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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
09-15-2009
AWK code for finding distances between atoms in two different files
Hi
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.....
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.....
Last edited by ananyob; 09-15-2009 at 11:48 PM..
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LEARN ABOUT OSF1
xlsatoms
xlsatoms(1X) xlsatoms(1X) NAME
xlsatoms - list interned atoms defined on server SYNOPSIS
xlsatoms [-options...] OPTIONS
This option specifies the X server to which to connect. This option specifies a printf-style string used to list each atom <value,name> pair, printed in that order (value is an unsigned long and name is a char *). xlsatoms will supply a newline at the end of each line. The default is %ld %s. This option specifies the range of atom values to check. If low is not given, a value of 1 assumed. If high is not given, xlsatoms will stop at the first undefined atom at or above low. This option specifies the name of an atom to list. If the atom does not exist, a message will be printed on the standard error. DESCRIPTION
The xlsatoms command lists the interned atoms. By default, all atoms starting from 1 (the lowest atom value defined by the protocol) are listed until unknown atom is found. If an explicit range is given, xlsatoms will try all atoms in the range, regardless of whether or not any are undefined. ENVIRONMENT
to get the default host and display to use. SEE ALSO
X(1X), Xserver(1X), xprop(1X) AUTHOR
Jim Fulton, MIT X Consortium xlsatoms(1X)