My software notes

June 2, 2006

NOE constraints counter

Filed under: softwares and scripts,xplor/xplor-nih/cns — kpwu @ 7:12 pm
Tags: , ,

Yesterday, I spent 1.5 hours writing a shell script which can take xplor-nih NOE table files as inputs and output the numbers of NOEs of each residue and report the numbers of intra residual, sequential, short, medium and long range NOEs after sorting. The current script doesn’t take ambiguous and hydrogen bond constraints as input. To run the script well, users have to remove those ambiguous and hydrogen bond constraints first. Oh, also, I won’t calculate complex structure, the script doesn’t support complex structure constraints as inputs (which means the file has segid “a”, segid “b” in each line).

The example results are like:

residue 5 has 1 NOEs
residue 6 has 2 NOEs
residue 7 has 1 NOEs
residue 8 has 4 NOEs
residue 9 has 0 NOEs
residue 10 has 1 NOEs
residue 11 has 4 NOEs
residue 12 has 7 NOEs
residue 13 has 9 NOEs
residue 14 has 5 NOEs
residue 15 has 6 NOEs
residue 16 has 7 NOEs
residue 17 has 7 NOEs
residue 18 has 13 NOEs
residue 19 has 8 NOEs
residue 20 has 11 NOEs
and the statistics look like:

=====================================
total counted NOEs are: 717
=====================================
intra_residual (j-i = 0): 205
sequential (j-i = 1): 263
medium range (j-i = 2 ): 34
medium range (j-i = 3 ): 6
medium range (j-i = 4 ): 3
long range (j-i >= 5 ): 206

(more…)

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