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HexagonalBipyramidal.pm
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HexagonalBipyramidal.pm
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## HexagonalBipyramidal.pm
############################################################################################
###
### Written by Sen Yao, 07/20/2016
### Copyright Sen Yao, Robert Flight, and Hunter Moseley, 07/20/2016. All rights reserved.
###
############################################################################################
package HexagonalBipyramidal;
use strict;
use AtomShell;
use base "Coordination";
our @defaultDataMembers = (
"numAtoms" => 8
);
our $expectedAngle60 = 60;
our $expectedAngle90 = 90;
our $expectedAngle120 = 120;
our $expectedAngle180 = 180;
our $invCorrM = [
[ 0.181, -0.090, 0.035, -0.069, 0.035, -0.090, 0.090, -0.056, -0.035, -0.035, -0.056, 0.090, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.090, 0.181, -0.090, 0.035, -0.069, 0.035, 0.090, 0.090, -0.056, -0.035, -0.035, -0.056, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[ 0.035, -0.090, 0.181, -0.090, 0.035, -0.069, -0.056, 0.090, 0.090, -0.056, -0.035, -0.035, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.069, 0.035, -0.090, 0.181, -0.090, 0.035, -0.035, -0.056, 0.090, 0.090, -0.056, -0.035, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[ 0.035, -0.069, 0.035, -0.090, 0.181, -0.090, -0.035, -0.035, -0.056, 0.090, 0.090, -0.056, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.090, 0.035, -0.069, 0.035, -0.090, 0.181, -0.056, -0.035, -0.035, -0.056, 0.090, 0.090, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[ 0.090, 0.090, -0.056, -0.035, -0.035, -0.056, 0.181, 0.035, -0.090, -0.069, -0.090, 0.035, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.056, 0.090, 0.090, -0.056, -0.035, -0.035, 0.035, 0.181, 0.035, -0.090, -0.069, -0.090, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.035, -0.056, 0.090, 0.090, -0.056, -0.035, -0.090, 0.035, 0.181, 0.035, -0.090, -0.069, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.035, -0.035, -0.056, 0.090, 0.090, -0.056, -0.069, -0.090, 0.035, 0.181, 0.035, -0.090, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[-0.056, -0.035, -0.035, -0.056, 0.090, 0.090, -0.090, -0.069, -0.090, 0.035, 0.181, 0.035, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[ 0.090, -0.056, -0.035, -0.035, -0.056, 0.090, 0.035, -0.090, -0.069, -0.090, 0.035, 0.181, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.511, 0.006, -0.006, -0.011, -0.006, 0.006, -0.289, 0.106, -0.106, -0.211, -0.106, 0.106],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.006, 0.511, 0.006, -0.006, -0.011, -0.006, 0.106, -0.289, 0.106, -0.106, -0.211, -0.106],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.006, 0.006, 0.511, 0.006, -0.006, -0.011, -0.106, 0.106, -0.289, 0.106, -0.106, -0.211],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.011, -0.006, 0.006, 0.511, 0.006, -0.006, -0.211, -0.106, 0.106, -0.289, 0.106, -0.106],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.006, -0.011, -0.006, 0.006, 0.511, 0.006, -0.106, -0.211, -0.106, 0.106, -0.289, 0.106],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.006, -0.006, -0.011, -0.006, 0.006, 0.511, 0.106, -0.106, -0.211, -0.106, 0.106, -0.289],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.289, 0.106, -0.106, -0.211, -0.106, 0.106, 0.511, 0.006, -0.006, -0.011, -0.006, 0.006],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.106, -0.289, 0.106, -0.106, -0.211, -0.106, 0.006, 0.511, 0.006, -0.006, -0.011, -0.006],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.106, 0.106, -0.289, 0.106, -0.106, -0.211, -0.006, 0.006, 0.511, 0.006, -0.006, -0.011],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.211, -0.106, 0.106, -0.289, 0.106, -0.106, -0.011, -0.006, 0.006, 0.511, 0.006, -0.006],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, -0.106, -0.211, -0.106, 0.106, -0.289, 0.106, -0.006, -0.011, -0.006, 0.006, 0.511, 0.006],
[ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.106, -0.106, -0.211, -0.106, 0.106, -0.289, 0.006, -0.006, -0.011, -0.006, 0.006, 0.511]
];
sub new
{
my $class = shift @_;
my $self = Coordination->new(@defaultDataMembers, @_);
