I have this array:
dihedrals=['na-2e-na-cd 4 1.200 180.000 2.000', 'Pd-2e-na-cd 4 1.200 180.000 2.000', 'Pd-2e-na-ca 4 1.200 180.000 2.000', 'Pd-4n-na-hn 4 4.800 0.000 2.000', 'na-4n-cc-cc 4 4.200 180.000 2.000', 'na-2e-na-ca 4 1.200 180.000 2.000', 'Pd-2e-na-ca 4 1.200 180.000 2.000', 'cc-4n-na-hn 4 4.800 0.000 2.000', 'Pd-4n-na-cd 4 4.800 0.000 2.000', 'Pd-2e-na-cc 4 1.200 180.000 2.000', 'X -4n-na-X 2 3.400 180.000 2.000', 'Pd-4n-cc-h4 4 4.200 180.000 2.000', 'Pd-4n-cc-cc 4 4.200 180.000 2.000', 'na-2e-na-cd 4 1.200 180.000 2.000', 'na-2e-na-cc 4 1.200 180.000 2.000', 'cc-4n-na-cd 4 4.800 0.000 2.000', 'na-2e-na-ca 4 1.200 180.000 2.000', 'Pd-2e-na-cc 4 1.200 180.000 2.000', 'na-2e-na-cc 4 1.200 180.000 2.000', 'Pd-2e-na-cd 4 1.200 180.000 2.000', 'na-4n-cc-h4 4 4.200 180.000 2.000']
and I want to write it in a file like this:
na-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
Pd-4n-na-hn 4 4.800 0.000 2.000
na-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
cc-4n-na-hn 4 4.800 0.000 2.000
Pd-4n-na-cd 4 4.800 0.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
X -4n-na-X 2 3.400 180.000 2.000
Pd-4n-cc-h4 4 4.200 180.000 2.000
Pd-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
cc-4n-na-cd 4 4.800 0.000 2.000
na-4n-cc-h4 4 4.200 180.000 2.000
I tried:
!awk '{print $1" "$2" "$3" "$4" "$5}' a.txt
But awk sees extra field in this row: "X -4n-na-X " because there is a space next to X . I tried to change the field separator as two spaces with-F="[[:space:]][[:space:]] ":
import os
for x in range(len(dihedrals)):
dihedrals[x]=os.popen('echo "{}" |awk -F="[[:space:]][[:space:]] " \'{{ printf "%0s %0s %0s %0s %0s",$1,$2,$3,$4,$5,$6}}\' '.format(dihedrals[x])).read()
print(dihedrals[x])
But nothing changed.
I also tried printf %s:
import os
for x in range(len(dihedrals)):
dihedrals[x]=os.popen('echo "{}"|awk \'{{printf "%0s %3s %8s s s",$1,$2,$3,$4,$5}}\' '.format(dihedrals[x])).read()
But again it didn't work. How can I write my variable into a file as I explained above?
I also tried python formatting, regex, exc... but I couldn't accomplish.
NOTE: I also tried column -t a.txt but again I am in trouble with X space row (X -4n-na-X) Here is result:
na-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-ca 4 1.200 180.000 2.000
Pd-4n-na-hn 4 4.800 0.000 2.000
na-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
Pd-2e-na-ca 4 1.200 180.000 2.000
cc-4n-na-hn 4 4.800 0.000 2.000
Pd-4n-na-cd 4 4.800 0.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
X -4n-na-X 2 3.400 180.000 2.000
Pd-4n-cc-h4 4 4.200 180.000 2.000
Pd-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-cd 4 1.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
cc-4n-na-cd 4 4.800 0.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
CodePudding user response：
You can use formatted output in python for this array. We just need to split each line using 2 spaces to get individual fields.
