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PROGRAM RODS
*------------------------------------------------------------------------------
* Program to set up input for RENDER with CYLINDERs drawn between
* each pair of atoms lying closer than 0.6 * (sum of VanderWaals radii).
* This program is the same as SETUP, except for what is generated.
* Input matrix or angles are taken from setup.matrix or setup.angles
* (NB: same files as setup)
*
* Eric Swanson Oct 1991
* Modified to generate cylinders with half bond colors, where needed.
* EAM Feb 1997
* -radius XX to set cylinder radius
* EAM Sep 1997
* -default colors; option for coloring by B-value
* -more generous output formats (FORMATs 130 and 140)
* EAM Jun 1999
* -brad XX to set ball radius as fraction of Van der Waals radius
* EAM Jul 1999
* don't draw bonds across alternate chain locations
* EAM Nov 2019
* new gfortran requires a decimal point in floating constants
*
*------------------------------------------------------------------------------
INCLUDE 'VERSION.incl'
*
* I/O units for colour/co-ordinate input, specs output, user output
INTEGER INPUT, OUTPUT, NOISE
PARAMETER (INPUT=5, OUTPUT=6, NOISE=0)
PARAMETER (MAXCOL=5000, MAXATM=100000)
REAL RGB(3,MAXCOL),VDW(MAXCOL)
REAL SPAM(6,MAXATM)
REAL CEN(3)
CHARACTER*24 MASK(MAXCOL),TEST
CHARACTER*80 ATOM(MAXATM),CARD
LOGICAL MATCH
C
C flags include
C -b (ball and stick)
C -h (suppress header records in output)
C -radius XX (set cylinder radius)
C -brad XX (set ball radius as fraction of VdW)
C
character*64 options
logical bflag, hflag, bcflag, brflag
real cylrad, ballrad
c
c Read in 3x3 view matrix from file setup.matrix.
c Matrix is applied before finding translation, center, and scale.
c Afterwards the input matrix to RENDER is therefore the identity matrix.
C
common /matrix/ matrix, coords
real matrix(3,3), 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
bflag = .FALSE.
bcflag = .FALSE.
hflag = .FALSE.
brflag = .FALSE.
cylrad = 0.2
ballrad= 0.2
narg = iargc()
i = 1
500 continue
call getarg( i, options )
if (options(1:2) .eq. '-h') hflag = .true.
if (options(1:5) .eq. '-Bcol') then
bcflag = .true.
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, options )
read (options,*,err=701) Bmin
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, options )
read (options,*,err=701) Bmax
endif
if (options(1:2) .eq. '-b') bflag = .true.
if (options(1:2) .eq. '-r') then
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, options )
read (options,*,err=701) cylrad
if (cylrad.le.0) stop 'illegal radius value'
end if
if (options(1:3) .eq. '-br') then
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, options )
read (options,*,err=701) ballrad
if (ballrad.le.0) stop 'illegal ball radius value'
bflag = .true.
end if
i = i + 1
if (i.le.narg) goto 500
c
goto 799
701 write (noise,'(A)')
& 'syntax: rods [-h] [-b] [-Bcolor Bmin Bmax] [-radius R]'
call exit(-1)
799 continue
c
write (noise,*) 'Raster3D rods program ',VERSION
if (bcflag) then
write (noise,*) 'Atom colors will be assigned based on Biso'
write (noise,*) ' from dark blue = Bmin =', Bmin
write (noise,*) ' to light red = Bmax =', Bmax
endif
c
C
do i=1,3
do j=1,3
matrix(i,j)=0.
enddo
matrix(i,i)=1.
enddo
call view_matrix
c
if (.not. hflag) then
WRITE(OUTPUT,'(A,A)') 'rods ',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'
WRITE(OUTPUT,'(A)') '0 0 0 black background'
WRITE(OUTPUT,'(A)') 'F no, shadowed rods look funny'
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)',ERR=49)
& MASK(NCOL), (RGB(I,NCOL),I=1,3),VDW(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
* Problems reading input record
49 continue
write(noise,*) 'rods: Cannot parse input record ',CARD
call exit(-1)
* 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), VDW(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)',err=49) X,Y,Z
c EAM Oct88
READ(CARD,'(30X,3F8.3,6X,F8.2)',err=49) coords, Biso
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 = VDW(ICOL)
SPAM(1,IATM) = X
SPAM(2,IATM) = Y
SPAM(3,IATM) = Z
SPAM(4,IATM) = RAD
SPAM(5,IATM) = ICOL
SPAM(6,IATM) = Biso
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
C Here's the real loop.
C Look for pairs closer to each other than 0.60 times the
C sum of the vanderWaals radii.
C Draw all cylinders with 0.2A cylindrical radius.
C For ball and stick pictures, shrink vanderWaals radius
C of balls by 0.20
C If two atoms of different colors are bonded, make half-bond
C cylinders with each color.
