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dna-array.lisp
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(in-package :small)
(progn
(defun dna-array-from-list (lst &key (cube-type 'dna-cube))
(let* ((box-size 70)
(x (v3 0 0 0))
(y (v3 0 0 0))
(y (v3 0 0 0))
(z (v3 0 0 0))
(inc-x (v3 box-size 0 0))
(inc-y (v3 0 box-size 0))
(inc-z (v3 0 0 box-size))
(cube-array
(mapcar #'(lambda (zframe)
(setf z (.+ z inc-z))
(setf x (v3 0 0 0))
(mapcar #'(lambda (xrow)
(setf x (.+ x inc-x))
(setf y (v3 0 0 0))
(mapcar #'(lambda (has-cube)
(setf y (.+ y inc-y))
(let ((cube (if has-cube
(make-instance 'dna-cube)
nil)))
(when cube
(format t "~A~%" (.+ x
(.+ y z)))
(translate-obj cube
(.+ x
(.+ y z))))))
xrow))
zframe))
lst)))
cube-array))
(time
(defparameter *sq*
(list
(list
(list nil nil nil nil)
(list nil nil nil nil)
(list nil nil nil nil)
(list nil nil nil nil))
(list
(list nil nil nil nil)
(list nil t t nil)
(list nil t t nil)
(list nil nil nil nil))
(list
(list nil nil nil nil)
(list nil t t nil)
(list nil t t nil)
(list nil nil nil nil))
(list
(list nil nil nil nil)
(list nil nil nil nil)
(list nil nil nil nil)
(list nil nil nil nil)))))
(time (defparameter *arr* (dna-array-from-list *sq*)))
)(break "~A" *arr*)
(setf *arr* t)
(sb-profile:profile "SMALL")
(sb-profile:report)
(sb-profile:reset)
(stap-bridges (make-instance 'dna-cone))
(time
(wmdna "shuttleworth"
(alexandria:flatten (mapcar #'all-to-write (alexandria:flatten *arr*)))))
)
(setq j 1)
(1+ j)
(format nil "~A" 1)
(time
(let ((i 1))
(mapcar #'(lambda (cube)
(setf i (1+ i))
(wmdna (format nil "~A" i)
(all-to-write cube)))
(alexandria:flatten *arr*))))
(car (alexandria:flatten *arr*))
(dolist (x (alexandria:flatten (mapcar #'all-to-write (alexandria:flatten *arr*))))
(format t "~A~%" (length (all-tfms x))))
(mapcar #'(lambda (x)
(format t "~A~%" (parent x)))
(flatten (all-to-write (car (alexandria:flatten *arr*)))))
(count nil (mapcar #'(lambda (x)
(format t "~A~%" (parent x)))
(flatten (all-to-write (car (alexandria:flatten *arr*))))))
(filter #'(lambda (x)
x))
(alexandria:flatten (mapcar #'all-to-write (alexandria:flatten *arr*))))
(time
(wmdna "orc7"
(filter #'(lambda (x)
(when (typep x 'dna-nt)
x))
(alexandria:flatten (mapcar #'all-to-write (alexandria:flatten *arr*))))))
(time
(wmdna "orc3"
;; (all-to-write
;; (second (second (second *arr*)))
;; )
(filter #'(lambda (x)
(when (typep x 'dna-nt)
x))
(alexandria:flatten
(all-to-write
(second (second (second *arr*))))))
(filter #'(lambda (x)
(when (typep x 'dna-nt)
x))
(alexandria:flatten
(all-to-write
(second (second (third *arr*))))))
))
(all-tfms (second (second (third *arr*))))
(tfms (third (second (second *arr*))))
(wmdna "owl"
(all-to-write (second (second (third *arr*)))))
;; (wmdna (list (second (second (second *arr*)))
;; (second (second (third *arr*))))
;; :filename "bro")
(wmdna "so" (first
(alexandria:flatten
(mapcar #'all-to-write
(remove nil (alexandria:flatten
*arr*))))))
(wmdna "f" (first
(alexandria:flatten
(mapcar #'all-to-write
(remove nil (alexandria:flatten
*arr*))))))
(time (wmdna "arr" (mapcar #'all-to-write
(remove nil (alexandria:flatten
*arr*)))))
(let* ((t1 (SMALL::make-dna-tile))
(stap (SMALL::s-staple t1 1 2 '(23 16 16) '(8 15 7))))
(SMALL::wmdna "a-s" (append
(list (first (SMALL::scaffold t1)))
(small::internal-staples t1)))
(small::internal-staples t1))
;;; TODO EDGE STAPLS AND BRIDGE STAPS
;; OXDNA Model