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PROGRAM RASTEP
********************************************************************************
*
* Usage:
* rastep [-h] [-iso] [-Bcolor Bmin Bmax] [-prob xx] [-radius r] [-fancy[0-9]]
* [-tabulate histogram.file] [-by_atomtype] [-suv_check]
*
*
* -auto auto-orientation of viewpoint
* -h suppresses header records in output
* -iso forces isotropic B values (spheres rather than
* ellipsoids) even if ANISOU cards present
* -Bcolor Bmin Bmax
* color by Biso values; Bmin = dark blue, Bmax = light red
* -Acolor color by anisotropy; red < white (A=0.5) < green
* -prob xx draws ellipsoids to enclose this
* probability level (default = 0.50)
* -radius draws bonds with this radius in Angstroms
* (default = 0.10)
* -fancy[0-9] increasingly complex rendition of ellipsoids
* fancy0 [default] solid surface only
* fancy1 principle axes + transparent bounding ellipsoid
* fancy2 equatorial planes only
* fancy3 equatorial planes + transparent ellipsoid
* fancy4 longest principle axis only
* fancy5 for ORTEP lovers - one octant missing
* fancy6 same as fancy5, with missing octant colored grey
*
*===============================================================================
* The following options are used by parvati scripts
*
* -tabulate [file]instead of creating a Raster3D input file,
* list all atoms with principle axes and anisotropy.
* Optionally write a histogram of anisotropy to speficied
* output file; otherwise output is to stderr
*
* output from -tabulate for this version of rastep
* ATOM RESNAME RESNUM EIGEN1 EIGEN2 EIGEN3 ANISOTROPY Uiso
*
* -com [file] find <anisotropy> in shells from center of mass
* -nohydrogens don't plot hydrogens even if present
* -mini small size plot (176x208) with auto-orientation
* -suv_check use Suv to validate similarity of bonded ellipsoids
*
********************************************************************************
*
* EAM Jul 97 - initial version
* EAM Dec 97 - version 2.4b release
* EAM Jan 98 - add tabulation option
* EAM May 98 - integrate with PARVATI script
* EAM Jun 99 - fix bug (lack of sqrt) in -iso processing, trap read errors
* -Acolor flag to color by anisotropy (not yet entirely satisfactory)
* EAM Jul 99 - V2.4l -tab output revised slightly,
* NPD ellipsoids colored magenta
* -nohydro flag to suppress drawing hydrogens
* -mini flag to generate smaller pictures
* don't draw bonds between atoms with different ALT flags
* EAM Aug 99 - V2.4m
* work harder at suppressing hydrogens
* add auto-orientation (NB: scaling is wrong in this case!)
* EAM Dec 99 - V2.5
* clean up output formats a little
* EAM Jun 2000 - additional error reporting
* EAM Jul 2000 - apply Bcolor to bonds as well as atoms
* EAM Sep 2000 - Suv similarity test
* EAM Apr 2001 - V2.6
* ORTEP_LIKE ellipsoids (one octant missing)
* error count
* EAM Feb 2002 - rework ANISOU and Suv processing to gain back some speed
* maybe I should have an array of iso/aniso flags to save
* time during testing?
* the rest of CARD() array can go too?
* all the tests on IF ATOM(I)(1:).eq.'ATOM' are now unneeded
* EAM May 2003 - expand default color table to allow for off-by-one atom names
* EAM Oct 2003 - trap and report 0 values for axial Uij components in input
*
* 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), VDW(MAXCOL)
REAL SPAM(5,MAXATM)
REAL UIJ(6,MAXATM)
real center(3)
CHARACTER*24 MASK(MAXCOL),TEST
CHARACTER*80 ATOM(MAXATM),CARD
character*3 resname
character*1 spacer
LOGICAL MATCH
logical hflag, ellipses, bcflag, tflag, atflag, comflag
logical acflag, nohydro, mini, auto
integer fancy
character*80 flags
c
c Data structures used for auto-orientation
real Rr(3,3), U(4,4), Xmom(5)
c
COMMON /ASSCOM/ assout, verbose
integer assout
logical verbose
c
real quadric(10), anisou(6)
real eigens(4), evecs(4,4), evecinv(4,4), evecit(4,4)
real qq(4,4), qp(4,4), temp(4,4)
c
external anitoquad
integer anitoquad
c
real problevel(50)
c
real start(3),end(3)
real MARGIN
parameter (MARGIN = 1.15)
c
real Uprin(3), Umean, Usigma, anisotropy, ellipticity
integer histogram(20), hislun
real anisi(MAXATM), sum_a, sum_a2, anis_mean, anis_sigma
real Biso(MAXATM), sum_b, sum_b2, sum_ab
integer nanis, niso, nhyd, nonpos
logical hwhacky
integer nerrors
c
character*2 atomtype
integer natype
c
real*8 wsum, xsum, ysum, zsum
real*8 xcom, ycom, zcom
real adist(110)
integer hdist(100), comlun, dshells
c
c Support for validation of similarity of bonded atoms
logical suvflag
integer suvlun, suvbad
real anisov(6)
c
c Default to CPK colors and VDW radii
integer DEFCOLS
parameter (DEFCOLS = 17)
character*60 defcol(DEFCOLS)
data defcol /
& 'COLOUR###### CA ############## 0.175 0.175 0.175 1.70',
& 'COLOUR###### C ############## 0.175 0.175 0.175 1.70',
& '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################ 0.050 0.750 0.050 1.80',
& 'COLOUR##### CA ############### 0.175 0.175 0.175 1.70',
& 'COLOUR##### C ############### 0.175 0.175 0.175 1.70',
& '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################# 0.050 0.750 0.050 1.80',
& 'COLOUR######################## 1.000 0.000 1.000 2.00'
& /
c
c Critical values for probability ellipsoids of a trivariate normal
c distribution. From Table 6.1 of ORTEP-III manual (Oak Ridge National
c Laboratory Report ORNL-6895, 1996). Tabulated below in increments of
c 2% in probability. Default contours enclose a probability level of
c 50% (critical value 1.5382).
