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|
* PROGRAM RIBBON
*
* Program to set up input for RENDER (RASTER3D package)
* to draw ribbon diagram. The RIBBON routine itself is simply
* extracted from CCP FRODO. The original invoked a bspline feature
* of the ps300; I have replaced this with a spline equation gotten
* from Larry Andrews. Conversion from ribbon edges to solid rendering
* is my own hacking.
* Ethan Merritt - 8-Nov-1988
* Slightly modified code to guarantee output of triangles with
* vertices in correct order for triangular mesh algorithms EAM Sep 90
*
* Usage: ribbon [-h] [-dn] pdbfile > setup.r3d
* ribbon [-h] -dn - to take pdb records from stdin
*
* Input: pdbfile
* Brookhaven PDB-format file of atomic co-ordinates
* only C-alpha and O atoms are needed
* setup.matrix or setup.angles
* rotation matrix or angles applied to PDB coords
* (see writeup for SETUP/RENDER).
* Output: stdout (new for DS5000 version)
* file suitable for input to RENDER
*
* Interactive parameters:
* WIDTH of ribbon in Angstroms
* NUMBER of interpolated coordinates between successive C-alphas.
* COLOR scheme for ribbon
* 0 or 1: solid color (RGB values from color1 below)
* 2: shade from color1 at 1st res to color2 at last res
* 3: front of ribbon is color1, back of ribbon is color2
* 4: shade front as in scheme 2, back is color 3
* 5: each chain is new color (from successive input
* (COLOR cards at start of input file)
* 6: use prefixed COLOR cards (as in SETUP/RENDER)
* (implemented 4-Aug-1997 EAM)
* COLOR1,COLOR2,COLOR3 RGB components (9f8.0)
*
INCLUDE 'VERSION.incl'
c
INTEGER INPUT, OUTPUT, NOISE
PARAMETER (OUTPUT=6, NOISE=0)
PARAMETER (MAXCOL=5000, MAXATM=10000)
C REAL RGB(3,MAXCOL)
REAL RADIUS(MAXCOL)
REAL RAD
CHARACTER*24 MASK(MAXCOL),TEST
CHARACTER*80 ATOM(MAXATM),CARD
LOGICAL SMATCH
c
C Ethan Merritt Oct 1988
C Modified to read in 3x3 view matrix (e.g. from CCP FRODO view command)
C from file. Matrix is applied before
C finding translation, center, and scale. Afterwards the input matrix
C to RENDER is therefore the identity matrix.
C EAM Aug 1997 - Honor COLOUR requests
C EAM Nov 1999 - remove all (q) formats
C EAM Jan 2010 - declare and initialize RAD
C
c
common /COLORS/ ischeme, cindex, COLOR1(3), COLOR2(3), COLOR3(3)
& ,RGB(3,MAXCOL)
integer cindex
common /SPAM/ natm, SPAM(4,MAXATM), SCAM(MAXATM)
integer SCAM
common /FLAGS/ mflag, hflag, dflag
logical mflag, hflag, dflag
c
character*64 in_file
character*32 flags
character*80 line
common /matrix/ matrix, coords
real matrix(3,3), coords(3)
data matrix / 1.,0.,0.,0.,1.,0.,0.,0.,1. /
c
c -h causes the header records not to be printed
c -m [now obsolete because always in force] uses format
c mixed object types in output file
c -d suppresses interactive input
c
hflag = .FALSE.
dflag = .FALSE.
mflag = .TRUE.
c
narg = iargc()
do i = 1,narg
call getarg( i, flags )
if (flags(1:2) .eq. '-h') then
hflag = .TRUE.
else if (flags(1:2) .eq. '-d') then
dflag = .TRUE.
read (flags(3:4),'(I1)') ischeme
end if
end do
c
call getarg( narg, in_file )
if (in_file(1:1) .eq. '-') then
INPUT = 5
else
INPUT = 1
open( unit=INPUT, file=in_file, status='OLD' )
end if
c
3 format(a,a)
c
call view_matrix
c
NCOL = 0
NATM = 0
ASPECT = 1280./1024.
