The ChemDoodle Web Components library is licensed under version 3 of the GNU GENERAL PUBLIC LICENSE. This library also has complete access to the entire ChemDoodle desktop API through AJAX, allowing for quick access to one of the most robust chemical graphics and informatics packages in existence directly through Javascript. Beyond graphics, this tool provides a framework for user interaction to create dynamic applications through web browsers, desktop platforms and mobile devices such as the iPhone, iPad and Android devices. ChemDoodle Web Components allow the wielder to present publication quality 2D and 3D graphics and animations for chemical structures, reactions and spectra. While minimizations of several discrete structures using through-space forces may look correct, please understand the theory behind the force field you are using and that any force field not specifically developed or parameterized for intermolecular forces will not lead to experimentally accurate coordinates.The ChemDoodle Web Components library is a pure Javascript chemical graphics and cheminformatics library derived from the ChemDoodle(R) application and produced by iChemLabs. Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. To do this, you can change the optimization scope to optimize the entire scene.
However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other.
ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. Most small molecule force fields are optimized for describing individual discrete molecular structures.
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