YARM Samples

Measure rijs of all protons in a pdb file less than 6 angs apart.

Notes: This script will build a minimal %rij hash, in that only rijs between 0-6 angs will be retained.

#!/usr/local/bin/perl
require "/usr/local/yarm/yarm_lib.pl";

################################################
# Define variables
################################################
# Name of input pdb file
$pdb_file = "dick_xtal.pdb";

# Minimum and maximum distances to use in building %rij
$min = 0; $max = 6;

################################################
# Call YARM subroutines
################################################
print "$yarm_version\n";

# Get non-exchangeable nucleic acid protons from a PDB file
%xyz = &Pdb_Read_All( $pdb_file );
%xyz = &Get_Atom_Type( \%xyz, \%nonX_NA );
%xyz = &Pseudo_Methyl(\%xyz);

# Measure distances of all atom pairs between 
# min to max angstroms
%rij  = &Rij_Hash( \%xyz, $min, $max );

# A list of all the i atoms in %rij
@atoms_i = sort keys %rij;

# Loop through every @rij_atoms_i
foreach $atom_i ( @atoms_i ) {

    # A list of all the j atoms for this particular i atom
    @atoms_j = sort keys %{$rij{$atom_i}};

    # Loop through every @rij_atoms_j
    foreach $atom_j ( @atoms_j ) {
        $rij = $rij{$atom_i}{$atom_j};
        print "$atom_i $atom_j rij=$rij\n";
    }
}