Hei, I am trying to use an already existing code to convert a protein PDB file into a GIT vector. I am trying to run it, but it doesn't seem to work. I believe I am just doing it wrong. What I am trying to do is to get the script running so that it can access a folder of pdb files and calculate the GIT vectors.
The preexisting code I want to get running is given here: http://www2.mat.dtu.dk/people/Peter.Roegen/Gauss_Integrals_Tuned.html and the instructions on how to compile and run the code seem fairly simple:
Compile: GIT is compiled entering >gcc GIT.c -lm -O3 -o GIT
Run: To run GIT enter >GIT /path/to/pdb_file_directory/ Averge-gauss_integral_file output.file error.file
I have not really worked with C before and all my attempts of getting it to run failed. I use a Mac and normally code in python. I downloaded the Command line tools for Xcode and made sure gcc was installed. From what I understand this is enough to compile the c file. I got the Git.c from the above website but running it lead to a bunch of errors:
(base) Jennifers-MBP:Binf jenniferan$ gcc Git.c -lm -O3 -o GIT
Git.c:1808:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
main(int argc, char *argv[])
^
Git.c:1823:7: error: non-void function 'main' should return a value [-Wreturn-type]
return;
^
Git.c:1831:7: error: non-void function 'main' should return a value [-Wreturn-type]
return;
^
Git.c:1837:7: error: non-void function 'main' should return a value [-Wreturn-type]
return;
^
Git.c:1844:7: error: non-void function 'main' should return a value [-Wreturn-type]
return;
^
Git.c:1850:143: warning: format specifies type 'long *' but the argument has type 'int *' [-Wformat]
sscanf(line,"%li %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf\n",&nres,&inv[0],&inv[1]...
~~~ ^~~~~
%i
Git.c:1858:11: error: non-void function 'main' should return a value [-Wreturn-type]
return;
^
Git.c:1867:7: error: non-void function 'main' should return a value [-Wreturn-type]
return ;
^
2 warnings and 6 errors generated.
After that I just tried the next step, which also didn't work:
(base) Jennifers-MBP:Binf jenniferan$ >GIT /Users/jenniferan/Desktop/Binf/ Averge-gauss_integral_file output.file error.file
bash: /Users/jenniferan/Desktop/Binf/: is a directory
(base) Jennifers-MBP:Binf jenniferan$
("Binf" is the fold my .pdb files is located in).
Maybe it is a mistake to do this in the terminal, maybe it's something else. I just have no clue at all how I can successfully run this script.
Do you guys have any advice?