c
data problevel / 0.4299, 0.5479, 0.6334, 0.7035, 0.7644,
& 0.8192, 0.8694, 0.9162, 0.9605, 1.0026,
& 1.0430, 1.0821, 1.1200, 1.1570, 1.1932,
& 1.2288, 1.2638, 1.2985, 1.3330, 1.3672,
& 1.4013, 1.4354, 1.4695, 1.5037, 1.5382,
& 1.5729, 1.6080, 1.6436, 1.6797, 1.7164,
& 1.7540, 1.7924, 1.8318, 1.8724, 1.9144,
& 1.9580, 2.0034, 2.0510, 2.1012, 2.1544,
& 2.2114, 2.2730, 2.3404, 2.4153, 2.5003,
& 2.5997, 2.7216, 2.8829, 3.1365, 6.0000 /
c
c
assout = noise
verbose = .false.
hflag = .false.
acflag = .false.
bcflag = .false.
tflag = .false.
atflag = .false.
comflag = .false.
suvflag = .false.
ellipses = .true.
hwhacky = .false.
nohydro = .false.
mini = .false.
auto = .false.
fancy = 0
prob = 0.50
radius = 0.10
nerrors = 0
narg = iargc()
i = 1
5 continue
call getarg( i, flags )
if (flags(1:5) .eq. '-help') goto 701
if (flags(1:6) .eq. '-debug') verbose = .true.
if (flags(1:2) .eq. '-h') hflag = .true.
if (flags(1:4) .eq. '-iso') ellipses = .false.
if (flags(1:4) .eq. '-rad') then
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, flags )
read (flags,*,err=701) radius
if (radius.lt.0) radius = 0.0
end if
if (flags(1:4) .eq. '-pro') then
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, flags )
read (flags,*,err=701) prob
if (prob.le.0.) stop 'illegal probability level'
* If prob > 1 assume they meant it in percent
if (prob.gt.1.) prob = prob / 100.
end if
if (flags(1:5) .eq. '-Acol') then
acflag = .true.
bcflag = .false.
end if
if (flags(1:5) .eq. '-Bcol') then
bcflag = .true.
acflag = .false.
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, flags )
read (flags,*,err=701) Bmin
i = i + 1
if (i.gt.narg) goto 701
call getarg( i, flags )
read (flags,*,err=701) Bmax
endif
if (flags(1:6) .eq. '-fancy') then
if (flags(7:7).eq.'0') then
fancy = 0
else if (flags(7:7).eq.'1') then
fancy = 1
else if (flags(7:7).eq.'2') then
fancy = 2
else if (flags(7:7).eq.'3') then
fancy = 3
else if (flags(7:7).eq.'4') then
fancy = 4
else if (flags(7:7).eq.'5') then
fancy = 5
else if (flags(7:7).eq.'6') then
fancy = 6
else
fancy = 1
endif
endif
if (flags(1:4) .eq. '-tab') then
tflag = .true.
hflag = .true.
acflag = .false.
bcflag = .false.
fancy = 0
do j=1,MAXATM
anisi(j) = 0.0
end do
hislun = NOISE
if (i.ge.narg) goto 799
call getarg(i+1,flags)
if (flags(1:1) .ne. '-') then
hislun = 1
open(unit=hislun,file=flags,status='UNKNOWN'
& , CARRIAGECONTROL='LIST'
& )
endif
endif
if (flags(1:4) .eq. '-com') then
comflag = .true.
comlun = NOISE
if (i.ge.narg) goto 799
call getarg(i+1,flags)
if (flags(1:1) .ne. '-') then
comlun = 2
open(unit=comlun,file=flags,status='UNKNOWN'
& , CARRIAGECONTROL='LIST'
& )
endif
endif
if (flags(1:4) .eq. '-suv') then
suvflag = .true.
suvlun = NOISE
suvlimit = 0.975
if (i.ge.narg) goto 799
call getarg(i+1,flags)
if (flags(1:1) .ne. '-') then
read (flags,*,err=701) suvlimit
endif
endif
if (flags(1:8) .eq. '-by_atom') then
atflag = .true.
endif
if (flags(1:8) .eq. '-nohydro') then
nohydro = .true.
endif
if (flags(1:8) .eq. '-mini') then
mini = .true.
auto = .true.
endif
if (flags(1:8) .eq. '-auto') then
auto = .true.
endif
c
i = i + 1
if (i.le.narg) goto 5
goto 799
701 continue
write (noise,*) 'Raster3D Thermal Ellipsoid Program ',
& VERSION
write (noise,'(/,A)') 'syntax:'
write (noise,'(A)')
& 'rastep [-h] [-iso] [-Bcolor Bmin Bmax] [-prob Plevel]'
write (noise,'(A)')
& ' [-fancy[0-6]] [-radius R] [-auto]'
write (noise,'(A,A)')
& ' [-nohydrogens] [-suv [suv_limit]]'
write (noise,'(A,A)')
& ' [-tabulate [tabfile]] [-by_atomtype] [-com [comfile]]'
call exit(-1)
799 continue
c
c Critical values for the radius corresponding to a sphere
c enclosing the requested probability level are taken from
c Table 6.1 of the ORTEP manual
iprob = (prob+0.01)*50.
pradius = problevel(iprob)
c
write (noise,800)
write (noise,*) 'Raster3D Thermal Ellipsoid Program ',
& VERSION
write (noise,*) 'E A Merritt - 2 Feb 2002'
write (noise,800)
800 format('************************************************')
c
if (.not.ellipses) then
write (noise,801) float(iprob)/50.
