# Pastebin AWYX0oJg
(defun part-positions-from-extended-strand-positions (origami extended-strand-position)
  "Generate the positions of the parts from extended-helix positions"
  (let ((part-position (make-array (* 7 (length (parts origami))) :element-type 'double-float :adjustable nil)))
    (loop for part in (parts origami)
          for extended-helix = (gethash part (map-part-to-extended-strand origami))
          for extended-helix-number-of-nodes = (number-of-nodes extended-helix)
          for extended-helix-z-start = (nonbond-node-z-offset-and-length extended-helix-number-of-nodes)
          for (p5-node-index p3-node-index) = (multiple-value-list (node-indices-for-part part extended-helix))
          for p5-z-offset = (node-z-offset extended-helix-z-start p5-node-index)
          for p3-z-offset = (node-z-offset extended-helix-z-start p3-node-index)
          for part-centroid-z-offset = (* (+ p5-z-offset p3-z-offset) 0.5)
          for eha = (elt extended-strand-position 0)
          for ehb = (elt extended-strand-position 1)
          for ehc = (elt extended-strand-position 2)
          for ehd = (elt extended-strand-position 3)
          for ehx = (elt extended-strand-position 4)
          for ehy = (elt extended-strand-position 5)
          for ehz = (elt extended-strand-position 6)
          for transform = (let ((m (geom:make-matrix nil)))
                            (geom:set-from-quaternion m eha ehb ehc ehd ehx ehy ehz)
                            m)
          for zvec = (geom:vec 0.0 0.0 part-centroid-z-offset)
          for part-centroid = (geom:m*v transform zvec)
          for part-order-id = (order-id part)
          for part-pos-start = (* 7 order-id)
          do (setf (elt part-position (+ part-pos-start 0)) eha
                   (elt part-position (+ part-pos-start 1)) ehb
                   (elt part-position (+ part-pos-start 2)) ehc
                   (elt part-position (+ part-pos-start 3)) ehd
                   (elt part-position (+ part-pos-start 4)) (geom:vx part-centroid)
                   (elt part-position (+ part-pos-start 5)) (geom:vy part-centroid)
                   (elt part-position (+ part-pos-start 6)) (geom:vz part-centroid)))
    part-position))