PerlMol - Download and Installation

The PerlMol modules are being developed for perl 5.8.x and are known to work under Windows, Linux, FreeBSD, Solaris, and OS X. They are backward-compatible with perl 5.6.x, but you are strongly encouraged to upgrade to 5.8.x because support for older versions may be removed in the future. PerlMol depends on other modules available on CPAN, such as Math::VectorReal. See the README files for details.

There are three main ways of installing the PerlMol modules:

  1. Automated installation using the module - recommended way for UNIX-compatible systems.
  2. Manual install of the PerlMol bundle - alternative way if is not an option for some reason.
  3. PPM package for Windows ActivePerl 5.8 - easiest way of installing under Windows.
  4. CVS Repository - for developers that know what they are doing and are interested in trying the latest unreleased development versions.

Automated installation via

If you have the CPAN module configured properly, you can install each module separately by using perl -MCPAN -e 'install Chemistry::Mol' (to give an example). To install the latest bundle do perl -MCPAN -e 'install PerlMol'. But note that some of the most recent modules may not be included in the bundle yet.

You can also download the tarballs for individual modules and install them yourself by following the instructions on the README files, either from CPAN or from

PerlMol bundle - manual installation

If you don't have or can't get the CPAN module configured and/or you want to install everything as one bundle instead of module by module, follow these instructions (this works for Unix-like systems, including Cygwin and OS X, and for ActivePerl under Windows):

  1. Get the latest version of the PerlMol bundle. Note that some of the most recent modules may not be included in the bundle yet.
  2. Untar it in a temporary directory and change to that directory:
    tar xvzf PerlMol-0.3500.tar.gz
    cd PerlMol-0.3500
  3. Build and install the modules:
    perl Makefile.PL
    make test
    make install

NOTE: If you are using ActivePerl/Windows, you may have to install and use nmake instead of make. Or see the next section for how to install using PPM.

The last step may require root or administrator access. If you don't have it or you prefer to install everything in your home directory, you can use perl Makefile.PL PREFIX=/home/my_username or something like that. In that case you also need to make sure that perl knows how to find the modules by adding the installation directory to your include path. Add these to your profile (.bashrc, .cshrc, etc.)

# for sh, bash, ksh, etc.
export PERL5LIB

# for example:
export PERL5LIB

# for csh, tcsh
setenv PERL5LIB /home/my_username/lib/perl5/site_perl/perl_version

# for example:
setenv PERL5LIB /home/ivan/lib/perl5/site_perl/5.8.8

PPM Package for Windows/ActivePerl

The easiest way of installing PerlMol if you are using ActivePerl for Windows is to use PPM. Note, however, that several of the PerlMol modules in the official ActiveState repositories are outdated or built incorrectly, so don't use them or use them at your own risk!

The PerlMol bundle (but not the separate modules) is available as a ppm package for Perl 5.8.x on CPAN; to install it do the following:


Perl 5.6 PPM packages are not supplied or supported.

A note about Perl versions

If you have perl-5.8.0 or more recent, the PerlMol bundle has everything you need. If you have an earlier version of Perl, you will need these additional modules (which are included with perl-5.8.0):

    Test::Simple        0.45
    Scalar::Util        1.07
    Storable            2.04
    Text::Balanced      1.89

CVS (development version)

If you are interested in helping develop PerlMol or you want to take a look at the latest developments, you can take a look at the CVS repository, either through the ViewVC web interface, or through any CVS client. To connect anonymously using the command-line CVS client, use the following commands:

cvs login
cvs -z3 co modulename

Where modulename corresponds to one of the CPAN distribution names, in all lowercase (for example, chemistry-mol), or all to get all the CVS modules at once.