small requests

[auffinger]

Dear Xiang-Jun,

1) I would appreciate a --silent option since I am running your programs on a large number of files.

2) with snap, I would appreciate a count of the files that are written out by your program and something like a zero output file message if they are no proteins processed. This would be helpful for parsing (I know that there is a screen message, but writing it in the output file should be interesting).

Thanks for considering this if you have time.

Best,

Pascal

[xiangjun]

Hi Pascal,

1) I would appreciate a --silent option since I am running your programs on a large number of files.

Try to run the program with --silent to see what you get. In any event, you can use file redirection to achieve your goal. For example,

Code: [Select]

x3dna-dssr -i=1ehz.pdb -o=1ehz.out 2> msg

2) with snap, I would appreciate a count of the files that are written out by your program and something like a zero output file message if they are no proteins processed. This would be helpful for parsing (I know that there is a screen message, but writing it in the output file should be interesting).

See reply above.

Xiang-Jun

[auffinger]

Hi Xiang-Jun,

I will use --silent, thanks for this. May be this option could be mentioned in the help file (-h).

Fot the second point:

in dssr, you have

 ****************************************************************************
List of 12 additional files
   1 dssr-stems.pdb -- MODEL/ENDMDL delineated stems
   2 dssr-helices.pdb -- MODEL/ENDMDL delineated helices (pseudo/coaxial)
   3 dssr-pairs.pdb -- MODEL/ENDMDL delineated base pairs
   4 dssr-multiplets.pdb -- MODEL/ENDMDL delineated multiplets
   5 dssr-hairpins.pdb -- MODEL/ENDMDL delineated hairpin loops
   6 dssr-4pas.pdb -- MODEL/ENDMDL delineated loop/turn interactions for Pascal
   7 dssr-2ndstrs.bpseq -- secondary structures in bpseq format
   8 dssr-2ndstrs.ct -- secondary structures in connect format
   9 dssr-2ndstrs.dbn -- secondary structures in dot-bracket notation
  10 dssr-torsions.txt -- Backbone torsion angles and suite names
  11 dssr-Uturns.pdb -- MODEL/ENDMDL delineated U-turn motifs
  12 dssr-a2bases.pdb -- MODEL/ENDMDL delineated atom-base stacking interactions

at the end of the output file. I was suggesting adding such a feature that would provide easier to
read/parse outputs.
This could be useful also in find_pair for example but seems particularly important in Snap that is a new program.

I suggest to include the line appearing on the screen (saying that the structure contains less than 5 amino acids) in the output of dssr.

Best,

Pascal