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comparison PLIDflow/scripts/separateChain.sh @ 6:795e11fac81b draft default tip

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Included new tools for standardization
author bitlab
date Wed, 22 Apr 2020 06:12:00 -0400
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5:97f12f7cc852 6:795e11fac81b
1 #!/bin/bash
2
3 # Arguments
4 # $1 = pdb
5
6
7
8 nbad=$(awk '{if(length($5) > 1) print $0 }' $1 | wc -l)
9
10 if [[ $nbad -ne 0 ]]; then
11
12 #cat $1 | awk 'BEGIN{FS="\t"}{ split($0, array, " "); a=substr(array[5],1,1); b=substr(array[5],2); }'
13 cat $1 | gawk 'BEGIN{FS="\t"}{ split($0, array, " "); if(array[5] ~ /([A-Z][0-9]+)/){ a=substr(array[5],1,1); b=substr(array[5],2); gsub(array[5], a" "b, $0); gsub(a" "b" ", a" "b, $0) ; print $0; }else{ print $0}}' > $1.temp.awk
14 grep "ATOM\|HETATM" $1.temp.awk | awk '{ if(length($5)==1) updateName=$5; if($1 == "ATOM" || $1 == "HETATM"){ print $0 > "chain"updateName".pdb"; }}' ;
15 rm $1.temp.awk
16
17 else
18
19 grep "ATOM\|HETATM" $1 | awk '{ if(length($5)==1) updateName=$5; if($1 == "ATOM" || $1 == "HETATM"){ print $0 > "chain"updateName".pdb"; }}' ;
20
21 fi
22
23 #grep "ATOM\|HETATM" $1 | awk '{ if(length($5)==1) updateName=$5; if($1 == "ATOM" || $1 == "HETATM"){ print $0 > "chain"updateName".pdb"; }}' ;
24 for i in chain* ; do echo "TER" >> $i ; echo "END" >> $i ; done