File Coverage

blib/lib/HackaMol/Roles/NERFRole.pm
Criterion Covered Total %
statement 14 38 36.8
branch 0 4 0.0
condition n/a
subroutine 5 9 55.5
pod 4 4 100.0
total 23 55 41.8


line stmt bran cond sub pod time code
1             # ABSTRACT: Role providing Natural extension reference frame implementation for molecular building
2             $HackaMol::Roles::NERFRole::VERSION = '0.052';
3             use 5.008;
4 11     11   6947 use Moose::Role;
  11         57  
5 11     11   59 use Math::Vector::Real;
  11         28  
  11         81  
6 11     11   52548 use Math::Trig;
  11         31  
  11         595  
7 11     11   61  
  11         36  
  11         4320  
8             my $orig = V(0,0,0);
9              
10             # adding the first vector
11             my $self = shift;
12             if (@_ == 3){
13 0     0 1   return V(@_);
14 0 0         }
15 0           else {
16             return $orig;
17             }
18 0           }
19              
20             #allow the use of optvec to give control over the addition
21             my ($self, $a, $R, $optvec) = @_;
22             $optvec = V(1,0,0) unless defined($optvec);
23             return ($a + $R*$optvec->versor);
24 0     0 1   }
25 0 0          
26 0           my ($self,$a,$b,$R,$ang) = @_;
27             $ang = deg2rad(180-$ang);
28             my ($ba, $j, $k) = ($b-$a)->rotation_base_3d;
29             my $c = $b+$ba*$R;
30 0     0 1   $c = $j->rotate_3d($ang, $c-$b) + $b;
31 0           return ($c);
32 0           }
33 0            
34 0           my ($self,$a,$b,$c,$R,$ang,$tors) = @_;
35 0           $ang = deg2rad(180-$ang);
36             $tors = deg2rad($tors);
37             my $cang = cos($ang);
38             my $sang = sin($ang);
39 0     0 1   my $ctor = cos($tors);
40 0           my $stor = sin($tors);
41 0            
42 0           my $bc = ($c-$b)->versor;
43 0           my $n = (($b-$a) x $bc)->versor;
44 0            
45 0           my $D = $R*($bc*$cang + ($n x $bc)*$sang*$ctor + $n*$sang*$stor) + $c;
46             return $D;
47 0           }
48 0            
49             no Moose::Role;
50 0            
51 0           1;
52              
53              
54 11     11   79 =pod
  11         23  
  11         57  
55              
56             =head1 NAME
57              
58             HackaMol::Roles::NERFRole - Role providing Natural extension reference frame implementation for molecular building
59              
60             =head1 VERSION
61              
62             version 0.052
63              
64             =head1 SYNOPSIS
65              
66             # Adds the NERF capabilities to consuming classes
67             # Let's say that the $bld object below consumes this Role
68             #Let's build a six member ring
69              
70             push @vecs, $bld->init() ;
71             push @vecs, $bld->extend_a( $vecs[0] , 1.47 );
72             push @vecs, $bld->extend_ab( @vecs[0,1], 1.47, 109.5 );
73             push @vecs, $bld->extend_abc(@vecs[0,1,2], 1.47, 109.5, 60 );
74             push @vecs, $bld->extend_abc(@vecs[1,2,3], 1.47, 109.5, -60 );
75             push @vecs, $bld->extend_abc(@vecs[2,3,4], 1.47, 109.5, 60 );
76              
77             printf ("C %10.6f %10.6f %10.6f\n", @$_ ) foreach @vecs;
78              
79             =head1 DESCRIPTION
80              
81             The HackaMol::X::NERF library is a quick implementation of the Natural
82             Extension Reference Frame method for building cartesian coordinates from
83             internal coordinates. It is experimental. In fact, there are
84             no substantial tests yet! They will be added soon.
85             The API will change and expand. Currently, the class provides four methods four initializing and extending a vector space. Lend me a hand if you are interested!
86              
87             Study Z-matrices and the synopsis should be easy to understand. All angles are in degrees.
88              
89             =head1 METHODS
90              
91             =head2 init
92              
93             optional argument is list of three numbers: x, y, and z.
94              
95             Returns an MVR object constructed from V(0,0,0) or V(x,y,z).
96              
97             =head2 extend_a(MVR1, R)
98              
99             two arguments MVR1 and R, along with optional argument MVR2.
100              
101             Returns an MVR object that is a distance R from MVR1. This new vector will be
102             displaced along the x axis unless the optional MVR2 is passed. If MVR2 the
103             MVR returned is displace by R times the unit vector parallel to MVR1.
104              
105             =head2 extend_ab(MVR1, MVR2, R, ANGLE)
106              
107             four arguments MVR1, MVR2, R, and ANGLE.
108              
109             Returns an MVR object that is a distance R from MVR2 and at ANGLE from MVR1.
110              
111             =head2 extend_abc(MVR1, MVR2, MVR3, R, ANGLE, TORSION)
112              
113             six arguments MVR1, MVR2, MVR3, R, ANGLE, and TORSION.
114              
115             Returns an MVR object that is a distance R from MVR3, at ANGLE from MVR2,
116             and at TORSION from MVR1 via the vector between MVR2 and MVR3.
117              
118             =head1 AUTHOR
119              
120             Demian Riccardi <demianriccardi@gmail.com>
121              
122             =head1 COPYRIGHT AND LICENSE
123              
124             This software is copyright (c) 2017 by Demian Riccardi.
125              
126             This is free software; you can redistribute it and/or modify it under
127             the same terms as the Perl 5 programming language system itself.
128              
129             =cut