when I find the ring and then print the normal vector for the attached molecule, it says the norm is along the z-axis, yet, if you look at the input, the norm should be along the y-axis.
The molecule
sorry, I forgot to include: Perl v5.8.8 built for x86_64-linux-thread-multi PerlMol-0.35
Here is a short piece of code:
use Chemistry::File ':auto'; use Chemistry::Mol; use Chemistry::InternalCoords::Builder 'build_zmat'; use Chemistry::Ring::Find 'find_rings';
$mol = Chemistry::Mol->read("tmp.xyz"); build_zmat($mol); @rings = find_rings($mol); ($norm1, $d1) = $rings[0]->plane; print $norm1;
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The molecule
sorry, I forgot to include:
Perl v5.8.8 built for x86_64-linux-thread-multi
PerlMol-0.35
Here is a short piece of code:
use Chemistry::File ':auto';
use Chemistry::Mol;
use Chemistry::InternalCoords::Builder 'build_zmat';
use Chemistry::Ring::Find 'find_rings';
$mol = Chemistry::Mol->read("tmp.xyz");
build_zmat($mol);
@rings = find_rings($mol);
($norm1, $d1) = $rings[0]->plane;
print $norm1;