Configuration Generator

[debeshmandal]

Cleanup the configuration generator and ensure proper checks are done and messages are printed, but can be suppressed.

• [x] Move all existing molecules to molecules folder
• [x] Update main class to use molecules to parse dictionaries
• [x] Change the name of the main functions
• [x] Other checks and tidying of variables
• [ ] Ensure that more than one non-salt molecule can be placed non-overlapping
• [ ] print warnings when the minimum image convention is being broken
• [ ] ensure all necessary functions are present for configuration generation