bash: dynamical variables with multiple files in for loop-CodePudding

I am working with some bash pipeline, which loop several pdb filles located in the receptors folder and post-process each file using some python script that required some expression defined as the flex_residues variable in the begining of the same scirpt:

home="$PWD"
receptors="${home}"/receptors
flex_residues='MET49_ASN142_CYS145_GLU166_GLN189'

# process each pdb file using the same %flex_residues 
for prot in "${receptors}"/*.pdb; do
receptor=$(basename "$prot" .pdb)
prepare_flexreceptor.py -r "${receptors}"/"${receptor}".pdb -s "${flex_residues}"
done

Now I would like to customize my pipeline to define different expressions of the $flex_residues depending on the processed pdb file. For example if I have 3 different pdb file in the receptors, I would like to define them in the begining of the script with the corresponded flex_residues. e.g.

receptor1.pdb >> flex_residues (for receptor1)='MET44_ASN142_CYS145_HIE163_GLN189'
receptor2.pdb >> flex_residues (for receptor 2) ='TRP12_ASN142_GLN188_GLU166_GLN189'
receptor3.pdb >> flex_residues (for receptor 3) ='ALA49_ASN142_MET111_HIS164_GLN189'

therefore the used flex_residues should automatically changes according to each processed receptor in the for loop. Could you suggest me the possibilities to modify my bash pipeline ?

CodePudding user response：

You can make use of an associative array. Would you please try:

#!/bin/bash

# initialize associative array
declare -A flex_residues=(
    ["receptor1"]="MET44_ASN142_CYS145_HIE163_GLN189"
    ["receptor2"]="TRP12_ASN142_GLN188_GLU166_GLN189"
    ["receptor3"]="ALA49_ASN142_MET111_HIS164_GLN189"
)

home="$PWD"
receptors="$home"/receptors

# process each pdb file using the same %flex_residues
for prot in "$receptors"/*.pdb; do
    receptor=$(basename "$prot" .pdb)
    prepare_flexreceptor.py -r "$temp/$receptor".pdbqt -s "${flex_residues[$receptor]}"
done

You can grow the declare line with as many lines as you want to initialize, or create a separate file which contains key-value pairs and read the file at the beginning of the script assigning the associative array.