C
CLOSE = 1.6 * 1.6
C
IF (BFLAG) THEN
DO 135 IATM=1,NATM
RAD = SPAM(4,IATM) * ballrad
ICOL = SPAM(5,IATM)
if (bcflag) then
call B2RGB( SPAM(6,IATM), Bmin, Bmax, RED, GREEN, BLUE )
RED = RED*RED
GREEN = GREEN*GREEN
BLUE = BLUE*BLUE
else
RED = RGB(1,ICOL)
GREEN = RGB(2,ICOL)
BLUE = RGB(3,ICOL)
endif
WRITE(OUTPUT,130)
2 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),RAD,
3 RED,GREEN,BLUE
C130 FORMAT(1H2,/,7f8.3)
130 FORMAT(1H2,/,7(1X,F8.3))
135 CONTINUE
ENDIF
C
DO 160 IATM=1,NATM
DO 150 JATM=IATM+1,NATM
DX = SPAM(1,IATM) - SPAM(1,JATM)
DY = SPAM(2,IATM) - SPAM(2,JATM)
DZ = SPAM(3,IATM) - SPAM(3,JATM)
DIST = DX*DX + DY*DY + DZ*DZ
CLOSE = 0.6 * (SPAM(4,IATM) + SPAM(4,JATM))
CLOSE = CLOSE**2
IF (ATOM(IATM)(17:17).NE.' ' .AND. ATOM(JATM)(17:17).NE.' '
& .AND. ATOM(IATM)(17:17).NE.ATOM(JATM)(17:17)) GOTO 150
c
c 4-Feb-2000 also force chain ID's to be the same
c
IF (ATOM(IATM)(22:22).NE.' ' .AND. ATOM(JATM)(22:22).NE.' '
& .AND. ATOM(IATM)(22:22).NE.ATOM(JATM)(22:22)) GOTO 150
IF (DIST .LE. CLOSE) THEN
if (bcflag) then
ICOL = 1
JCOL = 2
call B2RGB( SPAM(6,IATM), Bmin, Bmax, RED, GREEN, BLUE )
RGB(1,ICOL) = RED*RED
RGB(2,ICOL) = GREEN*GREEN
RGB(3,ICOL) = BLUE*BLUE
call B2RGB( SPAM(6,JATM), Bmin, Bmax, RED, GREEN, BLUE )
RGB(1,JCOL) = RED*RED
RGB(2,JCOL) = GREEN*GREEN
RGB(3,JCOL) = BLUE*BLUE
else
ICOL = SPAM(5,IATM)
JCOL = SPAM(5,JATM)
endif
IF(ICOL.EQ.JCOL) THEN
WRITE(OUTPUT,140)
1 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),CYLRAD,
2 SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),CYLRAD,
3 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
else if (bcflag) then
write(output,140)
1 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),CYLRAD,
2 SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),CYLRAD,
3 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
write(output,141)
1 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL),
2 RGB(1,JCOL),RGB(2,JCOL),RGB(3,JCOL),
3 0.0, 0.0, 0.0
ELSE
DO 136 K=1,3
136 CEN(K) = (SPAM(K,IATM)+SPAM(K,JATM))/2
WRITE(OUTPUT,140)
1 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),CYLRAD,
2 CEN(1),CEN(2),CEN(3),CYLRAD,
3 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
WRITE(OUTPUT,140)
1 CEN(1),CEN(2),CEN(3),CYLRAD,
2 SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),CYLRAD,
3 RGB(1,JCOL),RGB(2,JCOL),RGB(3,JCOL)
ENDIF
ENDIF
C140 FORMAT(1H3,/,11f8.3)
140 FORMAT(1H3,/,2(1X,F8.3,1X,F8.3,1X,F8.3,1X,F7.3),3F7.3)
141 format(2H17,/3(1X,3F6.3))
150 CONTINUE
160 CONTINUE
C
C
C
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, coords
real matrix(3,3), coords(3)
c
real phiX, phiY, phiZ
integer noise
parameter (noise = 0)
parameter (R2D = 180./3.1415927)
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
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
CCC Return RGB triple that runs from dark blue at Bmin
CC to light red at Bmax
C
subroutine B2RGB( Biso, Bmin, Bmax, R, G, B )
real Biso, Bmin, Bmax, R, G, B
c
real fraction, h, s, v
c
fraction = (Biso-Bmin) / (Bmax-Bmin)
if (fraction.lt.0.) fraction = 0.
if (fraction.gt.1.) fraction = 1.
h = 240. * (1.-fraction)
s = 0.8
v = 0.5 + fraction/2.
call hsv2rgb( h, s, v, r, g, b )
return
end
CCC Color format conversion from Hue/Saturation/Value to Red/Green/Blue
CC minimal (i.e. NO) error checking
C
subroutine hsv2rgb( h, s, v, r, g, b )
real h, s, v, r, g, b
c
real f, p, q, t
integer i
c
i = h /60.
f = h/60. - float(i)
p = v * (1. - s)
q = v * (1. - s*f)
t = v * (1. - s*(1. - f))
if (i.eq.5) then
r = v
g = p
b = q
else if (i.eq.4) then
r = t
g = p
b = v
else if (i.eq.3) then
r = p
g = q
b = v
else if (i.eq.2) then
r = p
g = v
b = t
else if (i.eq.1) then
r = q
g = v
b = p
else
r = v
g = t
b = p
endif
return
end
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