= MoleCuilder =

Molecuilder began as a simple code to handle the config files of [ParallelCarParrinello 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)

Below, you find some links to get you started or considering guidelines.
   * GettingStarted.
   * FirstSteps into the code.
   * AddingCode helps with adding files and how to get them compiled.
   * EclipseAndMoleCuilder for help on configuring Eclipse.
   * WhatAndWhere has all the code can do and where to find it.