initial commit keeneland
Use goap to prefilter trajectory and cluster based on that
Added restraints for the clusters that are going to seed next stage
Changed master script and cycles for short fragments
Fixed several bugs to perform clustering
made restraints for every cluster in TEMPLATES directory
removed hydrophobic restraints in CKY
Added confinement restraints, for now fixed at 30 Angs sphere
Do the assembly inside directory
fixed typos for restraint setup
Changed the creation of restraints: was taking the autoassmebly genearted pdb as template and should be using the fragments as templates
Renumbering of second fragment to create restraints
bug in renumbering 2 off
Fixed Bug numbering residues in auto assemble
Multiple changes to tackle the correct numbering of residues/restraints when combining fragments into
Merge branch 'master' of https://github.com/alberto99/CKY