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Running a program multiple times to search pattern and assign structure

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# 1  
Old 01-27-2013
Running a program multiple times to search pattern and assign structure
Hi all,
I have a big file (n.txt) with following pattern:

Code:
ATOM      1  N    SER A   1     122.392 152.261 138.190  1.00  0.00     N  
ATOM      2  CA  SER A   1     122.726 151.241 139.183  1.00  0.00     C  
TER
ENDMDL
ATOM      1  N    SER A   1     114.207 142.287 135.439  1.00  0.00      N  
ATOM      2  CA  SER A   1     113.667 143.509 134.894  1.00  0.00      C 
TER
ENDMDL

I am using following script to read pattern and assign structure to them using another program st giving 2 output files-fn.str -m.mol:
Code:
pattern_txt=n.txt
npattern=`grep -c ENDMDL $pattern_txt`
echo $npattern patterns. Assigning_structure:
echo $npattern > st_input
seq -w 1 $npattern >> st_input
st $pattern_txt -fn.str -mn.mol

But this script is reading only first pattern and giving structure of that pattern by running st program. I wish to have structure for all patterns.

Please guide.
# 2  
Old 01-28-2013
What are the parameters to st? Does it need other input than the pattern file? So you produced
Code:
cat st_input
2
1
2

- what do you do with it? It is not used anywhere.
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# 3  
Old 01-28-2013
Thanks.
st is a program that read a pattern and produces 2 files n.str (for summary) and n.mol (detail).
I want st to read each pattern from big file, predict the structure and compile all in one n.str and n.mol
# 4  
Old 01-29-2013
So you need to extract each of the (multi line?) patterns from "big file" and provide it to st? I still don't have the slightest clue what you need, or, what st needs resp., and what st_input is/was for.
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