c
if (hflag) goto 10
c
WRITE(OUTPUT,'(A,A)') 'C-alpha ribbon - Raster3D ',VERSION
WRITE(OUTPUT,'(A)') '80 64 tiles in x,y'
WRITE(OUTPUT,'(A)') ' 8 8 pixels (x,y) per tile'
WRITE(OUTPUT,'(A)') '4 anti-aliasing 3x3 into 2x2 pixels'
WRITE(OUTPUT,'(A)') '0 0 0 black background'
WRITE(OUTPUT,'(A)') 'F no, ribbons cast funny shadows'
WRITE(OUTPUT,'(A)') '25 Phong power'
WRITE(OUTPUT,'(A)') '0.15 secondary light contribution'
WRITE(OUTPUT,'(A)') '0.05 ambient light contribution'
WRITE(OUTPUT,'(A)') '0.25 specular reflection component'
WRITE(OUTPUT,'(A)') '4.0 eye position'
WRITE(OUTPUT,'(A)') '1 1 1 main light source position'
c
10 CONTINUE
READ(INPUT,'(A80)',END=50) CARD
IF (CARD(1:4).EQ.'COLO') THEN
NCOL = NCOL + 1
IF (NCOL.GT.MAXCOL) THEN
WRITE(NOISE,*) 'Colour table overflow. Increase ',
& 'MAXCOL and recompile.'
STOP 10
ENDIF
READ(CARD,'(6X,A24,3F8.3,F6.2)') MASK(NCOL),
& (RGB(I,NCOL),I=1,3),RADIUS(NCOL)
ELSEIF ((CARD(1:4).EQ.'ATOM') .AND.
& ( CARD(14:16).EQ.'CA ' .OR. CARD(14:16).EQ.'O ')) THEN
NATM = NATM + 1
IF (NATM.GT.MAXATM) THEN
WRITE(NOISE,*) 'Atom array overflow. Increase ',
& 'MAXATM and recompile.'
STOP 20
ENDIF
ATOM(NATM) = CARD
ELSEIF (CARD(1:3).EQ.'END') THEN
GO TO 50
ENDIF
GO TO 10
* Come here when EOF or 'END' record is reached
50 CONTINUE
IF (NATM.EQ.0) THEN
WRITE(NOISE,*) 'No atoms in input.'
STOP 30
ELSE
WRITE(NOISE,*) NATM,' atoms accepted from input.'
ENDIF
IF (NCOL.EQ.0) THEN
WRITE(NOISE,*) 'No colours in input.'
c STOP 40
ENDIF
C
XMAX = -1E20
XMIN = 1E20
YMAX = -1E20
YMIN = 1E20
ZMAX = -1E20
ZMIN = 1E20
RAD = 1.7
DO 100 IATM=1,NATM
CARD = ATOM(IATM)
TEST = CARD(7:30)
READ(CARD,82) coords
82 format(30x,3f8.3)
x = coords(1)*matrix(1,1) + coords(2)*matrix(2,1)
1 + coords(3)*matrix(3,1)
y = coords(1)*matrix(1,2) + coords(2)*matrix(2,2)
1 + coords(3)*matrix(3,2)
z = coords(1)*matrix(1,3) + coords(2)*matrix(2,3)
1 + coords(3)*matrix(3,3)
SPAM(1,IATM) = X
SPAM(2,IATM) = Y
SPAM(3,IATM) = Z
c SPAM(4,IATM) = RAD
C
C EAM Aug 1997 - finally get around to honoring atom colors
DO 84 ICOL = 1, NCOL
IF (SMATCH(TEST,MASK(ICOL))) THEN
SCAM(IATM) = ICOL
RAD = RADIUS(ICOL)
SPAM(4,IATM) = RAD
GOTO 86
ENDIF
84 CONTINUE
86 CONTINUE
C
XMAX = MAX(XMAX,X+RAD)
XMIN = MIN(XMIN,X-RAD)
YMAX = MAX(YMAX,Y+RAD)
YMIN = MIN(YMIN,Y-RAD)
ZMAX = MAX(ZMAX,Z+RAD)
ZMIN = MIN(ZMIN,Z-RAD)
100 CONTINUE
XMID = (XMAX+XMIN)/2.