801 format(' Spheres will bound Biso probability level', f5.2)
else
write (noise,802) float(iprob)/50.
802 format(' Ellipsoids will bound probability level', f5.2)
endif
write (noise,803) pradius
803 format(' Corresponding critical value ', f7.4)
c
if (acflag) then
write (noise,*) 'Atoms will be colored based on Anisotropy'
endif
c
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
Umin = Bmin / (8. * 3.14159*3.14159)
Umax = Bmax / (8. * 3.14159*3.14159)
Umin = Umin
Umax = Umax
endif
c
if (.not. hflag) then
WRITE(OUTPUT,'(A,A,I5,A)')
& 'Raster3D thermal ellipsoid program ',VERSION,
& INT(prob*100.+0.5), '% probability bounds'
if (mini) then
WRITE(OUTPUT,'(A)') '22 26 tiles in x,y'
else
WRITE(OUTPUT,'(A)') '80 64 tiles in x,y'
endif
WRITE(OUTPUT,'(A)') ' 8 8 pixels (x,y) per tile'
WRITE(OUTPUT,'(A)') '4 3x3 virtual pixels -> 2x2 pixels'
WRITE(OUTPUT,'(A)') '1 1 1 white background'
WRITE(OUTPUT,'(A)') 'F no, shadows are dorky'
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)') '0.0 No perspective'
WRITE(OUTPUT,'(A)') '1 1 1 main light source position'
end if
c
if (auto) then
ASPECT = 22./26.
else
ASPECT = 80./64.
endif
c
NCOL = 0
NATM = 0
NANI = 0
nanis = 0
niso = 0
nhyd = 0
nonpos = 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), VDW(NCOL)
ELSEIF (nohydro .AND. CARD(77:78).EQ.' H') THEN
goto 10
ELSEIF (CARD(1:6).EQ.'ANISOU') THEN
nani = nani + 1
if (card(13:27).ne.atom(natm)(13:27)) goto 14
read (card(29:70),*,err=12,end=12) (uij(i,natm),i=1,6)
do i=1,6
uij(i,natm) = uij(i,natm) * 0.0001
enddo
noerr = 1
do i=1,3
if (uij(i,natm).eq.0.0) then
uij(i,natm) = 0.0001
noerr = 0
endif
enddo
if (noerr.eq.0) goto 15
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
uij(1,natm) = -1.0
ELSEIF (CARD(1:3).EQ.'END') THEN
GO TO 50
ENDIF
GO TO 10
12 write(noise,*) '*** Format problem - ', card(13:70)
nerrors = nerrors + 1
goto 10
14 write(noise,*) '*** ANISOU record out of order - ', card(13:70)
nerrors = nerrors + 1
goto 10
15 write(noise,*) '*** Illegal ANISOU values - ', card(13:70)
nerrors = nerrors + 1
goto 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.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
*
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)
c
c Do a little pre-processing to make later bookkeeping easier
c At least screen out non-conformant PDB files that contain
c something obviously not an element type in columns 77:78
c Hydrogen naming conventions are totally messed up.
c
if (atflag) then
resname = card(18:20)
c if (resname.eq.'MET' .and. card(14:15).eq.'SD') then
c atom(iatm)(77:78) = 'SD'
c end if
if ( resname.eq.'HOH' .or. resname.eq.'H2O'
& .or. resname.eq.'WAT') then
atom(iatm)(77:78) = 'OW'
end if
if (atom(iatm)(78:78).ge.'0' .and. atom(iatm)(78:78).le.'9')
& atom(iatm)(77:78) = ' '
end if
if (nohydro .and. atom(iatm)(77:78).eq.' ') then
do 70 i = 13,16
if (atom(iatm)(i:i).eq.' ') goto 70
if (atom(iatm)(i:i).ge.'1'
& .and. atom(iatm)(i:i).le.'4') goto 70
if (atom(iatm)(i:i).ne.'H') goto 71
atom(iatm)(77:78) = ' H'
70 continue
71 continue
end if
c
TEST = CARD(7:30)
DO 80 ICOL=1,NCOL
IF (MATCH(TEST,MASK(ICOL))) THEN
READ(CARD,'(30X,3F8.3,6X,F6.2)',end=82,err=82)
& X,Y,Z, Biso(IATM)
IF (Biso(IATM).LE.0.0) THEN
nerrors = nerrors + 1
write(noise,*) '*** Illegal Biso ',Biso(IATM),' - ',
& atom(iatm)(13:27)
Biso(IATM) = 0.0
ENDIF
Uiso = Biso(IATM) / (8. * 3.14159*3.14159)
SPAM(1,IATM) = X
SPAM(2,IATM) = Y
SPAM(3,IATM) = Z
SPAM(4,IATM) = Uiso
SPAM(5,IATM) = ICOL
RAD = sqrt(Uiso) * PRADIUS
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)
c atomtype = CARD(77:78)
c if (atomtype.ne.' ') then
c weight = amass(atomtype)
c else
weight = 13.4
wsum = wsum + weight
xsum = xsum + weight * X
ysum = ysum + weight * Y
zsum = zsum + weight * Z
GO TO 100
ENDIF
80 CONTINUE
WRITE(NOISE,*) 'No colour table mask matches this atom:'
WRITE(NOISE,*) ATOM(IATM)
STOP 90
82 continue
write(noise,*) 'Input format problem in record'
write(noise,*) CARD
STOP 90
100 CONTINUE
XMID = (XMAX+XMIN)/2.
