; Searches for molecular signature
; new_sigsloop.pam JAN 2003 Bimal Rath
; Parallelized MAY 2003 ArDean Leith
; Altered for tomography OCT 2006 Christian Renken
; Rewritten JUL 2008 ArDean Leith
; Improved JAN 2011 ArDean Leith
;
; PURPOSE: Locates molecular signature (motif) inside search volume.
; Be sure both volumes have same magnification
; (1 Pixel = "n" nanometer)
;
; SAMPLE USAGE : ./spider spi/dat @new_sigsloop 99 num=1
[num] ; NEEDED FROM STARTUP LINE!!!!
; Read input variables and file names
@new_sigs_settings([n],[phi0],[the0],[psi0],[phid],[thed],[nphi],[nthe],[psin],[mskval],[peaks],[msktype])
MY fl
MD
VB OFF ; Minimize results file output
MD
TR OFF ; Minimize results file output
MD
SET MP ; Set number of OMP processors
[n]
[key] = 0 ; Initial doc. file output line number
IQ FI [have_tomo_wedge] ; Are using tomo. wedge filter
[WEDGE_FILTER]
; Euler angle search is done here
[nrots] =0
[phi] = [phi0] + ([num]-1)*[phid] ; Current phi counter is sent from caller
DO [it] = 1, [nthe] ; Theta loop --------------------------------- THETA
[theta] = [the0]+([it]-1)*[thed]
; Modulate psid to uniformly sample unit sphere
[sint] = SIN([theta])
[dsint] = ABS([sint])
IF ([dsint] .LE. 0.01) THEN
[psid] = 360
[npsi] = 1
ELSE
[psid] = [thed] / [sint]
[npsi] = INT((([psin]-[psi0])/[psid])+1)
if ([npsi] .LT. 1) [npsi] = 1
ENDIF
!vm
!echo ' For theta: {***[theta]} {%f5.1%[psid]} {***[npsi]}'
DO [jt] = 1, [npsi] ; Psi loop -------------------------------- PSI
[psi] = [psi0]+([jt]-1)*[psid]
[nrots]=[nrots]+1
VM
echo ' Rotation: {****[nrots]} Phi,the,psi: {***[phi]}, {***[theta]}, {***[psi]}'
[loopcount] = ([it]-1)*[nphi] + [jt] ; Do-loop counter
; Using an asymmetric mask, Rotate mask vol
RT 3D ; Rotate
[MOTIF_MASK] ; Cubic motif mask vol (input)
_1 ; Rotated cubic mask vol (output)
[phi],[theta],[psi] ; Rotation angle
; Threshold cubic rotated mask
TH M ; Threshold to create mask
_1 ; Rotated mask vol (input)
_2 ; Thresholded, rotated mask (output)
B ; Below = 0
(.3) ; Threshold value
!fi h [min],[max]
![SEARCH_VOL]
!fmin,fmax
!vm
!echo ' Search vol:',{%1pg13.3%[min]} .... {%1pg13.3%[max]}
!fi h [min],[max]
!_2
!fmin,fmax
!vm
!echo ' Rotated mask vol:',{%1pg13.3%[min]} .... {%1pg13.3%[max]}
!vm
!echo ' Oper: LO I'
; Pad rotated mask and create FFT -------------------------- LO I
LO I ; Padded FFT creation for mask
M ; Make FFT of mask only
[SEARCH_VOL] ; Large search vol (input)
_2 ; Rotated cubic motif mask (input)
[MOTIF_MASK_FFT] ; FFT of padded, rotated mask (output)
!vm
!echo ' Oper: LO LSD'
; Create local SD vol using rotated mask ------------------ LO LSD
LO LSD ; LSD creation
_2 ; Rotated cubic motif mask (input)
[MOTIF_MASK_FFT] ; FFT of padded, rotated mask (input)
[SEARCH_VOL_FFT] ; FFT of search vol (input)
[SEARCH_VOL_SQ_FFT] ; FFT of sq. search vol (input)
[LSD_VOL] ; Local SD vol (output)
!vm
!echo ' Oper: RT 3D on cubic motif vol'
; Rotate the cubic motif vol
RT 3D ; Rotate
[CUBE_MOTIF_VOL] ; Cubic motif (input)
_3 ; Rotated cubic motif (output)
[phi],[theta],[psi] ; Rotation angle
VM
echo ' Rotation angle: {****[phi]} {****[theta]} {****[psi]}'
!vm
!echo ' Oper: LO'
; Locate rotated motif within search vol -------------------- LO
LO ; Locate motif
[phi],[theta],[psi] ; Angles for doc. file
_3 ; Rotated cubic motif (input)
_2 ; Rotated mask for motif (input)
[SEARCH_VOL_FFT] ; Search vol fft (input)
[LSD_VOL] ; Local SD vol (input)
[peaks] ; Number of peaks wanted
[PEAK] ; Peaks image (output)
[DOC_FILE_OUT] ; Peak location doc file (output)
MY FL ; Flush results file
ENDDO ; End of: Psi loop
ENDDO ; End of: Theta loop
@signal_pub([num]) ; Signal this parallel job is finished
[SYNC_DOC_BASE]
EN
;