YMID = (YMAX+YMIN)/2.
ZMID = (ZMAX+ZMIN)/2.
TX = -XMID
TY = -YMID
TZ = -ZMID
IF (ASPECT.GE.1.) THEN
* The X direction is wider than the Y
XROOM = ASPECT
YROOM = 1.
ZROOM = 2.
ELSE
XROOM = 1.
YROOM = ASPECT
ZROOM = 2.
ENDIF
XSPAN = XMAX-XMIN
YSPAN = YMAX-YMIN
ZSPAN = ZMAX-ZMIN
SCALE = MAX(XSPAN/XROOM,YSPAN/YROOM,ZSPAN/ZROOM)
* Leave a little extra room as a border:
SCALE = SCALE / 0.90
if (hflag) goto 129
WRITE(OUTPUT,120) TX,TY,TZ,SCALE
120 FORMAT('1 0 0 0 input co-ordinate + radius transformation'/
& '0 1 0 0'/
& '0 0 1 0'/
& 4F10.3)
if (mflag) then
WRITE (OUTPUT,'(A)') '3 mixed object types'
WRITE (OUTPUT,'(A)') '(9F8.3,2x,3f5.2)'
WRITE (OUTPUT,'(A)') '(11F8.3)'
WRITE (OUTPUT,'(A)') '(11F8.3)'
else
WRITE (OUTPUT,'(A)') '1 all objects are triangles'
WRITE (OUTPUT,'(A)') '(9F8.3,2x,3f5.2)'
end if
129 continue
write (noise,'(/)')
write (noise,153) 'X min max:', XMIN, XMAX
write (noise,153) 'Y min max:', YMIN, YMAX
write (noise,153) 'Z min max:', ZMIN, ZMAX
write (noise,153) ' scale:', SCALE
153 format(1x,a,3f8.2)
c
c
if (dflag) then
width = 1.5
offset = 1.2
nchord = 5
if (ischeme .le. 0 .or. ischeme .gt. 6) ischeme = 2
call vload( color1, 0.0, 0.0, 0.4 )
call vload( color2, 0.5, 0.0, 0.0 )
call vload( color3, 0.6, 0.6, 0.6 )
else
width = 0
write (noise,3) 'Width of ribbon (default 1.5A): '
read (5,'(A80)') line
read (line,*,end=154,err=154) width
154 continue
if (width.le.0) width = 1.5
c Original RIBBON used bspline smoothing, which requires "offset"
c because smoothed curve doesn't go through guide points.
