Manual Reference Pages - CHEMISTRY::FILE::VRML (3)
Chemistry::File::VRML - Generate VRML models for molecules
use Chemistry::Bond::Find find_bonds;
my $mol = Chemistry::Mol->read(test.pdb);
find_bonds($mol, orders => 1);
$mol->write(test.wrl, format => vrml,
center => 1,
style => ballAndWire,
color => byAtom,
This module generates a VRML (Virtual Reality Modeling Language) representation
of a molecule, which can then be visualized with any VRML viewer. This is a
PerlMol file I/O plugin, and registers the vrml format with
Chemistry::Mol. Note however that this file plugin is write-only; theres no
way of reading a VRML file back into a molecule.
This module is a modification of PDB2VRML by Horst Vollhardt, adapted to the
The following options may be passed to $mol->write.
If true, shift the molecules center of geometry into the origin of the
coordinate system. Note: this only affects the output; it does not affect
the coordinates of the atoms in the original Chemistry::Mol object.
Sets the style for the VRML representation of the molecular structure.
Default is Wireframe. Currently supported styles are:
Set the overall color of the molecular structure. If the color is
set to byAtom, the color the for atoms and bonds is defined by
the atom type. Default is byAtom. Currently supported colors are:
yellow, blue, red,
green, white, brown,
Defines the radius in Angstrom for the cylinders in the Stick
and BallAndStick style. Default is 0.15 .
Defines the factor which is multiplied with the VDW radius for
the spheres in the BallAndWire and BallAndStick style. Default
is 0.2 .
Turns on/off compression of the output. If turned on, all leading
whitespaces are removed. This produces a less readable but approx.
20% smaller output, the speed is increased by 10% as well.
PDB2VRML originally by Horst Vollhardt, firstname.lastname@example.org, 1998.
Modified and adapted as Chemistry::File::VRML by Ivan Tubert-Brohman,
PDB2VRML Copyright (c) 1998 by Horst Vollhardt. All rights reserved.
Chemistry::File::VRML modifications Copyright (c) 2005 by Ivan Tubert-Brohman.
All rights reserved. This program is free software; you can redistribute it
and/or modify it under the same terms as Perl itself.
PDB2VRML found at
PerlMol project at http://www.perlmol.org/
|perl v5.20.3 ||CHEMISTRY::FILE::VRML (3) ||2005-05-16 |
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