YMID = (YMAX+YMIN)/2.
ZMID = (ZMAX+ZMIN)/2.
TX = -XMID
TY = -YMID
TZ = -ZMID
xcom = xsum / wsum
ycom = ysum / wsum
zcom = zsum / wsum
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 (mini) then
scale = sqrt(xspan**2+yspan**2+zspan**2) * aspect
if (scale .lt. 9.) scale = 9.
end if
*
* These are for the center-of-mass table
DMAX = MAX( ABS(XMAX-XCOM), ABS(XMIN-XCOM) )**2
& + MAX( ABS(YMAX-YCOM), ABS(YMIN-YCOM) )**2
& + MAX( ABS(ZMAX-ZCOM), ABS(ZMIN-ZCOM) )**2
DMAX = SQRT(DMAX)
dshells = 100
*
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 Auto-orientation
c 25-Aug-1999
c Find Eigenvectors of moment of inertia tensor.
c Arrange smallest Eigenvalue along Y, largest along Z.
c Problems:
c - Could emphasize side-chain over backbone by ignoring
c atoms O and N, but in practice this doesn't seem to help much.
c - Scaling is wrong, because it was done before rotation.
c
if (auto) then
do 125 iatm = 1, natm
if (atom(iatm)(1:4).ne.'ATOM'
& .and. atom(iatm)(1:4).ne.'HETA') goto 125
C if (atom(iatm)(13:15).eq.' O ') goto 125
C if (atom(iatm)(13:15).eq.' N ') goto 125
if (atom(iatm)(77:78).eq.' H' .and. nohydro) goto 125
x = spam(1,iatm) - xcom
y = spam(2,iatm) - ycom
z = spam(3,iatm) - zcom
Rq = (x*x + y*y + z*z)
Rv = sqrt(Rq)
Rr(1,1) = Rr(1,1) + x*x
Rr(1,2) = Rr(1,2) + x*y
Rr(1,3) = Rr(1,3) + x*z
Rr(2,1) = Rr(2,1) + y*x
Rr(2,2) = Rr(2,2) + y*y
Rr(2,3) = Rr(2,3) + y*z
Rr(3,1) = Rr(3,1) + z*x
Rr(3,2) = Rr(3,2) + z*y
Rr(3,3) = Rr(3,3) + z*z
Xmom(1) = Xmom(1) + 1.
Xmom(2) = Xmom(2) + Rv
Xmom(3) = Xmom(3) + Rq
Xmom(4) = Xmom(4) + Rv*Rq
Xmom(5) = Xmom(5) + Rq*Rq
125 continue
if (verbose) then
write (NOISE,'(/,A,5G13.5)') ' Radial moments:',Xmom
write (NOISE,'(A)') ' Moment of inertia tensor'
end if
Rg = sqrt(Xmom(3)/Xmom(1))
U(1,1) = Xmom(3)
U(2,2) = Xmom(3)
U(3,3) = Xmom(3)
do k = 1,3
do l = 1,3
U(k,l) = (U(k,l) - Rr(k,l)) / Xmom(1)
end do
if (verbose) write (NOISE,'(3G13.6)') (U(k,l),l=1,3)
end do
call jacobi( U, 3, 4, Eigens, Evecs )
c Re-order so that long axis is vertical, short axis towards viewer
kmax = 1
if (Eigens(2).gt.Eigens(kmax)) kmax = 2
if (Eigens(3).gt.Eigens(kmax)) kmax = 3
kmin = 1
if (Eigens(2).le.Eigens(kmin)) kmin = 2
if (Eigens(3).le.Eigens(kmin)) kmin = 3
kmid = 6 - (kmin + kmax)
if (verbose) then
write (NOISE,'(A,/,3F13.5,10X,3i2)') ' Eigenvalues:',
& Eigens(kmin),Eigens(kmid),Eigens(kmax)
& ,kmin,kmid,kmax
write (NOISE,'(A)') ' Eigenvectors:'
do k = 1,3
write (NOISE,'(3F13.5)')
& Evecs(k,kmin),Evecs(k,kmid),Evecs(k,kmax)
enddo
end if
do k = 1,3
U(k,1) = Evecs(k,kmid)
U(k,2) = Evecs(k,kmin)
U(k,3) = Evecs(k,kmax)
U(k,4) = 0.0
U(4,k) = 0.0
enddo
U(4,4) = 1.0
c Beware! may be left-handed at this point!