write (noise,3) 'Offset from CA position (default 1.2A): '
read (5,'(A80)') line
read (line,*,end=156,err=156) offset
156 continue
if (offset.le.0) offset = 1.2
write (noise,3) 'Chords per residue (default = 10): '
read (5,'(A80)') line
read (line,*,end=158,err=158) nchord
158 continue
if (nchord.le.1) nchord = 10
write (noise,160)
160 format(' Coloring schemes available:',
1 /,' 0 or 1: solid color (RGB values from color1 below)',
2 /,' 2: shade from color1 at 1st res to color2 at last res',
3 /,' 3: front of ribbon is color1, back of ribbon is color2',
4 /,' 4: shade front as in scheme 2, back is color 3',
5 /,' 5: new color for each chain (requires COLOUR cards)')
write (noise,3) 'Coloring scheme: '
read (5,'(A80)') line
read (line,*,end=161,err=161) ischeme
161 continue
if (ischeme.le.0 .or. ischeme.gt.6) ischeme = 1
if (ischeme .eq. 1) write (noise,3)
1 'COLOR1 (RGB values, 3f8.0): '
if (ischeme .eq. 2) write (noise,3)
1 'COLOR1, COLOR2 (RGB values, 6f8.0): '
if (ischeme .eq. 3) write (noise,3)
1 'COLOR1, COLOR2 (RGB values, 6f8.0): '
if (ischeme .eq. 4) write (noise,3)
1 'COLOR1, COLOR2, COLOR3 (RGB values, 9f8.0): '
if (ischeme .lt. 5) then
read (5,'(A80)') line
if (line.eq.' ') goto 163
read (line,*,end=163,err=163) color1,color2,color3
endif
goto 164
163 continue
call vload( color1, 0.0, 0.0, 0.4 )
call vload( color2, 0.5, 0.0, 0.0 )
call vload( color3, 0.6, 0.6, 0.6 )
164 continue
if (ischeme .eq. 3) then
color3(1) = color2(1)
color3(2) = color2(2)
color3(3) = color2(3)
end if
c end of -d suppression
end if
write (noise,169) ischeme,color1,color2,color3
169 format(' color scheme',i3,/,3(3x,3f6.3))
cindex = 1
c
call ribbon( 2, width, nchord, offset, natm )
c
END
LOGICAL FUNCTION SMATCH (SUBJ, MASK)
CHARACTER*24 SUBJ,MASK
SMATCH = .FALSE.
DO 10 I = 1, 24
IF (SUBJ(I:I).NE.MASK(I:I) .AND. MASK(I:I).NE.'#') RETURN
10 CONTINUE
SMATCH = .TRUE.
RETURN
END
subroutine view_matrix
c
common /matrix/ matrix, coords
real matrix(3,3), coords(3)
c
real phiX, phiY, phiZ
parameter (noise = 0)
parameter (R2D = 180./3.1415927)
open (unit=3, file='setup.matrix', status='OLD', err=100)
write (noise,3) ' View Matrix from file '
read (3,*) ((matrix(i,j),i=1,3),j=1,3)
write (noise,'(1x,3f9.5)') ((matrix(i,j),i=1,3),j=1,3)
close (3)
det = matrix(1,1) * matrix(2,2) * matrix(3,3)
1 + matrix(1,2) * matrix(2,3) * matrix(3,1)
2 + matrix(2,1) * matrix(3,2) * matrix(1,3)
3 - matrix(1,3) * matrix(2,2) * matrix(3,1)
4 - matrix(1,2) * matrix(2,1) * matrix(3,3)
5 - matrix(1,1) * matrix(2,3) * matrix(3,2)
write (noise,'('' determinant ='',f8.3)') det
phiX = atan2( -matrix(3,2), matrix(3,3) )
phiY = atan2( matrix(3,1), matrix(3,3) / cos(phiX) )
phiZ = atan2( -matrix(2,1), matrix(1,1) )
write (noise,3) ' View Angles from matrix',' '
write (noise,2) phiZ*R2D, phiY*R2D, phiX*R2D
return
100 continue
open (unit=3, file='setup.angles', status='OLD', err=200)
write (noise,3) ' View Angles from file '
