MoleCuilder

Molecuilder began as a simple code to handle the config files of pcp which was meant to allow for:

• Adding atoms by absolute coordinates or bond lengths and angles ...
• Removing atoms
• Storing and loading of config files, also of old versions (Jan's)

However, it grew and grew and as of now it can do quite a lot more:

• Estimated guess of the volume of a given cluster (by calculating volume of convex envelope)
• many-body bond order fragmentation (to an adaptive or fixed order and also from a previous fragmentation)
• Depth-First-Search Analysis of a given structure finding tree/back edges, all disconnected subgraphs and rings (however not the "SPSS" set)
• Principal Axis System (either only printout or also rotation to it)
• Alignment of molecule along a given axis
• Measurements of bond lengths and angles
• Duplication/Mirroring of a molecule in any axial direction by any positive factor
• Scaling, translations and many more operations on a system
• Molecular Dynamics (given a force file, Verlet integration is performed)