Samples: B-form DNA, 6 Atracts and two 20 degree bends

#! /usr/bin/perl -w
# 
require $ENV{'CYCLIZE_HOME'}."lib/cyclize_lib.pl";

# Build the cyclize parameters hash
%cyclize_parameters = (
    "whole_chains"     => 1e8,
    "nrad_stats"       => 1e7,
    "icalcs"           => 100,
    "radial_cutoff"    => 60,
    "axial_cutoff"     => 40,
    "torsional_cutoff" => 36,
    "nkeepers"         => 10,
);

# Set the default values for generating the DNA
$Temp = 300;
$nnuc = 156;

# Build the parameter hashes defined below
&build_parameter_hashes; 

# The positions of the A-tracts
@atract_positions = ( 25..30, 36..41, 46..51, 57..62, 67..72, 78..82 );

for $linker ( 1..10 ) {

    # The first kink site is at nt 100+linker, the second is in phase
    $kink_site1 = 100+$linker;
    $kink_site2 = 100+$linker+10;
    @kink_positions = ( $kink_site1, $kink_site2 );

    # Set the value of the "kink" (a tilt) for the %KINK parameters hash.
    $kink = 20;
    $KINK{tilt} = $kink;

    # Create the generic sequence, with nts named "B"
    # and fill the sequence with standard Bform parameters
    %seq = &create_sequence( B, $nnuc );
    %seq = &fill_params( \%seq, \%BDNA );

    # Change the name of the nts in the A-tract sites to "A"
    # and fill these regions with A-tract parameters
    %seq = &fill_name( \%seq, "A", @atract_positions );
    %seq = &fill_Atract_params( \%seq, \%Atract, \%Atract_3, \%Atract_5 );

    # Create the generic sequence, with nts named "B"
    # and fill the sequence with standard Bform parameters
    %seq = &fill_name( \%seq, "K", @kink_positions );
    %seq = &fill_params( \%seq, \%KINK, @kink_positions );

    &Cyclize( \%seq, \%cyclize_parameters, "phasing_example_$linker" );

}

exit;

############################################################
# build_parameters_hashes
# 
# USAGE: 
# &build_parameter_hashes;
#
# -This subroutine initialize the defaults for the "parameter hashes" used
#  to construct the "sequence hash".  
# -A single parameter hash contains six keys: tilt, tilt_flex, roll,
#  roll_flex, twist and twist_flex.
############################################################
sub build_parameter_hashes {

    #####################################################
    # BDNA site parameter definitions
    $BDNA_tormod         = 2.4e-19; # torsional modulus (erg*cm)
    $BDNA_rpb            = 3.4e-8;  # rise/bp (cm)
    $BDNA_helical_repeat = 10.45;   # helical repeat (bp/360 degrees)

    %BDNA = (
        tilt       => 0,
        roll       => 0,
        twist      => 360/$BDNA_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $BDNA_rpb*$k*$Temp/$BDNA_tormod )*180/$PI,
        dz         => 3.4,
    );

    #####################################################
    # KINK site parameter definitions
    $KINK_tormod         = 2.4e-19; # torsional modulus (erg*cm)
    $KINK_rpb            = 3.4e-8;  # rise/bp (cm)
    $KINK_helical_repeat = 10.45;   # helical repeat (bp/360 degrees)

    %KINK = (
        tilt       => 0,
        roll       => 0,
        twist      => 360/$KINK_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $KINK_rpb*$k*$Temp/$KINK_tormod )*180/$PI,
        dz         => 3.4,
    );
    
    #####################################################
    # Atract site parameter definitions
    $Atract_tormod         = 2.4e-19; # torsional modulus (erg*cm)
    $Atract_rpb            = 3.4e-8;  # rise/bp (cm)
    $Atract_helical_repeat = 10.33;   # helical repeat (bp/360 degrees)

    # Default Atract values for middle of Atract region
    %Atract = (
        tilt       => 0,        
        roll       => 0,        
        twist      => 360/$Atract_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
        dz         => 3.4,
    );
    $Atract{min} = 4;       # minimum number of A's in Atract
    $Atract{max} = 6;       # maximum number of A's in Atract

    # Default Atract values for 5' junction of Atract
    %Atract_5 = (
        tilt       => -7.7,
        roll       => 4.6,   
        twist      => 360/$Atract_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
        dz         => 3.4,
    );

    # Default Atract values for 3' junction
    %Atract_3 = (
        tilt       => 9.7,
        roll       => 0,
        twist      => 360/$Atract_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
        dz         => 3.4,
    );
}