/ 
HackaMol-0.035
River stage one • 3 direct dependents • 3 total dependents
/ HackaMol::Roles::NERFRole

NAME

HackaMol::Roles::NERFRole - Role providing Natural extension reference frame implementation for molecular building

VERSION

version 0.035

SYNOPSIS

# Adds the NERF capabilities to consuming classes        
# Let's say that the $bld object below consumes this Role 
#Let's build a six member ring 

push @vecs, $bld->init() ; 
push @vecs, $bld->extend_a(  $vecs[0]  ,   1.47              );
push @vecs, $bld->extend_ab( @vecs[0,1],   1.47, 109.5       );
push @vecs, $bld->extend_abc(@vecs[0,1,2], 1.47, 109.5,  60 );
push @vecs, $bld->extend_abc(@vecs[1,2,3], 1.47, 109.5, -60 );
push @vecs, $bld->extend_abc(@vecs[2,3,4], 1.47, 109.5,  60 );

printf ("C %10.6f %10.6f %10.6f\n", @$_ ) foreach @vecs;

DESCRIPTION

The HackaMol::X::NERF library is a quick implementation of the Natural Extension Reference Frame method for building cartesian coordinates from internal coordinates. This library currently uses Moo and Math::Vector::Real objects, and is thus reasonably fast. It is experimental. In fact, there are no substantial tests yet! They will be added soon. 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!

Study Z-matrices and the synopsis should be easy to understand. All angles are in degrees.

METHODS

init

optional argument is list of three numbers: x, y, and z.

Returns an MVR object constructed from V(0,0,0) or V(x,y,z).

extend_a(MVR1, R)

two arguments MVR1 and R, along with optional argument MVR2.

Returns an MVR object that is a distance R from MVR1. This new vector will be displaced along the x axis unless the optional MVR2 is passed. If MVR2 the MVR returned is displace by R times the unit vector parallel to MVR1.

extend_ab(MVR1, MVR2, R, ANGLE)

four arguments MVR1, MVR2, R, and ANGLE.

Returns an MVR object that is a distance R from MVR2 and at ANGLE from MVR1.

extend_abc(MVR1, MVR2, MVR3, R, ANGLE, TORSION)

six arguments MVR1, MVR2, MVR3, R, ANGLE, and TORSION.

Returns an MVR object that is a distance R from MVR3, at ANGLE from MVR2, and at TORSION from MVR1 via the vector between MVR2 and MVR3.

AUTHOR

Demian Riccardi <demianriccardi@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2015 by Demian Riccardi.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.