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Top Forums Shell Programming and Scripting AWK code for finding distances between atoms in two different files Post 302353611 by ananyob on Tuesday 15th of September 2009 06:41:03 PM
Old 09-15-2009
Question AWK code for finding distances between atoms in two different files

HiSmilie

I have two separate data files (.xyz) type and I want to see distances between the coordinates of atoms of the two files. For example:-
My first files contains
1 1 1 11.50910000 5.17730000 16.49360000
3 1 2 11.21790000 6.36062000 15.60660000
6 1 2 11.43950000 7.66053000 16.07200000
2 1 3 11.87750000 7.81529000 17.04670000
where the last three columns are the coordinates, 1st column is Atom ID, 2nd column is Molecule ID and 3rd column is Atom type. I have another file that has coordinates of different atoms like
14 1 7 9.22151000 9.21624000 11.08350000
21 1 8 8.24299000 10.25310000 11.12120000
7 1 6 9.68004000 8.92467000 9.65365000
22 1 2 11.06970000 3.75903000 16.75830000

I want to make an awk code where AWK will read both files and find distance between atom ID 1 and atom ID 14 and will show the output with the atom IDs and the distance like
1 14 7.1284841 where 7.1284841 is the distance between coordinates of atom ID 1 and atom ID 14. The distance calculating formula is
SQRT ((X1-X2)^2 + (Y1-Y2)^2 + (Z1-Z2)^2)
I want the code to check distance between each single atom in file 1 and all the atoms in file 2. Like, it should give outputs of distances between atom id1 from file 1 and atom IDs 14, 21 7 and 22 from file 2 and then do the same for atom IDs 3, 6 and 2 from file 1. I do not know how to proceed with writing a code for this. I am new to awk.
Please suggest.....Smilie

Last edited by ananyob; 09-15-2009 at 11:48 PM..
 

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Tk_InternAtom(3)					       Tk Library Procedures						  Tk_InternAtom(3)

__________________________________________________________________________________________________________________________________________________

NAME
Tk_InternAtom, Tk_GetAtomName - manage cache of X atoms SYNOPSIS
#include <tk.h> Atom Tk_InternAtom(tkwin, name) const char * Tk_GetAtomName(tkwin, atom) ARGUMENTS
Tk_Window tkwin (in) Token for window. Used to map atom or name relative to a particular display. const char *name (in) String name for which atom is desired. Atom atom (in) Atom for which corresponding string name is desired. _________________________________________________________________ DESCRIPTION
These procedures are similar to the Xlib procedures XInternAtom and XGetAtomName. Tk_InternAtom returns the atom identifier associated with string given by name; the atom identifier is only valid for the display associated with tkwin. Tk_GetAtomName returns the string associated with atom on tkwin's display. The string returned by Tk_GetAtomName is in Tk's storage: the caller need not free this space when finished with the string, and the caller should not modify the contents of the returned string. If there is no atom atom on tkwin's display, then Tk_GetAtomName returns the string "?bad atom?". Tk caches the information returned by Tk_InternAtom and Tk_GetAtomName so that future calls for the same information can be serviced from the cache without contacting the server. Thus Tk_InternAtom and Tk_GetAtomName are generally much faster than their Xlib counterparts, and they should be used in place of the Xlib procedures. KEYWORDS
atom, cache, display Tk Tk_InternAtom(3)
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