Indeed, Bioclipse is an excellent way of integrating your tools with other tools. You'll have good use from the modular GUI, the scripting environment etc. JMol, as Michael mentioned, is already integrated, and building a plugin for your tool should not be a biggie. You shuold be able to get started in an hour using a guide such as this.
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Ram
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Samuel Lampa
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Samuel Lampa
What exactly do you want to happen at compile time? I'm not sure I understand what you are trying to achieve.
Please post link to related question to describe the background of the problem or explain the question in detail. Are you developing a web application or a desktop application?
I am doing superposition. Thus I want to integrate the above mentioned so that when my Java program is compiled, the result of the rotation & translation will be shown at Jmol when 2 protein structures are on top of one another.