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PROGRAM RINGS3D
*------------------------------------------------------------------------------
* Program to set up input for RENDER by filling in 5- and 6-member rings
* with triangles.
*
* EAM May 1999 - initial version
* residue types are hard-wired in DATA statements
* planes are not smoothed
* EAM Nov 2008 - revise for use with TLSMD
*------------------------------------------------------------------------------
implicit none
c
include 'VERSION.incl'
c
c I/O units and environmental control
c
integer input, output, noise
parameter (input=5, output=6, noise=0)
integer narg
c integer iargc
c external iargc
character*64 options
logical bflag, pflag, sflag, rflag
c
c Data arrays
c
integer MAXATOM, MAXCOL
parameter (MAXATOM=10000, MAXCOL=1000)
real rgb(3,MAXCOL), vdw(MAXCOL)
real x(MAXATOM), y(MAXATOM), z(MAXATOM)
integer resno(MAXATOM), color(MAXATOM)
character*1 chain(MAXATOM)
character*4 resname(MAXATOM), name(MAXATOM)
c
character*24 mask(MAXCOL),test
character*80 card
logical match
c
c General storage
c
integer i,j,n
integer ncol, icol, nrings
integer natm, iatm, jatm
integer ind(10)
integer ringsize
real red,grn,blu
C
C Known residue types containing one or two rings
C Each row contains a residue name (type) in the first entry
C followed by up to 9 atom names which define the ring[s].
C A blank name terminates the list for this residue type.
C
C Five-membered rings (e.g. furanose)
C connect atoms (1,2,5)(2,3,5)(3,4,5)
C => atoms 1 and/or 4 can be out-of-plane, but not 2,3,5
C Six-membered rings (e.g. pyranose)
C connect atoms (1,2,6)(2,3,5)(2,5,6)(3,4,5)
C => atoms 1 and/or 4 can be out-of-plane, but not 2,3,5,6
C Nine-membered rings are assumed to be a conjugated ring system
C
C
C To add a new residue type:
c increase NTYPES by 1
c add row of atom names to type array
c adjust start/end indices of protein/base/sugar flags
c optional: add default colour record
C
integer NTYPES
parameter (NTYPES=28)
character*4 type( 10, NTYPES )
integer nhits( NTYPES )
integer p_start, p_end, b_start, b_end, s_start, s_end
C
C Default to solid color
C
integer DEFCOLS
parameter (DEFCOLS=6)
character*60 defcol(DEFCOLS)
data defcol /
& 'COLOUR########### A########## 0.501 0.501 1.000 2.00',
& 'COLOUR########### C########## 1.000 0.398 0.063 2.00',
& 'COLOUR########### G########## 1.000 0.101 0.101 2.00',
& 'COLOUR########### T########## 0.501 1.000 0.501 2.00',
& 'COLOUR########### U########## 0.501 1.000 0.501 2.00',
& 'COLOUR######################## 0.800 0.800 0.800 2.00'
& /
c
data type /
& ' HIS',' CG ',' ND1',' CE1',' NE2',' CD2', ' ',' ',' ',' ',
& ' PHE',' CG ',' CD1',' CE1',' CZ ',' CE2',' CD2',' ',' ',' ',
& ' TYR',' CG ',' CD1',' CE1',' CZ ',' CE2',' CD2',' ',' ',' ',
& ' TRP',' CZ2',' CH2',' CZ3',' CE3',' CD2',' CE2',
& ' CG ',' CD1',' NE1',
& ' GAL',' C1 ',' C2 ',' C3 ',' C4 ',' C5 ',' O5 ',' ',' ',' ',
& ' NAG',' C1 ',' C2 ',' C3 ',' C4 ',' C5 ',' O5 ',' ',' ',' ',
& ' NGA',' C1 ',' C2 ',' C3 ',' C4 ',' C5 ',' O5 ',' ',' ',' ',
& ' GLC',' C1 ',' C2 ',' C3 ',' C4 ',' C5 ',' O5 ',' ',' ',' ',
& ' MAN',' C1 ',' C2 ',' C3 ',' C4 ',' C5 ',' O5 ',' ',' ',' ',
& ' MNG',' C1 ',' C2 ',' C3 ',' C4 ',' C5 ',' O5 ',' ',' ',' ',
& ' SIA',' C2 ',' C3 ',' C4 ',' C5 ',' C6 ',' O6 ',' ',' ',' ',
& ' RIP',' O4''',' C4''',' C3''',' C2''',' C1''',' ',' ',' ',' ',
& ' +C',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' +T',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' +U',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' +A',' N3 ',' C2 ',' N1 ',' C6 ',' C5 ',' C4 ',
& ' N7 ',' C8 ',' N9 ',
& ' +G',' N3 ',' C2 ',' N1 ',' C6 ',' C5 ',' C4 ',
& ' N7 ',' C8 ',' N9 ',
& ' C',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' T',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' U',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' A',' N3 ',' C2 ',' N1 ',' C6 ',' C5 ',' C4 ',' N7 ',' C8 ',' N9 ',
& ' G',' N3 ',' C2 ',' N1 ',' C6 ',' C5 ',' C4 ',' N7 ',' C8 ',' N9 ',
& ' DC',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' DT',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' DU',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' ',' ',' ',
& ' DA',' N3 ',' C2 ',' N1 ',' C6 ',' C5 ',' C4 ',' N7 ',' C8 ',' N9 ',
& ' DG',' N3 ',' C2 ',' N1 ',' C6 ',' C5 ',' C4 ',' N7 ',' C8 ',' N9 ',
& ' PDC',' N1 ',' C2 ',' N3 ',' C4 ',' C5 ',' C6 ',' C9 ',' C8 ',' N7 '
& /
c
data p_start, p_end / 1, 4 /
data s_start, s_end / 5, 12 /
data b_start, b_end /13, 28 /
c
do i = 1, NTYPES
nhits(i) = 0
enddo
c
bflag = .FALSE.