read (3,*) phiZ, phiY, phiX
close (3)
write (noise,2) phiZ, phiY, phiX
cx = cos(phiX/R2D)
sx = sin(phiX/R2D)
cy = cos(phiY/R2D)
sy = sin(phiY/R2D)
cz = cos(phiZ/R2D)
sz = sin(phiZ/R2D)
matrix(1,1) = cz*cy
matrix(1,2) = sz*cx + cz*sy*sx
matrix(1,3) = sz*sx - cz*sy*cx
matrix(2,1) = -sz*cy
matrix(2,2) = cz*cx - sx*sy*sz
matrix(2,3) = cz*sx + sz*sy*cx
matrix(3,1) = sy
matrix(3,2) = -sx*cy
matrix(3,3) = cx*cy
write (noise,3) ' View Matrix from angles',' '
write (noise,'(1x,3f9.5)') ((matrix(i,j),i=1,3),j=1,3)
return
200 continue
2 format(1x,' phiZ =',f8.2,' phiY =',f8.2,' phiX =',f8.2)
3 format(/a,a)
write (noise,*) ' No view matrix or angles provided'
return
end
C
SUBROUTINE RIBDRW(GUIDE,NRIB,MAXRES,NPT,NCHORD)
integer npt ! number of guide points
real guide(4,MAXRES,NRIB) ! 4 dim because E&S wanted it that way
integer nchord ! how many interpolations per guide pt
parameter (MAXCOL = 5000)
integer OUTPUT
parameter (OUTPUT = 6)
C
C splining from Larry Andrews 7-Nov-1988
C
parameter (nspln = 5000) ! maximum of (npt*nchord)
parameter (ndata = 500) ! maximum # guidepoints
parameter (ndata1 = 501)
c
common /COLORS/ ischeme, cindex, COLOR1(3), COLOR2(3), COLOR3(3)
& ,RGB(3,MAXCOL)
integer cindex
common /FLAGS/ mflag, hflag, dflag
logical mflag, hflag, dflag
c
c real s(ndata1)
c REAL XP(4,NDATA)
real smooth(4,nspln,2) ! npt*nchord points on splined curve
real color(3)
c
if (npt .gt. ndata) stop 'spline - TOO MANY GUIDE POINTS'
if (npt*nchord .gt. nspln) stop 'spline - NPT*NCHORD > 5000'
c
c fill 4th coord with fraction of chain traced
c
color_inc = 1.000 / float(npt)
fraction = 0.0
if (ischeme.le.5) then
do i = 1, npt
guide(4,i,1) = fraction
guide(4,i,2) = fraction
fraction = fraction + color_inc
end do
endif
c
c calculate spline segments
c
tinc = 1./float(nchord)
do 1000 irib = 1, 2
iout = 1
do 900 ipt = 2, npt-1
t = 0.0
do i = 1, nchord
iout = iout + 1
call bspline( guide(1,ipt-1,irib), guide(1,ipt,irib),
1 guide(1,ipt+1,irib), t, smooth(1,iout,irib) )
t = t + tinc
end do
900 continue
1000 continue
c
c Add end segments (splines go midpoint-to-midpoint)
c
iout = iout + 1
do 1100 irib = 1, 2
do i = 1, 4
smooth(i, 1, irib) = guide(i, 1, irib )
smooth(i, iout, irib) = guide(i, npt, irib )
end do
1100 continue
C
2 format(9f8.3,2x,3f5.2)
3 format('1',/,9f8.3,2x,3f5.2)
c
c Start loop over spline segments
c
ires = 1
jres = 1
kres = 2
2000 continue
c do 2100 ires = 1, iout-1
fraction = smooth(4,ires, 1)
c
c Make sure the two sides of the ribbon stay in register
c
inext = ires + 1
55 dist0 = dist(smooth(1,inext,1),smooth(1,kres,2))
dist1 = dist(smooth(1,inext,1),smooth(1,kres+1,2))
if ((dist1 .lt. dist0) .and. (kres .lt. iout)) then
kres = kres + 1
goto 55
end if
56 dist0 = dist(smooth(1,inext,1),smooth(1,kres,2))
dist1 = dist(smooth(1,inext+1,1),smooth(1,kres,2))
if ((dist1 .lt. dist0) .and. (inext .lt. iout)) then
inext = inext + 1
goto 56
end if
c
call colorit( color, fraction,
