-
Notifications
You must be signed in to change notification settings - Fork 0
/
conformation-debug.lisp
111 lines (100 loc) · 6.49 KB
/
conformation-debug.lisp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
(in-package :topology)
(defclass conformation-selector ()
((all-conformations :initarg :all-conformations :accessor all-conformations)
(consistent-conformations :initform nil :initarg :consistent-conformations :accessor consistent-conformations)
(consistent-index :initform 0 :initarg :consistent-index :accessor consistent-index)))
(defun classify-dihedral-angle (angle-degrees)
(when (< angle-degrees 0.0)
(setf angle-degrees (+ 360.0 angle-degrees)))
(let* ((rounded (round (/ angle-degrees 30.0)))
(result (if (= rounded 12) 0 rounded)))
result))
(defun classify-dihedral-angles (angles)
(loop with accumulator = 0
for angle in angles
for classified-angle = (classify-dihedral-angle angle)
do (setf accumulator (+ (* accumulator 12) classified-angle))
finally (return-from classify-dihedral-angles accumulator)))
(defparameter *saved-fi* nil)
(defun fill-internals-from-fragments-debug (conf fragments &optional index)
"Fill internal coordinates from the fragments"
(let ((monomer-to-conformation-selector (make-hash-table))
(all-classified (make-hash-table :test 'eql)))
(loop with atagg = (ataggregate conf)
with atmol = (elt (atmolecules atagg) 0)
for monomer across (monomers (oligomer conf))
for monomer-context = (gethash monomer (monomer-contexts conf))
for _mc = (format t "monomer-context = ~a~%" monomer-context)
for frags = (gethash monomer-context (monomer-context-to-fragment-conformations fragments))
for monomer-index = (gethash monomer (monomer-positions conf))
for atres = (elt (atresidues atmol) monomer-index)
for fragment-conformations = (let ((fp (gethash monomer-context (monomer-context-to-fragment-conformations fragments))))
(unless fp
(error "Cannot find context ~a in conformations" monomer-context))
fp)
for conformations = (fragments fragment-conformations)
for conformation-selector = (make-instance 'conformation-selector
:all-conformations conformations)
do (setf (gethash monomer monomer-to-conformation-selector) conformation-selector))
(let ((ordered-monomers (ordered-monomers (oligomer conf))))
(loop with previous-monomer = nil
with previous-conformation-selector = nil
for monomer in ordered-monomers
for conformation-selector = (gethash monomer monomer-to-conformation-selector)
do (progn
(if (null previous-monomer)
(setf (consistent-index conformation-selector) 0
(consistent-conformations conformation-selector) (all-conformations conformation-selector))
(let* ((previous-conformation (elt (consistent-conformations previous-conformation-selector)
(consistent-index previous-conformation-selector)))
(out-of-focus (out-of-focus-internals previous-conformation)))
(format t "Look for consistent-conformations for ~a : ~a~%" monomer (length (all-conformations conformation-selector)))
(format t "out-of-focus ~s~%" out-of-focus)
(loop for conf in (all-conformations conformation-selector)
for internals = (internals conf)
for internal0 = (first internals)
for internal1 = (second internals)
for internal2 = (third internals)
for dihedral0 = (/ (topology:dihedral internal0) 0.0174533)
for dihedral1 = (/ (topology:dihedral internal1) 0.0174533)
for dihedral2 = (/ (topology:dihedral internal2) 0.0174533)
for classify0 = (classify-dihedral-angle dihedral0)
for classify1 = (classify-dihedral-angle dihedral1)
for classify2 = (classify-dihedral-angle dihedral2)
for classified = (classify-dihedral-angles (list dihedral0 dihedral1 dihedral2))
do (format t "internals = ~a, ~a, ~a = ~a~%"
(topology:name internal0)
(topology:name internal1)
(topology:name internal2)
classified)
do (incf (gethash classified all-classified 0))))))
(setf previous-monomer monomer
previous-conformation-selector conformation-selector)))
monomer-to-conformation-selector))
#|
(loop with atagg = (ataggregate conf)
with atmol = (elt (atmolecules atagg) 0)
for monomer across (monomers (oligomer conf))
for monomer-context = (gethash monomer (monomer-contexts conf))
for _mc = (format t "monomer-context = ~a~%" monomer-context)
for frags = (gethash monomer-context (monomer-context-to-fragment-conformations fragments))
for monomer-index = (gethash monomer (monomer-positions conf))
for atres = (elt (atresidues atmol) monomer-index)
for fragment-conformations = (let ((fp (gethash monomer-context (monomer-context-to-fragment-conformations fragments))))
(unless fp
(error "Cannot find context ~a in conformations" monomer-context))
fp)
for _fp = (format t "fragment-conformations = ~a~%" fragment-conformations)
for rand-limit = (length (fragments fragment-conformations))
for rand-index = (if index index (random rand-limit))
for fragment-internals = (let ((fragments (fragments fragment-conformations)))
(unless fragments
(error "fragments is NIL for context ~a" monomer-context))
(elt (fragments fragment-conformations) rand-index))
for _fi = (format t "fragment-internals = ~a~%" fragment-internals)
do (push fragment-internals *saved-fi*)
do (loop for joint across (joints atres)
for internal in (internals fragment-internals)
do (fill-joint-internals joint internal))
))
|#