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Classes to manipulate chemical objects: atoms, molecules, etc.

This package is unmaintained.

Download latest release 1.1.2 (archived versions might be outdated)

License: PHP License

Description

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.

Maintainers

• Jesus M. Castagnetto (jmcastagnetto) — lead, active

Dependencies

Required

• PHP (>= 4.0.0)
• PEAR Installer (>= 1.4.0b1)

Releases

• 1.1.2 (stable, 2012-04-09)
  Release notes

  License: PHP License

  QA release
  Remove call time pass by references -- fatal in PHP 5.4.
  Bug #12264 Warnings & notices
  PHPUnit 3.6+ compatibility

• 1.1.1 (stable, 2010-10-04)
  Release notes

  License: PHP License

  QA release
  Bug #895 PEAR QA: improvement for get_class()-usage jmcastagnetto
  Bug #4493 forgotten $this-> jmcastagnetto
  Added PHPUnit test coverage (fragile)
  Fixed undefined constant bugs

• 1.1.0 (stable, 2003-05-13)
  Release notes

  License: PHP License

  Modified the parsing algorithm for atom records in a residue
  Added toXYZ() methods, and made toString() aliases of those
  Added one more example for converting PDB to XYZ

• 1.0.3 (stable, 2002-07-31)
  Release notes

  License: PHP License

  Change calls to "new Element()" to the current
  "new Science_Chemistry_Element()"

• 1.0.2 (stable, 2002-04-23)
  Release notes

  License: PHP License

  Fixed package.xml to be able to install the test scripts

• 1.0.1 (stable, 2002-04-23)
  Release notes

  License: PHP License

  Fixed an install problem. It should now install properly on
  $PEAR/Science/Chemistry

• 1.0 (stable, 2002-04-23)
  Release notes

  License: PHP License

  This is the initial release of the classes after conversion to PEAR
  standards.
  Includes tests/examples of use and PHPDoc generated documentation.
  On 2001-08-26 renamed to conform to new PEAR directory structure.

Bugs