pflag = .FALSE.
sflag = .FALSE.
rflag = .FALSE.
narg = iargc()
i = 0
100 continue
i = i + 1
if (i.gt.narg) goto 199
call getarg( i, options )
if (options(1:2) .eq. '-b') then
bflag = .true.
else if (options(1:2) .eq. '-p') then
pflag = .true.
else if (options(1:2) .eq. '-s') then
sflag = .true.
else if (options(1:2) .eq. '-r') then
rflag = .true.
else
goto 101
endif
goto 100
c
101 continue
write (noise,'(A)')
& 'syntax: rings3d [-options] < infile.pdb > outfile.r3d'
write (noise,'(A)')
& ' -bases A/C/G/T/U DA/+A/etc'
write (noise,'(A)')
& ' -ribose sugar in A/C/G/T/U DA/+A/etc'
write (noise,'(A)')
& ' -protein HIS/PHE/TRP/TYR'
write (noise,'(A)')
& ' -sugars GAL/GLC/MAN/NAG/NGA/SIA'
call exit(-1)
199 continue
if (.not.bflag .and. .not.pflag .and. .not.rflag) sflag = .true.
c
write (noise,*) 'Raster3D rings3d program ',VERSION
c
c Read in colours first
c
ncol = 0
natm = 0
200 continue
read(input,'(a80)',end=250) 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),vdw(ncol)
elseif (card(1:4).eq.'ATOM'.or.card(1:4).eq.'HETA') then
* Load default colors after any that were read in
if (natm.eq.0.and.ncol.le.MAXCOL-DEFCOLS) then
do i = 1,DEFCOLS
ncol = ncol + 1
read(defcol(I),'(6x,a24,3f8.3,f6.2)') mask(ncol),
& (rgb(j,ncol),j=1,3), vdw(ncol)
enddo
endif
* Now we read in ATOM record
natm = natm + 1
if (natm.gt.MAXATOM) then
write(noise,*) 'Atom array overflow. Increase ',
& 'MAXATOM and recompile.'
stop 20
endif
test = card(7:30)
do icol = 1, ncol
if (match(test,mask(icol))) then
color(natm) = icol
read(card,901) resno(natm),x(natm),y(natm),z(natm)
901 format(22x,i4,4x,3f8.3)
name(natm) = card(13:16)
resname(natm) = card(17:20)
chain(natm) = card(22:22)
goto 220
endif
enddo
220 continue
elseif (card(1:3).eq.'END') then
go to 250
endif
go to 200
* Come here when EOF or 'END' record is reached
250 continue
if (natm.eq.0) then
write(noise,*) 'No atoms in input.'
stop 30
else
write(noise,*) 'Input atoms: ',natm
endif
c
C Here's the real loop.
