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PerlMol - Perl Modules for Molecular Chemistry
Keywords
perl, molecule, molecular, chemistry, chemical, cheminformatics, chemoinformatics, computational chemistry, molecular modelling, molecular modeling, perlmol, perl module, atom, bond, atoms, bonds, molecules, connection table, z-matrix, internal coordinate
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PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry. It provides objects and methods for representing molecules, atoms, and bonds in Perl; doing substructure matching; and reading and writing files in various formats.
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<title>PerlMol - Perl Modules for Molecular Chemistry</title>
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<meta name="description" content='PerlMol is a collection of Perl modules for
chemoinformatics and computational chemistry. It provides objects and methods
for representing molecules, atoms, and bonds in Perl; doing substructure
matching; and reading and writing files in various formats.' />
<meta name="keywords" content="perl, molecule, molecular, chemistry, chemical,
cheminformatics, chemoinformatics, computational chemistry, molecular
modelling, molecular modeling, perlmol, perl module, atom, bond, atoms,
bonds, molecules, connection table, z-matrix, internal coordinates, pdb,
mdl, mol, molfile, sdf, sdfile, smiles, smarts, sln, sybyl, line notation,
canonicalization, canonical, ring, perception, structure, substrucure,
sssr, essr, xyz, mopac, midas, chimera, protein, macromolecule" />
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<p class="button_sel">Introduction
<p class="button"><a href="/features.html">Features</a>
<p class="button"><a href="/pod/Chemistry/Tutorial.html">Quick Tutorial</a>
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<h1>PerlMol - Perl Modules for Molecular Chemistry</h1>
<p>PerlMol is a collection of Perl modules for chemoinformatics and
computational chemistry with the philosophy that "simple things should be
simple". It should be possible to write one-liners that use this toolkit to do
meaningful "molecular munging". The PerlMol toolkit provides objects and
methods for representing molecules, atoms, and bonds in Perl; doing
substructure matching; and reading and writing files in various formats.
For a more detailed feature list, see the <a href="features.html">Features</a>
section.
<h2>Recent News</h2>
<ul>
<li><b>2009-05-10</b> Updated distributions: Chemistry-Mol-0.37, Chemistry-Pattern-0.27,
Chemistry-Ring-0.20, Chemistry-Canonicalize-0.11, Chemistry-Bond-Find-0.23
Chemistry-File-MDLMol-0.21, Chemistry-File-PDB-0.23, Chemistry-File-SMILES-0.46,
</ul>
<h2>Project status</h2>
<p>The current status could be called "alpha", because there are still many
missing or untested features, but there is enough for being useful for some
real work.
The <a href="features.html">Feature list</a> shows how complete the
current implementation for a given feature is.
<p>The following CPAN distributions have been released:
<ul>
<li><a href="http://search.cpan.org/dist/Chemistry-Mol/">Chemistry-Mol</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Pattern/">Chemistry-Pattern</a>
<li><a href="http://search.cpan.org/dist/Chemistry-FormulaPattern/">Chemistry-FormulaPattern</a>
<li><a href="http://search.cpan.org/dist/Chemistry-MidasPattern/">Chemistry-MidasPattern</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Reaction/">Chemistry-Reaction</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Bond-Find/">Chemistry-Bond-Find</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Canonicalize/">Chemistry-Canonicalize</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Ring/">Chemistry-Ring</a>
<li><a href="http://search.cpan.org/dist/Chemistry-InternalCoords/">Chemistry-InternalCoords</a>
<li><a href="http://search.cpan.org/dist/Chemistry-3DBuilder/">Chemistry-3DBuilder</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-SLN/">Chemistry-File-SLN</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-SMILES/">Chemistry-File-SMILES</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-SMARTS/">Chemistry-File-SMARTS</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-MDLMol/">Chemistry-File-MDLMol</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-Mopac/">Chemistry-File-Mopac</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-PDB/">Chemistry-File-PDB</a>
<li><a href="http://search.cpan.org/dist/Chemistry-MacroMol/">Chemistry-MacroMol</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-VRML/">Chemistry-File-VRML</a>
<li><a href="http://search.cpan.org/dist/Chemistry-File-XYZ/">Chemistry-File-XYZ</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Isotope/">Chemistry-Isotope</a>
<li><a href="http://search.cpan.org/dist/Chemistry-Mok/">Chemistry-Mok</a>
<li><a href="http://search.cpan.org/dist/PerlMol/">PerlMol</a>
</ul>
<h2>Authors</h2> <p>The PerlMol project was started and is being led and
maintained by <a href="http://ivan.tubert.org/">Ivan Tubert-Brohman</a>.
Other contributors include:
<ul>
<li>Gabriel Valiente (Technical University of Catalonia)
- Chemistry::Reaction module.</li>
<li>Brent Gregersen - formula parsing patch for Chemistry::File::Formula.</li>
<li>... and many people that have sent helpful suggestions, questions, tests,
and bug reports.</li>
</ul>
<p>If anyone else would like to help, please
<a href="mailto:itubert@users.sourceforge.net">send me an email</a>.
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