1 smooth(1,ires,1), smooth(1,jres,2), smooth(1,inext,1))
c
if (mflag) then
write (output,3) (smooth(i,ires, 1),i=1,3),
1 (smooth(i,jres, 2),i=1,3),
2 (smooth(i,inext,1),i=1,3),
3 color
else
write (output,2) (smooth(i,ires, 1),i=1,3),
1 (smooth(i,jres, 2),i=1,3),
2 (smooth(i,inext,1),i=1,3),
3 color
endif
c
if (jres .eq. kres) goto 2100
call colorit( color, fraction,
1 smooth(1,kres,2), smooth(1,inext,1), smooth(1,jres,2))
if (mflag) then
write (output,3) (smooth(i,jres, 2),i=1,3),
1 (smooth(i,inext,1),i=1,3),
2 (smooth(i,kres, 2),i=1,3),
3 color
else
write (output,2) (smooth(i,jres, 2),i=1,3),
1 (smooth(i,inext,1),i=1,3),
2 (smooth(i,kres, 2),i=1,3),
3 color
end if
jres = kres
if (kres .lt. iout) kres = kres + 1
2100 continue
ires = inext
if (ires .lt. iout) goto 2000
c
c End loop over spline segments
c
cindex = cindex + 1
return
end
function dist(v1, v2)
real diff(3)
call vdif(diff,v1,v2)
dist = dot(diff,diff)
return
end
subroutine vload( v, s1, s2, s3 )
real v(3)
v(1) = s1
v(2) = s2
v(3) = s3
return
end
subroutine colorit( color, fraction, point1, point2, point3 )
real color(3), point1(3), point2(3), point3(3)
c
c scheme 1 solid color (COLOR1)
c scheme 2 shade from COLOR1 at 1st residue to COLOR2 at last
c scheme 3 COLOR1 on front, COLOR3 (=COLOR2) on back
c scheme 4 combination of 2 and 3 above
c scheme 5 color each new chain a new color from RGB
c
PARAMETER (MAXCOL=5000, MAXATM=10000)
common /COLORS/ ischeme, cindex, COLOR1(3), COLOR2(3), COLOR3(3)
& ,RGB(3,MAXCOL)
integer cindex
common /SPAM/ NATM, SPAM(4,MAXATM), SCAM(MAXATM)
integer SCAM
real vec1(3), vec2(3), vec3(3)
c
if ((ischeme .eq. 3) .or. (ischeme .eq. 4)) then
call vdif( vec1, point2, point1 )
call vdif( vec2, point3, point1 )
call cross( vec1, vec2, vec3 )
if (vec3(3) .lt. 0) then
color(1) = color3(1)
color(2) = color3(2)
color(3) = color3(3)
else if (ischeme .eq. 4) then
color(1) = fraction*color2(1)
& + (1.-fraction)*color1(1)
color(2) = fraction*color2(2)
& + (1.-fraction)*color1(2)
color(3) = fraction*color2(3)
& + (1.-fraction)*color1(3)
else
color(1) = color1(1)
color(2) = color1(2)
color(3) = color1(3)
end if
else if (ischeme .eq. 2) then
color(1) = fraction*color2(1) + (1.-fraction)*color1(1)
color(2) = fraction*color2(2) + (1.-fraction)*color1(2)
color(3) = fraction*color2(3) + (1.-fraction)*color1(3)
else if (ischeme .eq. 5) then
call vload( color,
& RGB(1,cindex), RGB(2,cindex), RGB(3,cindex))
c else if (ischeme .eq. 6) then
c ICOL = SCAM(fraction)
c color(1) = RGB(1,icol)
c color(2) = RGB(2,icol)
c color(3) = RGB(3,icol)
else
call vload( color, color1(1), color1(2), color1(3) )
end if
return
end
subroutine bspline( v1, v2, v3, t, v4 )
real v1(4), v2(4), v3(4)
real t
real v4(4)
c
frac3 = 0.5 * t*t
frac1 = 0.5 * (1.-t) * (1.-t)
frac2 = 1. - (frac1 + frac3)
do i = 1, 4
v4(i) = frac1 * v1(i) + frac2 * v2(i) + frac3 * v3(i)
end do
return
end
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