det = tinv4( evecinv, U )
if (det .lt. 0.0) then
do k = 1,3
U(k,3) = -U(k,3)
enddo
endif
c OK, now it should be right-handed
WRITE(OUTPUT,'(A)') '# Auto-orientation matrix'
WRITE(OUTPUT,'(A)') '16'
WRITE(OUTPUT,'(A)') 'ROTATION'
do k = 1,3
write (OUTPUT,'(3F13.5)') U(1,k),U(2,k),U(3,k)
enddo
WRITE(OUTPUT,'(A)') '# End auto-orientation'
end if
c
c Label output records
c
if (.not. tflag) then
WRITE(OUTPUT,'(A,A)')
& '# Thermal ellipsoids from Rastep Version ',VERSION
WRITE(OUTPUT,'(A,F5.2)') '# Probability level',float(iprob)/50.
end if
c
c Write ellipsoids to input file for render
c
IF (fancy.eq.0 .and. .not.tflag) GOTO 139
c
c First, optional pass, to write fancy stuff associated with ellipsoids
c
IATM = 1
130 CONTINUE
IF (ATOM(IATM)(1:4).EQ.'ATOM' .OR.
& ATOM(IATM)(1:4).EQ.'HETA') THEN
X = SPAM(1,IATM)
Y = SPAM(2,IATM)
Z = SPAM(3,IATM)
ICOL = SPAM(5,IATM)
if (bcflag) then
call U2RGB( SPAM(4,IATM), Umin, Umax, RED, GREEN, BLUE )
RED = RED*RED
GREEN = GREEN*GREEN
BLUE = BLUE*BLUE
else if (acflag) then
call A2RGB( 1.0, 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
IF (ellipses .and. uij(1,iatm).ge.0.) THEN
do i=1,6
anisou(i) = uij(i,iatm)
enddo
if (anitoquad(anisou,pradius,quadric,eigens,evecs).lt.0)then
write(noise,*) '*** Non-positive definite ellipsoid - ',
& atom(iatm)(13:27)
nonpos = nonpos + 1
nerrors = nerrors + 1
Biso(iatm) = 0.0
goto 138
endif
goto 132
132 continue
radlim = pradius * max( eigens(1),eigens(2),eigens(3) )
radlim = radlim * MARGIN
c
c Only for debugging ellipsoids
if (verbose) then
write (noise,901) 'ANISOU ',X,Y,Z,ANISOU
write (noise,902) 'QUADRIC',QUADRIC
write (noise,903) 'Eigenvalues', (EIGENS(i),i=1,3),
& 'prob', prob,'limiting radius', radlim
write (noise,904) 'Evecs ',((evecs(i,j),i=1,3),j=1,3)
endif
901 format(a,3f8.3,6f8.4)
902 format(a,10f8.3)
903 format(a,3f8.3,4x,a,f8.3,4x,a,f8.3)
904 format(a,9f7.3)
c
c Tabulate principal axes of ellipsoid for each atom
if (tflag) then
do i=1,3
Uprin(i) = eigens(i)**2
enddo
if (Uprin(2).gt.Uprin(1)) then
Umean = Uprin(1)
Uprin(1) = Uprin(2)
Uprin(2) = Umean
endif
if (Uprin(3).gt.Uprin(1)) then
Umean = Uprin(1)
Uprin(1) = Uprin(3)
Uprin(3) = Umean
endif
if (Uprin(3).gt.Uprin(2)) then
Umean = Uprin(2)
Uprin(2) = Uprin(3)
Uprin(3) = Umean
endif
c
c Anisotropy we define as Umin / Umax
c as in shelxpro output
anisotropy = min(Uprin(1),Uprin(2),Uprin(3))
& / max(Uprin(1),Uprin(2),Uprin(3))
c
c But don't count atoms which are perfectly isotropic
if (atom(iatm)(77:78).eq.' H') then
nhyd = nhyd + 1
if (anisotropy .ne. 1.0) hwhacky = .true.
else if (anisotropy .eq. 1.0) then
niso = niso + 1
else
anisi(iatm) = anisotropy
sum_A = sum_A + anisotropy
sum_B = sum_B + Biso(iatm)
nanis = nanis + 1
end if
c
c Ellipticity we define as 1 / anisotropy
if (anisotropy.eq.0) then
ellipticity = 0
else
ellipticity = 1. / anisotropy
end if
c
c Longhi et al (1997) JMB 268, 779-799.
c proposed another measure A = sigU / meanU
Umean = (Uprin(1) + Uprin(2) + Uprin(3)) / 3.0
Usigma = (Uprin(1)-Umean)**2
& + (Uprin(2)-Umean)**2 + (Uprin(3)-Umean)**2
Usigma = sqrt( Usigma ) / 3.0
alonghi = Usigma / Umean
c
c Might want to check correlation with Uiso
Uiso = SPAM(4,iatm)
c
c Cosmetic changes to atom identifier for the sake of sorting
c We will force there to be exactly three entities printed.