import re
dihedrals=['na-2e-na-cd 4 1.200 180.000 2.000', 'Pd-2e-na-cd 4 1.200 180.000 2.000', 'Pd-2e-na-ca 4 1.200 180.000 2.000', 'Pd-4n-na-hn 4 4.800 0.000 2.000', 'na-4n-cc-cc 4 4.200 180.000 2.000', 'na-2e-na-ca 4 1.200 180.000 2.000', 'Pd-2e-na-ca 4 1.200 180.000 2.000', 'cc-4n-na-hn 4 4.800 0.000 2.000', 'Pd-4n-na-cd 4 4.800 0.000 2.000', 'Pd-2e-na-cc 4 1.200 180.000 2.000', 'X -4n-na-X 2 3.400 180.000 2.000', 'Pd-4n-cc-h4 4 4.200 180.000 2.000', 'Pd-4n-cc-cc 4 4.200 180.000 2.000', 'na-2e-na-cd 4 1.200 180.000 2.000', 'na-2e-na-cc 4 1.200 180.000 2.000', 'cc-4n-na-cd 4 4.800 0.000 2.000', 'na-2e-na-ca 4 1.200 180.000 2.000', 'Pd-2e-na-cc 4 1.200 180.000 2.000', 'na-2e-na-cc 4 1.200 180.000 2.000', 'Pd-2e-na-cd 4 1.200 180.000 2.000', 'na-4n-cc-h4 4 4.200 180.000 2.000']
for i in dihedrals:
a = re.split(' {2,}', i)
print( "%-11s %2s %8s s s" % (a[0], a[1], a[2], a[3], a[4]) )
Output:
na-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-ca 4 1.200 180.000 2.000
Pd-4n-na-hn 4 4.800 0.000 2.000
na-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
Pd-2e-na-ca 4 1.200 180.000 2.000
cc-4n-na-hn 4 4.800 0.000 2.000
Pd-4n-na-cd 4 4.800 0.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
X -4n-na-X 2 3.400 180.000 2.000
Pd-4n-cc-h4 4 4.200 180.000 2.000
Pd-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-cd 4 1.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
cc-4n-na-cd 4 4.800 0.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
na-4n-cc-h4 4 4.200 180.000 2.000
A gnu-awk solution would be:
... |
awk -F ' {2,}' -v RS=', *|\\]' '
gsub(/dihedrals=\[|\047/, "") {
printf( "%-11s %2s %8s s s\n", $1, $2, $3, $4, $5)
}'
CodePudding user response：
Assumptions:
- 1st column always consists of 11 characters
I don't use python so I'll simulate the behavior (python making repeated calls out to awk) with a bash array and a bash/for loop that calls awk:
Setup:
declare -a dihedrals=([0]="na-2e-na-cd 4 1.200 180.000 2.000" [1]="Pd-2e-na-cd 4 1.200 180.000 2.000" [2]="Pd-2e-na-ca 4 1.200 180.000 2.000" [3]="Pd-4n-na-hn 4 4.800 0.000 2.000" [4]="na-4n-cc-cc 4 4.200 180.000 2.000" [5]="na-2e-na-ca 4 1.200 180.000 2.000" [6]="Pd-2e-na-ca 4 1.200 180.000 2.000" [7]="cc-4n-na-hn 4 4.800 0.000 2.000" [8]="Pd-4n-na-cd 4 4.800 0.000 2.000" [9]="Pd-2e-na-cc 4 1.200 180.000 2.000" [10]="X -4n-na-X 2 3.400 180.000 2.000" [11]="Pd-4n-cc-h4 4 4.200 180.000 2.000" [12]="Pd-4n-cc-cc 4 4.200 180.000 2.000" [13]="na-2e-na-cd 4 1.200 180.000 2.000" [14]="na-2e-na-cc 4 1.200 180.000 2.000" [15]="cc-4n-na-cd 4 4.800 0.000 2.000" [16]="na-2e-na-ca 4 1.200 180.000 2.000" [17]="Pd-2e-na-cc 4 1.200 180.000 2.000" [18]="na-2e-na-cc 4 1.200 180.000 2.000" [19]="Pd-2e-na-cd 4 1.200 180.000 2.000" [20]="na-4n-cc-h4 4 4.200 180.000 2.000")
Proposed code:
for x in "${dihedrals[@]}"
do
awk '{ f1=substr($0,1,11)
split(substr($0,12),a)
printf "s %2s %7s s s\n",f1,a[1],a[2],a[3],a[4]}' <<< "${x}"
done
This generates:
na-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
Pd-2e-na-ca 4 1.200 180.000 2.000
Pd-4n-na-hn 4 4.800 0.000 2.000
na-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
Pd-2e-na-ca 4 1.200 180.000 2.000
cc-4n-na-hn 4 4.800 0.000 2.000
Pd-4n-na-cd 4 4.800 0.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
X -4n-na-X 2 3.400 180.000 2.000
Pd-4n-cc-h4 4 4.200 180.000 2.000
Pd-4n-cc-cc 4 4.200 180.000 2.000
na-2e-na-cd 4 1.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
cc-4n-na-cd 4 4.800 0.000 2.000
na-2e-na-ca 4 1.200 180.000 2.000
Pd-2e-na-cc 4 1.200 180.000 2.000
na-2e-na-cc 4 1.200 180.000 2.000
Pd-2e-na-cd 4 1.200 180.000 2.000
na-4n-cc-h4 4 4.200 180.000 2.000
From a performance perspective I'd think the same (awk) logic should be doable within python thus eliminating the need for the repeated calls out to awk ... ???
CodePudding user response：
Do you have to use awk? It seems like something along these lines would accomplish the same goal in plain Python:
with open('a.txt', 'w') as fp:
fp.write('\n'.join(dihedrals))