C
nrings = 0
jatm = 0
300 continue
iatm = jatm + 1
if (iatm.ge.natm) goto 399
c
do j = iatm, natm
if (resno(j).eq.resno(iatm)
& .and.chain(j).eq.chain(iatm)) then
jatm = j
else
goto 301
endif
enddo
301 continue
if (bflag) then
do n = b_start, b_end
if (resname(iatm)(2:4).eq.type(1,n)(2:4)) goto 310
enddo
endif
if (pflag) then
do n = p_start, p_end
if (resname(iatm)(2:4).eq.type(1,n)(2:4)) goto 310
enddo
endif
if (sflag) then
do n = s_start, s_end
if (resname(iatm)(2:4).eq.type(1,n)(2:4)) goto 310
enddo
endif
c Look for base names, but use sugar ring (ribopyranose)
if (rflag) then
do n = b_start, b_end
if (resname(iatm)(2:4).eq.type(1,n)(2:4)) then
goto 309
endif
enddo
endif
goto 300
309 continue
c Found a ribose inside a base
n = b_start - 1
310 continue
ringsize = 9
if (rflag) n = b_start - 1
do i = 2, 10
if (type(i,n).eq.' ') then
ringsize = i - 2
goto 320
endif
do j = iatm, jatm
if (type(i,n).eq.name(j)) then
ind(i-1) = j
goto 312
endif
c Allow for incorrect column
if ((type(1,n)(1:1).eq.' ') .and.
& (type(i,n)(2:4).eq.name(j)(1:3))) then
ind(i-1) = j
goto 312
endif
enddo
write(noise,*) 'Cannot find atom ',type(i,n),' in',
& type(1,n), resno(iatm), chain(iatm)
goto 300
312 continue
enddo
320 continue
c
c Found one
c
nrings = nrings + 1
nhits(n) = nhits(n) + 1
red = rgb(1,color(ind(1)))
grn = rgb(2,color(ind(1)))
blu = rgb(3,color(ind(1)))
write(output,321) type(1,n),resno(iatm),chain(iatm)
321 format('# ',a4,2x,i4,a1)
322 format('1',/,3(3f8.2),3f6.3)
if (ringsize.eq.5) then
write(output,322)
& x(ind(1)),y(ind(1)),z(ind(1)),
& x(ind(2)),y(ind(2)),z(ind(2)),
& x(ind(5)),y(ind(5)),z(ind(5)),
& red,grn,blu
write(output,322)
& x(ind(3)),y(ind(3)),z(ind(3)),
& x(ind(4)),y(ind(4)),z(ind(4)),
& x(ind(5)),y(ind(5)),z(ind(5)),
& red,grn,blu
write(output,322)
& x(ind(2)),y(ind(2)),z(ind(2)),
& x(ind(3)),y(ind(3)),z(ind(3)),
& x(ind(5)),y(ind(5)),z(ind(5)),
& red,grn,blu
endif
if (ringsize.ge.6) then
write(output,322)
& x(ind(2)),y(ind(2)),z(ind(2)),
& x(ind(3)),y(ind(3)),z(ind(3)),
& x(ind(5)),y(ind(5)),z(ind(5)),
& red,grn,blu
write(output,322)
& x(ind(1)),y(ind(1)),z(ind(1)),
& x(ind(2)),y(ind(2)),z(ind(2)),
& x(ind(6)),y(ind(6)),z(ind(6)),
& red,grn,blu
write(output,322)
& x(ind(3)),y(ind(3)),z(ind(3)),
& x(ind(4)),y(ind(4)),z(ind(4)),
& x(ind(5)),y(ind(5)),z(ind(5)),
& red,grn,blu
write(output,322)
& x(ind(2)),y(ind(2)),z(ind(2)),
& x(ind(5)),y(ind(5)),z(ind(5)),
& x(ind(6)),y(ind(6)),z(ind(6)),
& red,grn,blu
endif
if (ringsize.eq.9) then
write(output,322)
& x(ind(5)),y(ind(5)),z(ind(5)),
& x(ind(7)),y(ind(7)),z(ind(7)),
& x(ind(8)),y(ind(8)),z(ind(8)),
& red,grn,blu
write(output,322)
& x(ind(6)),y(ind(6)),z(ind(6)),
& x(ind(8)),y(ind(8)),z(ind(8)),
& x(ind(9)),y(ind(9)),z(ind(9)),
& red,grn,blu
write(output,322)
& x(ind(5)),y(ind(5)),z(ind(5)),
& x(ind(6)),y(ind(6)),z(ind(6)),
& x(ind(8)),y(ind(8)),z(ind(8)),
& red,grn,blu
endif
goto 300
399 continue
write (noise,*) 'Filled rings for',nrings,' residues'
do i = 1,NTYPES
if (nhits(i).gt.0) write (noise,*) ' ',type(1,i),nhits(i)
enddo
c
c
c
end
LOGICAL FUNCTION MATCH (SUBJ, MASK)
CHARACTER*24 SUBJ,MASK
MATCH = .FALSE.
DO I = 1, 24
IF (SUBJ(I:I).NE.MASK(I:I) .AND. MASK(I:I).NE.'#') RETURN
ENDDO
MATCH = .TRUE.
RETURN
END
|