c PDB format is just a mess:
c cols 13:16 atom
c col 17 alternate conf
c cols 18:20 residue
c col 22 chain
c cols 23:27 resnum
c
do i = 16, 13, -1
if (ATOM(iatm)(i:i) .ne. ' ') j = i
enddo
do i = 13, 17
if (ATOM(iatm)(i:i) .ne. ' ') k = i
enddo
do i = j, k
if (ATOM(iatm)(i:i) .eq. ' ') ATOM(iatm)(i:i) = '_'
enddo
c if (ATOM(iatm)(17:17) .ne. ' ') then
c do i = 18,19
c if (ATOM(iatm)(i:i) .eq. ' ') ATOM(iatm)(i:i) = '_'
c enddo
c endif
spacer = ' '
if (ATOM(iatm)(22:22) .ne. ' ') then
spacer = '_'
do i = 23,25
if (ATOM(iatm)(i:i) .eq. ' ') ATOM(iatm)(i:i) = '_'
enddo
endif
write (output,905) ATOM(iatm)(13:17),
& ATOM(iatm)(18:22),spacer,ATOM(iatm)(23:27),
& Uprin(1),Uprin(2),Uprin(3),anisotropy,Uiso
905 format(A5,1X,A5,A1,A5,3F9.4,2X,F9.4,F9.4,F9.4)
c
c Also make a histogram of anisotropies
i = anisotropy * 20. + 1
histogram(i) = histogram(i) + 1
c
c And a table of <anis> by distance from center of mass
if (comflag .and. anisotropy.lt.1.0) then
dist = sqrt( (SPAM(1,iatm)-XCOM)**2
& + (SPAM(2,iatm)-YCOM)**2
& + (SPAM(3,iatm)-ZCOM)**2 )
i = (dist/dmax) * float(dshells) + 1
adist(i) = adist(i) + anisotropy
hdist(i) = hdist(i) + 1
endif
c
c End tabulation code
endif
c
c Skip hydrogens if requested
if (nohydro .and. ATOM(IATM)(77:78).eq.' H') goto 138
c
c Draw principal axes inside bounding ellipsoid
if (fancy.eq.1) then
do i=1,3
size = eigens(i) * pradius - 0.02
start(1) = x - size*evecs(1,i)
start(2) = y - size*evecs(2,i)
start(3) = z - size*evecs(3,i)
end(1) = x + size*evecs(1,i)
end(2) = y + size*evecs(2,i)
end(3) = z + size*evecs(3,i)
write (output,907) start, end
907 format(' 3',/,
& 3f9.3,' 0.02',3f9.3,' 0.02',' 0.5 1.0 0.3')
enddo
endif
c
c Draw longest principle axis only
c (experimental use only - not supported or documented)
if (fancy.eq.4) then
imax = 1
if (eigens(2).gt.eigens(imax)) imax = 2
if (eigens(3).gt.eigens(imax)) imax = 3
size = eigens(imax) * pradius
imin = 1
if (eigens(2).lt.eigens(imin)) imin = 2
if (eigens(3).lt.eigens(imin)) imin = 3
imed = 6 - (imax+imin)
size = size * eigens(imax)/eigens(imed)
start(1) = x - size*evecs(1,imax)
start(2) = y - size*evecs(2,imax)
start(3) = z - size*evecs(3,imax)
end(1) = x + size*evecs(1,imax)
end(2) = y + size*evecs(2,imax)
end(3) = z + size*evecs(3,imax)
write (output,907) start, end
endif
c
c Construct 3 quadrics corresponding to the 3 orthogonal planes
c through the center of our ellipsoid
if (fancy.eq.2 .or. fancy.eq.3) then
eigens(4) = 1.0
evecs(4,4)= 1.0
det = tinv4( evecinv, evecs )
call trnsp4( evecit, evecinv )
do k = 1,3
do i = 1,4
do j = 1,4
QQ(i,j) = 0.0
enddo
QQ(i,i) = 1. / (eigens(i)*eigens(i))
enddo
QQ(k,k) = 1000.
QQ(4,4) = -pradius*pradius
call tmul4( TEMP, QQ, evecinv )
call tmul4( QP, evecit, TEMP )
if (acflag) then
call A2RGB( anisotropy, red, green, blue )
red = red*red
green = green*green
blue = blue*blue
endif
write (output,151) 14, X,Y,Z, radlim, red, green, blue
write (output,152) QP(1,1),QP(2,2),QP(3,3),QP(1,2),QP(2,3),
& QP(1,3),QP(1,4),QP(2,4),QP(3,4),QP(4,4)
enddo
endif
c
endif
ENDIF
138 continue
IATM = IATM + 1
IF (IATM.LE.NATM) GOTO 130
c
c Set transparency for enclosing ellipoids
if (fancy.eq.1 .or. fancy.eq.3) then
write (output,'(A,/,A)') '9 Begin transparent ellipsoids','8 '
write (output,'(A)') ' 15. 0.6 1.0 1.0 1.0 0.6 0 0 0 0'
else if (fancy.eq.2 .or. fancy.eq.4) then
goto 160
endif
c
139 CONTINUE
c
c If we're just tabulating ellipticity, start making tables
c
if (tflag) then
total = 0
do i = 1,20
total = total + histogram(i)
end do
if (total.eq.0) then
write (noise,*) 'No ANISOU records found'
call exit(-1)
end if
if (nanis.eq.0) then
write (noise,*) 'No anisotropic atoms found'
call exit(-1)
end if
if (hwhacky) then
write(noise,*)
& 'You seem to have anisotropic hydrogens',
& ' - is this some kind of joke?'
