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This an initial solution, but can be improved: out = system2("f:/stride/stride.exe", "f:/stride/1a11.pdb -h", stdout=T) nh = strsplit(out[grepl("HBT", out)], " ")[[1]][2] print(nh) # Output: 26 (hydrogen bonds) I compiled an Windows version of Stride and uploaded here: http://lcrserver.icmc.usp.br/~daniel/bin/stride.exe


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The number of hydrogen bonds cannot actually be said from software only inferred. But you could try using STRIDE (http://structure.usc.edu/stride/) which takes the file name with a -h flag to output the number of hydrogen bonds. You could then write a small shell script which would pass in each file and store the data you wanted in whatever format you liked. ...



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