTool.
They have -i and -o.
It's a little slow though; about 1s per reaction and you need to set a timeout (maybe something like 3s) so
that mapping some reactions doesn't take 20min...
Dear Developer,
Is there any option for reaction mapping from list of reaction smiles?
Currently I have file of reaction list and I would like to map many reactions.
Any suggestion and advices are appreciated.
Kind regards,
Taka