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PROGRAM BALLS
*
* Program to set up input for RENDER
*
* This program takes a Brookhaven PDB-format file of atomic coordinates
* concatenated with a "colours" file that specifies the colouring and spherical
* radius of atoms according to atom type, residue type, or any other criterion,
* and produces a file that can be used directly as input to RENDER.
*
* Usage: cat colors.pdb protein.pdb | balls [-h] | render
*
* auxiliary files: setup.matrix optional file containing 3x3 view matrix
* setup.angles optional file defining view matrix
* in terms of 3 rotation angles
*
* I/O units for colour/co-ordinate input, specs output, user output
*
INCLUDE 'VERSION.incl'
*
INTEGER INPUT, OUTPUT, NOISE
PARAMETER (INPUT=5, OUTPUT=6, NOISE=0)
PARAMETER (MAXCOL=5000, MAXATM=300000)
REAL RGB(3,MAXCOL),RADIUS(MAXCOL)
REAL SPAM(7,MAXATM)
CHARACTER*24 MASK(MAXCOL),TEST
CHARACTER*80 ATOM(MAXATM),CARD
LOGICAL MATCH
logical hflag
character*80 flags
c
C Ethan Merritt Oct 1988
C Modified to read in 3x3 view matrix (e.g. from CCP FRODO view command)
C from file setup.matrix. Matrix is applied before
C finding translation, center, and scale. Afterwards the input matrix
C to RENDER is therefore the identity matrix.
C
common /matrix/ matrix, postrn, coords
real*4 matrix(3,3), postrn(3), coords(3)
C
C Default to CPK colors and VDW radii
character*60 defcol(7)
data defcol /
& 'COLOUR#######C################ 0.625 0.625 0.625 1.70',
& 'COLOUR#######N################ 0.125 0.125 1.000 1.60',
& 'COLOUR#######O################ 0.750 0.050 0.050 1.50',
& 'COLOUR#######S################ 1.000 1.000 0.025 1.85',
& 'COLOUR#######H################ 1.000 1.000 1.000 1.20',
& 'COLOUR#######P################ 0.400 1.000 0.400 1.80',
& 'COLOUR######################## 1.000 0.000 1.000 2.00'
& /
c
3 format(a,a)
c
do i=1,3
do j=1,3
matrix(i,j)=0.
enddo
matrix(i,i)=1.
enddo
call view_matrix
c
c Ethan Merritt Apr 1992
c -h option suppresses header records in output
c
hflag = .false.
narg = iargc()
do i = 1, narg
call getarg( i, flags )
if (flags(1:2) .eq. '-h') hflag = .true.
end do
c
if (.not. hflag) then
WRITE(OUTPUT,'(A,A)') 'balls - 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 -> 2x2 pixels'
WRITE(OUTPUT,'(A)') '0 0 0 black background'
WRITE(OUTPUT,'(A)') 'T yes, I LIKE 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'
end if
c
ASPECT = 1280./1024.
NCOL = 0
NATM = 0
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'.OR.CARD(1:4).EQ.'HETA') 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
ENDIF
* Load default colors after any that were read in
IF (NCOL.LT.MAXCOL-8) THEN
DO i = 1,7
NCOL = NCOL + 1
READ(defcol(i),'(6X,A24,3F8.3,F6.2)') MASK(NCOL),
& (RGB(J,NCOL),J=1,3), RADIUS(NCOL)
ENDDO
ENDIF
*
IF (NCOL.EQ.0) THEN
WRITE(NOISE,*) 'No colours in input.'
STOP 40
ENDIF
XMAX = -1E20
XMIN = 1E20
YMAX = -1E20
YMIN = 1E20
ZMAX = -1E20
ZMIN = 1E20
DO 100 IATM=1,NATM
CARD = ATOM(IATM)
TEST = CARD(7:30)
DO 80 ICOL=1,NCOL
IF (MATCH(TEST,MASK(ICOL))) THEN
c READ(CARD,'(30X,3F8.3)') X,Y,Z
c EAM Oct88
READ(CARD,'(30X,3F8.3)') coords
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)
c EAM Oct88
RAD = RADIUS(ICOL)
SPAM(1,IATM) = X
SPAM(2,IATM) = Y
SPAM(3,IATM) = Z
SPAM(4,IATM) = RAD
SPAM(5,IATM) = RGB(1,ICOL)
SPAM(6,IATM) = RGB(2,ICOL)
SPAM(7,IATM) = RGB(3,ICOL)
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)
GO TO 100
ENDIF
80 CONTINUE
WRITE(NOISE,*) 'No colour table mask matches this atom:'
WRITE(NOISE,*) ATOM(IATM)
STOP 90
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
c
if (.not. hflag) then
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)
WRITE(OUTPUT,'(A)') '3 mixed object types'
WRITE(OUTPUT,'(A)') '*'
WRITE(OUTPUT,'(A)') '*'
WRITE(OUTPUT,'(A)') '*'
end if
c
DO 150 IATM=1,NATM
SPAM(1,IATM) = SPAM(1,IATM) + postrn(1)
SPAM(2,IATM) = SPAM(2,IATM) + postrn(2)
SPAM(3,IATM) = SPAM(3,IATM) + postrn(3)
WRITE(OUTPUT,140) (SPAM(I,IATM),I=1,7)
140 FORMAT(1H2,/,7(1X,F8.3))
150 CONTINUE
write (noise,'(/)')
write (noise,156) 'X min max:', XMIN, XMAX
write (noise,156) 'Y min max:', YMIN, YMAX
write (noise,156) 'Z min max:', ZMIN, ZMAX
write (noise,156) ' scale:', SCALE
156 format(1x,a,3f8.2)
END
LOGICAL FUNCTION MATCH (SUBJ, MASK)
CHARACTER*24 SUBJ,MASK
MATCH = .FALSE.
DO 10 I = 1, 24
IF (SUBJ(I:I).NE.MASK(I:I) .AND. MASK(I:I).NE.'#') RETURN
10 CONTINUE
MATCH = .TRUE.
RETURN
END
subroutine view_matrix
c
common /matrix/ matrix, postrn, coords
real*4 matrix(3,3), postrn(3), coords(3)
c
real*4 phiX, phiY, phiZ
integer noise
parameter (noise = 0)
parameter (R2D = 180./3.1415927)
postrn(1) = 0.
postrn(2) = 0.
postrn(3) = 0.
open (unit=3, file='setup.matrix', status='OLD', err=100)
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)
read (3,*) phiZ, phiY, phiX
read (3,*,err=101,end=101) postrn(1), postrn(2), postrn(3)
101 continue
close (3)
write (noise,2) phiZ, phiY, phiX
write (noise,4) postrn(1), postrn(2), postrn(3)
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)
4 format(1x,' tranX =',f8.2,' tranY =',f8.2,' tranZ =',f8.2)
write (noise,*) ' No view matrix or angles provided'
return
end
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