nerrors = nerrors + 1
end if
write (hislun,'(A)') '# Anisotropy Fraction Number'
write (hislun,'(A)') '# range of atoms of atoms'
do i = 1,20
write (hislun,'(2F5.2,3X,F8.3,I10)')
& (float(i)-1.)/20., float(i)/20.,
& float(histogram(i))/total, histogram(i)
end do
c Calculate mean and sigma of distribution
sum_a2 = 0.0
sum_b2 = 0.0
sum_ab = 0.0
anis_mean = sum_A / float(nanis)
anis_sigma = 0.0
biso_mean = sum_B / float(nanis)
ccoef = 0.0
do i = 1,NATM
if (anisi(i).ne.0) then
sum_a2 = sum_a2 + (anisi(i) - anis_mean)**2
sum_b2 = sum_b2 + (Biso(i) - biso_mean)**2
sum_ab = sum_ab
& + (anisi(i)-anis_mean) * (Biso(i)-biso_mean)
end if
end do
if (nanis.gt.1) then
anis_sigma = sqrt( sum_a2 / float(nanis-1) )
ccoef = sum_ab / sqrt(sum_a2 * sum_b2)
end if
write (hislun,'(A)') '#'
write (hislun,'(A,I10)')'# number of ANISOU records:',nani
write (hislun,'(A,I10)')'# non-isotropic atoms:',nanis
write (hislun,'(A,I10)')'# isotropic atoms:',niso
if (nonpos.gt.0)
& write (hislun,'(A,I10)')'# nonpositive-definite APDs:',nonpos
if (nhyd.gt.0)
& write (hislun,'(A,I10)')'# ANISOU hydrogens:',nhyd
write (hislun,'(A)') '#'
write (hislun,'(A,F7.3)')
& '# correlation between anisotropy and B_iso:', ccoef
write (hislun,'(A)') '#'
write (hislun,'(A)') '# Anisotropy B_iso'
write (hislun,'(A)') '# AtomType mean sigma mean number'
write (hislun,'(A)') '# --------- ----------- ------ ------'
write (hislun,'(A,F7.3,F7.3,F7.2,I8)')
& '#| Total',anis_mean,anis_sigma,biso_mean,nanis
c
c If we're tabulating ellipticity, but not by atom_type, then we're done
c
if (.not. atflag) goto 145
140 continue
c
C Find an atom type we haven't done yet, exit if none left
c This only works if the PDB file contains the atom type in
c columns 77:78 (standard since sometime in 1997, but many
c files do not conform to this standard)
c
do i = 1, NATM
if (anisi(i).ne.0.0 .and. atom(i)(77:78).ne.' ') then
atomtype = atom(i)(77:78)
goto 141
end if
end do
goto 145
141 continue
sum_A = 0.0
sum_a2 = 0.0
biso_mean = 0.0
natype = 0
c
c Loop over atoms looking for the right ones
c
do i = 1, NATM
if (anisi(i).ne.0.0 .and. atomtype.eq.atom(i)(77:78)) then
natype = natype + 1
sum_A = sum_A + anisi(i)
end if
end do
anis_mean = sum_A / float(natype)
anis_sigma = 0.0
do i = 1, NATM
if (anisi(i).ne.0.0 .and. atomtype.eq.atom(i)(77:78)) then
sum_a2 = sum_a2 + (anisi(i)-anis_mean)**2
biso_mean = biso_mean + Biso(i)
atom(i)(77:78) = ' '
end if
end do
if (natype.gt.1) anis_sigma = sqrt( sum_a2 / float(natype-1) )
biso_mean = biso_mean / float(natype)
write (hislun,'(A,4X,A,F7.3,F7.3,F7.2,I8)')
& '#| ',atomtype,anis_mean,anis_sigma,biso_mean,natype
goto 140
end if
IATM = 1
goto 150
c
c Write out plot of mean anisotropy as a function of distance from c.o.m.
c The hisclean routine is not strictly necessary; it collapses shells at
c the extreme ranges of distance that contain only a few atoms.
c
145 continue
if (comflag) then
write (comlun,'(A/A,A/A/A)') '#',
& '# Mean anisotropy as a function of distance',
& ' from center of mass',
& '#',
& '# Distance <anis> #atoms'
call hisclean( adist, hdist, dshells, nanis )
do i = 1, dshells
if (hdist(i).gt.0) then
adist(i) = adist(i) / float(hdist(i))
dmid = (dmax/float(dshells))*(float(i)-0.5)
write (comlun,146) dmid, adist(i), hdist(i)
endif
enddo
146 format(F10.3,F10.3,I10)
endif
if (suvflag) goto 160
call exit(0)
c
c Second pass write a single sphere or ellipsoid for each atom
c
150 CONTINUE
IF (ATOM(IATM)(1:4).EQ.'ATOM' .OR.