bless $self, ref $class || $class;
return $self;
}
sub orderedCombinations
{
my $self = shift @_;
my $combo = shift @_;
my $orderedCombos;
foreach my $twoAtoms (&Coordination::_restrictedCombinations(2, @$combo))
{
my @sixAtoms = grep { my $test = $_; ! (grep { $_ == $test; } (@$twoAtoms)); } (@$combo);
foreach my $idx1 (2..5)
{
foreach my $idx2 (2..5)
{
next if ($idx1 == $idx2);
foreach my $idx3 (2..5)
{
next if ($idx1 == $idx3 || $idx2 == $idx3);
my @rest = grep {$_ != $idx1 && $_ != $idx2 && $_ != $idx3} (2..5);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[1], $sixAtoms[$idx1], $sixAtoms[$idx2], $sixAtoms[$idx3], $sixAtoms[$rest[0]]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[$idx1], $sixAtoms[1], $sixAtoms[$idx2], $sixAtoms[$idx3], $sixAtoms[$rest[0]]]);
}
}
}
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[2], $sixAtoms[3], $sixAtoms[1], $sixAtoms[4], $sixAtoms[5]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[2], $sixAtoms[3], $sixAtoms[1], $sixAtoms[5], $sixAtoms[4]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[2], $sixAtoms[4], $sixAtoms[1], $sixAtoms[3], $sixAtoms[5]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[2], $sixAtoms[4], $sixAtoms[1], $sixAtoms[5], $sixAtoms[3]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[2], $sixAtoms[5], $sixAtoms[1], $sixAtoms[2], $sixAtoms[5]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[2], $sixAtoms[5], $sixAtoms[1], $sixAtoms[5], $sixAtoms[2]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[3], $sixAtoms[2], $sixAtoms[1], $sixAtoms[4], $sixAtoms[5]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[3], $sixAtoms[2], $sixAtoms[1], $sixAtoms[5], $sixAtoms[4]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[4], $sixAtoms[2], $sixAtoms[1], $sixAtoms[3], $sixAtoms[5]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[4], $sixAtoms[2], $sixAtoms[1], $sixAtoms[5], $sixAtoms[3]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[5], $sixAtoms[2], $sixAtoms[1], $sixAtoms[3], $sixAtoms[4]]);
push (@$orderedCombos, [@$twoAtoms, $sixAtoms[0], $sixAtoms[5], $sixAtoms[2], $sixAtoms[1], $sixAtoms[4], $sixAtoms[3]]);
}
return $orderedCombos;
}
sub angleTestStatistic
{
my $self = shift @_;
my $type = shift @_;
my $combo = shift @_;
my $angleStats = shift @_;
my $leaveOut = (@_)? shift @_: 0;
my ($mean60, $mean120, $mean90, $mean180, $varianceOrN60, $varianceOrN90, $varianceOrN120, $varianceOrN180);
if ($type eq "dev")
{
$varianceOrN60 = $self->numAngles() ;
$varianceOrN90 = $self->numAngles() ;
$varianceOrN120 = $self->numAngles() ;
$varianceOrN180 = $self->numAngles() ;
my $angleTestStat;
map { $angleTestStat += (($_ - $expectedAngle60) ** 2) / $varianceOrN60 ;} ($self->calcAllAngles60($combo)) ; #ideal mean, number of variable
map { $angleTestStat += (($_ - $expectedAngle90) ** 2) / $varianceOrN90 ;} ($self->calcAllAngles90($combo)) ;
map { $angleTestStat += (($_ - $expectedAngle120) ** 2) / $varianceOrN120 ;} ($self->calcAllAngles120($combo)) ;
map { $angleTestStat += (($_ - $expectedAngle180) ** 2) / $varianceOrN180 ;} ($self->calcAllAngles180($combo)) ;
return $angleTestStat;
}
else
{
if ($type eq "chi")
{
$mean60 = ($$angleStats{"HexagonalBipyramidal"}{"60"}{"mean"})? ($$angleStats{"HexagonalBipyramidal"}{"60"}{"mean"}) : $expectedAngle60; ## major coordinaiton mean
$mean90 = ($$angleStats{"HexagonalBipyramidal"}{"90"}{"mean"})? ($$angleStats{"HexagonalBipyramidal"}{"90"}{"mean"}) : $expectedAngle90;
$mean120 = ($$angleStats{"HexagonalBipyramidal"}{"120"}{"mean"})? ($$angleStats{"HexagonalBipyramidal"}{"120"}{"mean"}) : $expectedAngle120;
$varianceOrN60 = $$angleStats{"variance"}; ## overall variance
$varianceOrN90 = $$angleStats{"variance"};
$varianceOrN120 = $$angleStats{"variance"};
}
else
{
$varianceOrN60 = $$angleStats{"HexagonalBipyramidal"}{"60"}{"variance"};
$varianceOrN90 = $$angleStats{"HexagonalBipyramidal"}{"90"}{"variance"};
$varianceOrN120 = $$angleStats{"HexagonalBipyramidal"}{"120"}{"variance"};
}
my @means = ($mean60, $mean60, $mean60, $mean60, $mean60, $mean60, $mean120, $mean120, $mean120, $mean120, $mean120, $mean120, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90, $mean90);
my @angles = ($self->calcAllAngles60($combo), $self->calcAllAngles120($combo), $self->calcAllAngles90($combo));
