Package to manipulate Molecular structures. Starting with files from http://svn.php.net/repository/pear/packages/Science_Chemistry trunk (version 1.1.1)
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README.md

Science_Chemistry

General classes to represent Atoms, Molecules and Macromolecules. Also parsing code for PDB, CML and XYZ file formats. Examples of parsing and conversion to/from chemical structure formats. Includes a utility class with information on the Elements in the Periodic Table.

This is old code I wrote for PEAR. Originally it was tracked in CVS, then it was moved to SVN, and now I am importing it to git :-)

-- Jesus M. Castagnetto