YARM Samples

Find all protons in a pdb file less than 6 angs apart from a specific atom.

#!/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;

# Name of specific atom to look at
$atom_i = "A 3 CYT H6";

################################################
# 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);


%xyz = &Pdb_Read( $pdb_file );
%rij = &Rij_Hash( \%xyz, $min, $max );

@atoms_j = sort keys %{ $rij{ $atom_i } };
foreach $atom_j ( @atoms_j ) {
    $rij = $rij{$atom_i}{$atom_j};
    print "$atom_i $atom_j rij=$rij\n";
}