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RudiC, thanks for confirming my thought that different numerical values have to do with uneven spacings. Thanks!

Understood, but when I added field seperator and tried $6 as well as other values till $12 no one gave me 8. Where might be the problem?

Thank you very much Scrutinizer for a lengthy response!!! You're wonderfully generous :)

Everything in your response gives 8 or any other expected value depending on what you wrote except for the...

Hi, I would like to count the number of ALA occurences without having them to be repeated. In the script I have written now it has 40 repetitions of ALA but it has to be 8. ALA is chosen as one of...

I figured out that my input statement was a bit wrong. So no worries. Your suggestion worked. Thanks!

My input was:

#!/bin/bash
read -p "amino acid: " AAA
if [[ "ALA ARG ASN ASP CYS GLN GLY GLU HIS ILE \
LEU LYS MET PHE PRO SER THR TRP TYR VAL" =~ $AAA ]]
then
for i in HS_*.pdb;
do
...

Still no results. :-(. Any other way?

Dear forum members,

My question is simple. I want to pass a single quote (') to be read as belonging as an addition to the letters C1', C2', C3', C4', C5', O1', O2', O3', O4' & O5' to the program...

Thanks Scrutinizer for clarifying it. I assumed single and double quotes have the same qualities, but was wrong.

I get the numerical values when I write awk '{ if ($0 ~ /'$AAA'/) sum += $3} END...

What you mean by single quotes? When I put "" on $AAA in awk '{ if ($0 ~ /"$AAA"/) sum += $3} END {print sum}' $i I am still getting no output.
As what you mean by awk standard interface as...

Thank you. Also I have another question. Basically for the input file (calculate_contacts_HS_*.pdb.txt) I want that all lines that have ALA in first or second column sum the third column numerical...

Dear RudiC,

Can you please explain this part !OCC[$4]++ a bit more? I dont understand when you mention that it is not yet defined, what you mean by that?

Sincerely,
Aurimas

Thanks

Thanks. Can you also explain me what -v SRCH="$AAA" '$0 ~ SRCH && !OCC[$4]++ {CNT++ } END {print CNT+0}' does, especially !OCC and CNT? I cannot figure it out :/

Thank you it works and I edited my previous post. I also have a similar question for this code then:

#!/bin/bash
read -p "amino acid: " AAA
if [[ "ALA ARG ASN ASP CYS GLN GLY GLU HIS ILE \
...

Understood. I'll try to explain my situation in as much details as possible. The script I have now is:
#!/bin/bash
read -p "amino acid: " AAA
if [[ "ALA ARG ASN ASP CYS GLN GLY GLU HIS ILE \
...

As I told in the posts before the AAA value can be any of the 20 amino acids (ALA, ARG, ASN, ASP, CYS, GLN, GLY, GLU, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR or VAL). In the first ...

The output of the output of voronota get-balls-from-atoms-file --annotated for a certain .pdb file or input to awk looks like this (a sample, not full dataset) by your given code script:

...

Thank you, it works. However, the output now is 1 for all the cases, which is incorrect as I need to calculate AAA instances for 28 complexes (1st complex should give 8 as there are 8 times ALA is...

When I run your proposed code


#!/bin/bash
read -p "amino acid: " AAA
if [[ "ALA ARG ASN ASP CYS GLN GLY GLU HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL" =~ $AAA ]]
then for i in...

So the output for the given script is 10. When the script is run it first asks to enter amino acid (in this case ALA) that is taken the value of AAA with which the script works with. AAA can be any...

Dear forum members,

I want the script to count ALA as one (an example in quotes) and return an integer as 1 and not return 5 as an integer as it does now (look bash script). So how can I upgrade...

Thanks. I figured the rest out.

Dear forum members,

Below is my code, but I am getting permission denied when I try to run the script. Can someone explain what I am missing. I am using Mojave and try to run script on terminal.
...

Dear all,

How can I exit the script and return to terminal if domains is not equal to .pdb file, which i specifies . How could I make domains to be equal to "e" or any other string, number, etc....