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examples/Benchmarks/Atom-MVR-timer.pl  view on Meta::CPAN

#!/usr/bin/env perl
# 
use Modern::Perl;
use Math::Vector::Real;
use Time::HiRes qw(time);
use Benchmark qw(cmpthese);
use Scalar::Util qw(refaddr);
use HackaMol::Atom;

my $natoms = 100000;
print
"Atom-timer will time the construction of an array of  $natoms atoms to give idea about speed\n";

my $t1 = time;
my @atoms = map { HackaMol::Atom->new( Z => 80 ) } 1 .. $natoms;

my $t2 = time;
printf( "Time to Atom->new(Z => 80) for $natoms atoms: %10.3f\n", $t2 - $t1 );

my $t3;
foreach my $t ( 1 .. 3 ) {
    $_->push_coords( V( 2, 2, 2 ) ) foreach @atoms;
    $t3 = time;
    printf(
"$t time to push_coords( V(2.000,2.000,2.000) ) for $natoms atoms: %10.3f\n",
        $t3 - $t2 );
    $t2 = time;
}

foreach my $t ( 1 .. 3 ) {
    $atoms[$t]->push_coords( V( 2, 2, 2 ) ) foreach 1 .. 100;
    $t3 = time;
    printf(
"Time to push_coords( V(2.000,2.000,2.000) ) 100 times for atom $t: %.3g\n",
        $t3 - $t2 );
    $t2 = time;
}

$_->set_coords( 0, V( 1.000, 1.000, 1.000 ) ) foreach @atoms;
my $t4 = time;
printf(
    "Time to set_coords(0, V(1.000 ,1.000,1.000)) for $natoms atoms: %10.3f\n",
    $t4 - $t3 );

print "Dump the last atom: ", $#atoms, "\n";
print $atoms[$#atoms]->dump;

print "grep for some PdbRole defaults\n";

my @ala_atoms = grep { $_->resname eq 'ALA' } @atoms;
my $t5 = time;
printf( "time to grep resname eq ALA setting default: %10.3f\n", $t5 - $t4 );
print $atoms[$#atoms]->dump;
my @ala_atoms2 = grep { $_->resname eq 'ALA' } @atoms;
my $t6 = time;
printf( "time to grep resname eq ALA already set: %10.3f\n", $t6 - $t5 );

my $atoms_ala_atoms_match = 1;
foreach ( 0 .. $#ala_atoms ) {
    $atoms_ala_atoms_match = 0
      unless ( refaddr( $atoms[$_] ) == refaddr( $ala_atoms[$_] ) );
}
if ($atoms_ala_atoms_match) {