my $diff = [map { $angles[$_] - $means[$_]; } (0..(@angles-1))];
if ($leaveOut eq "l" || $leaveOut eq "leave" || $leaveOut eq "leaveOut")
{
my $n = 0;
for(my $x = 1; $x <= $#angles; $x++)
{ if ($angles[$x] < $angles[$n]) {$n = $x;} }
$$diff[$n] = 0;
}
my $std60 = 1/sqrt($varianceOrN60);
my $std90 = 1/sqrt($varianceOrN90);
my $std120 = 1/sqrt($varianceOrN120);
my $invStds = [$std60, $std60, $std60, $std60, $std60, $std60, $std120, $std120, $std120, $std120, $std120, $std120, $std90, $std90, $std90, $std90, $std90, $std90, $std90, $std90, $std90, $std90, $std90, $std90];
#my $chiStat = $self->covMatChi($diff, $invStds, $invCorrM);
my $chiStat = 0;
map {$chiStat += ($$diff[$_] * $$invStds[$_] / 1.5)**2;} (0..(@$diff-1));
#print join(", ", @angles), "\n";
#print join(", ", @means), "\n";
#print join(", ", @$diff), "\n";
#print $self->{shellObj}->metalID(), ", ", $$combo[0]->resID, ", ", $$combo[1]->resID, ", ", $$combo[1]->coordinates(), ", $chiStat, $distChi, $prob; $varianceOrN60, $varianceOrN90, $varianceOrN120\n\n";
#print "mean 90, $expect90\nangles: ";
##print map {"$_, "; } (@angles);
##print "\nstd90, $std90\n";
##print "covariance: ", $chiStat;#, "; previous: $angleTestStat\n";
return $chiStat;
}
}
sub calcAllAngles90
{
my $self = shift @_;
my $combo = (@_)? shift @_ : $self->{bestCombo}->{ligands};
my @angles;
my $axial = [$$combo[0], $$combo[1]];
my $planar = [$$combo[2], $$combo[3], $$combo[4], $$combo[5], $$combo[6], $$combo[7]];
my $center = $self->{shellObj}->{center};
for(my $x = 0; $x < @$axial; $x++) # axial atom to planar atom angles, 90 is ideal
{
for(my $y = 0; $y < @$planar; $y++)
{
push (@angles, $center->angle($$axial[$x], $$planar[$y]));
}
}
return @angles;
}
sub calcAllAngles180
{
my $self = shift @_;
my $combo = (@_)? shift @_ : $self->{bestCombo}->{ligands};
my @angles;
my $axial = [$$combo[0], $$combo[1]];
my $planar = [$$combo[2], $$combo[3], $$combo[4], $$combo[5], $$combo[6], $$combo[7]];
my $center = $self->{shellObj}->{center};
push (@angles, $center->angle($$axial[0], $$axial[1])) ; # axial atom to axial atom angles, 180 as ideal
push (@angles, $center->angle($$planar[0], $$planar[3])) ; # axial atom to axial atom angles, 180 as ideal
push (@angles, $center->angle($$planar[1], $$planar[4])) ; # axial atom to axial atom angles, 180 as ideal
push (@angles, $center->angle($$planar[2], $$planar[5])) ; # axial atom to axial atom angles, 180 as ideal
return @angles;
}
sub calcAllAngles60
{
my $self = shift @_;
my $combo = (@_)? shift @_ : $self->{bestCombo}->{ligands};
my @angles;
my $axial = [$$combo[0], $$combo[1]];
my $planar = [$$combo[2], $$combo[3], $$combo[4], $$combo[5], $$combo[6], $$combo[7]];
my $center = $self->{shellObj}->{center};
push (@angles, $center->angle($$planar[0], $$planar[1])); ## planar atom to adjacent planar atom angles, 60 is ideal
push (@angles, $center->angle($$planar[1], $$planar[2]));
push (@angles, $center->angle($$planar[2], $$planar[3]));
push (@angles, $center->angle($$planar[3], $$planar[4]));
push (@angles, $center->angle($$planar[4], $$planar[5]));
push (@angles, $center->angle($$planar[0], $$planar[5]));
return @angles;
}
sub calcAllAngles120
{
my $self = shift @_;
my $combo = (@_)? shift @_ : $self->{bestCombo}->{ligands};
my @angles;
my $axial = [$$combo[0], $$combo[1]];
my $planar = [$$combo[2], $$combo[3], $$combo[4], $$combo[5], $$combo[6], $$combo[7]];
my $center = $self->{shellObj}->{center};
push (@angles, $center->angle($$planar[0], $$planar[2])); ## planar atom to every other planar atom angles, 120 is ideal
push (@angles, $center->angle($$planar[1], $$planar[3]));
push (@angles, $center->angle($$planar[2], $$planar[4]));
push (@angles, $center->angle($$planar[3], $$planar[5]));
push (@angles, $center->angle($$planar[4], $$planar[0]));
push (@angles, $center->angle($$planar[5], $$planar[1]));
return @angles;
}
sub calcExpectedAngleStats
{
my $self = shift @_;
my $angleStats = shift @_;
push (@{$$angleStats{"HexagonalBipyramidal"}{"60"}}, $_->calcAllAngles60());
push (@{$$angleStats{"HexagonalBipyramidal"}{"120"}}, $_->calcAllAngles120());
push (@{$$angleStats{"HexagonalBipyramidal"}{"90"}}, $_->calcAllAngles90());
push (@{$$angleStats{"HexagonalBipyramidal"}{"180"}}, $_->calcAllAngles180());
return 0;
}