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?Doc file from AP MD?
;<1> docapmd
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? name of input particles?
;<2> original particles _1
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? name of prealigned particles?
;<3> rotated particles  _2
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? Reference images?<7>
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?Previous transformation parameters doc file?<4>
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?New transformation parameters doc file?<5>
;
; Format of the transformation parameters doc file is:
;  angle, Sx, Sy, 0-1 flag for Y-mirror (0-no mirror; 1-mirror)

ud n,x19
<1>


DO LB5 x55=1,x19
ud s,x55,x91,x92,x93
<1>
; Rotate the image
cp
<3>x55
_3
RT SQ
_3
_1
x93
(0,0)
; get corresponding projection, number is stored in apmd
if(x91.lt.0) then
; image has to be mirrored
x94=1
x91=-x91
MR
_1
_2
Y
cp
_2
_1
;
else
x94=0
endif
;
CC N
_1
<7>x91
_2
PK x10,x11,x12,x13,x31,x32,x33
_2
(0)
x31=-x31
x32=-x32
; combine rotation, mirror, and shift and use RT SQ
if(x94.eq.1) then
x31=-x31
endif
; combine with the previous transformation

ud ic,x55,x23,x24,x25,x29
<4>

@combat[x23,x24,x25,x29,x93,x31,x32,x94,x51,x52,x53,x54]



sd x55,x51,x52,x53,x54
<5>
if(x54.eq.0) then
rt sq
<2>x55
<3>x55
x51
x52,x53
else
rt sq
<2>x55
_1
x51
x52,x53
mr
_1
<3>x55
Y
endif
LB5

ud ice
<1>
ud ice
<4>
sd e
<5>
re