& ATOM(IATM)(1:4).EQ.'HETA') THEN
if (nohydro .and. ATOM(IATM)(77:78).eq.' H') goto 154
X = SPAM(1,IATM)
Y = SPAM(2,IATM)
Z = SPAM(3,IATM)
ICOL = SPAM(5,IATM)
if (bcflag) then
call U2RGB( SPAM(4,IATM), Umin, Umax, RED, GREEN, BLUE )
RED = RED*RED
GREEN = GREEN*GREEN
BLUE = BLUE*BLUE
else if (acflag) then
call A2RGB( 1.0, 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
IF (.not. ellipses) THEN
RAD = sqrt(SPAM(4,IATM)) * PRADIUS
WRITE(OUTPUT,151) 2, X,Y,Z,RAD,RED,GREEN,BLUE
ELSE IF (uij(1,iatm).gt.0.) THEN
do i=1,6
anisou(i) = uij(i,iatm)
enddo
if (anitoquad(anisou,pradius,quadric,eigens,evecs).lt.0)then
write(noise,*) '*** Non-positive definite ellipsoid - ',
& atom(iatm)(13:26)
nerrors = nerrors + 1
Biso(iatm) = 0.0
red = 1.0
green = 0.0
blue = 1.0
endif
radlim = pradius * max( eigens(1),eigens(2),eigens(3) )
radlim = radlim * MARGIN
if (acflag) then
anisotropy = min( eigens(1),eigens(2),eigens(3) )
& / max( eigens(1),eigens(2),eigens(3) )
anisotropy = anisotropy * anisotropy
call A2RGB( anisotropy, red, green, blue )
red = red*red
green = green*green
blue = blue*blue
endif
if (fancy.eq.5 .or. fancy.eq.6) then
write (output,'(I2,/,A,I2,/,A)') 8,
& ' -1.0 -1.0 -1.0 -1.0 -1.0 0.0 0 0 0',
& fancy-1, 'ORTEP_LIKE'
if (fancy.eq.6) write (output,171) 0.5, 0.5, 0.5
write (output,172) 0, x,y,z, (evecs(i,1),i=1,3)
write (output,172) 0, x,y,z, (evecs(i,2),i=1,3)
write (output,172) 0, x,y,z, (evecs(i,3),i=1,3)
171 format('BOUNDING_COLOR ',3F6.3)
172 format('BOUNDING_PLANE ',I2,6F10.4)
endif
write (output,151) 14, x,y,z,radlim,red,green,blue
write (output,152) (quadric(i),i=1,10)
ELSE
RAD = sqrt(SPAM(4,IATM)) * PRADIUS
WRITE(OUTPUT,151) 2, X,Y,Z,RAD,RED,GREEN,BLUE
151 FORMAT(I2,/,3(1X,F8.3),4F8.3)
152 FORMAT(10F12.4)
ENDIF
goto 154
ENDIF
154 continue
IATM = IATM + 1
IF (IATM.LE.NATM) GOTO 150
IF (fancy.eq.1 .or. fancy.eq.3) then
write (output,'(A)') '9 end transparent ellipsoids'
endif
IF (fancy.eq.5 .or. fancy.eq.6) then
write (output,'(A)') '9 end ortep ellipsoids'
endif
160 continue
c
c Write bonds to file also. Atoms are considered bonded if they lie
c closer to each other than 0.6 * sum of VDW radii.
C If two atoms of different colors are bonded, make half-bond
C cylinders with each color.
C
if (nerrors.eq.0) write(noise,*)
& '... no errors found in input file'
if (radius.eq.0.0 .and. .not.suvflag) goto 210
if (suvflag) then
write (suvlun,'(A,A,F5.3,A)')
& 'Checking for neighboring atoms with dissimilar Uij ',
& '(Suv < ',suvlimit,')...'
suvbad = 0
endif
c
DO 202 IATM=1,NATM
IF (nohydro .AND. ATOM(IATM)(77:78).EQ.' H') GOTO 202
if (suvflag) then
if (Biso(IATM).eq.0.0) goto 202
if (uij(1,IATM).lt.0.) goto 202
endif
XI = SPAM(1,IATM)
YI = SPAM(2,IATM)
ZI = SPAM(3,IATM)
ICOL = SPAM(5,IATM)
VDWI = VDW(ICOL)
DO 201 JATM=IATM+1,NATM
CLOSE2 = 4.537
DX2 = (XI - SPAM(1,JATM))**2
if (dx2 .gt. close2) goto 201
DY2 = (YI - SPAM(2,JATM))**2
DZ2 = (ZI - SPAM(3,JATM))**2
DIST2 = DX2 + DY2 + DZ2
c
c Checking for bonded atoms with dissimilar Uij
if (suvflag) then
IF (DIST2 .GT. CLOSE2) GOTO 201
IF (Biso(JATM).eq.0.0) goto 201
if (uij(1,jatm).lt.0.) goto 201
CDEBUG Version 2.6c used explicit test on 0.6*VdW distance
CDEBUG but this is very slow so I have fixed CLOSE2 at the C-S bond length
CDEBUG It might be worth doing a first cut using, say, 2.25A (>S-S bond)
CDEBUG and then only check the actual VdW distance for pairs making the cut
C JCOL = SPAM(5,JATM)
C VDWJ = VDW(JCOL)
C CLOSE2 = (0.6 * (VDWI + VDWJ)) **2
C IF (DIST2 .GT. CLOSE2) GOTO 201
CDEBUG Add this section back to see if results match V2.6c numbers
similarity = Suv( uij(1,iatm), uij(1,jatm) )
if (similarity .lt. suvlimit) then
write (suvlun,161)
& ATOM(IATM)(13:17),ATOM(IATM)(18:27),
& ATOM(JATM)(13:17),ATOM(JATM)(18:27),
& similarity
suvbad = suvbad + 1
161 format(1X,A5,1X,A10,8X,A5,1X,A10,4X,'Suv = ',F8.4)
endif
if (tflag) goto 201
endif
c More stringent distance test when drawing bonds
IF (nohydro .AND. ATOM(JATM)(77:78).EQ.' H') GOTO 201
JCOL = SPAM(5,JATM)
VDWJ = VDW(JCOL)
CLOSE2 = (0.6 * (VDWI + VDWJ)) **2
IF (DIST2 .GT. CLOSE2) GOTO 201
c Don't draw bonds between alternate conformers of same residue
IF (ATOM(IATM)(17:17).ne.' '.and.ATOM(JATM)(17:17).ne.' '
& .and. ATOM(IATM)(17:17).ne.ATOM(JATM)(17:17)) goto 201
c
c Atoms coloured by B value
if (bcflag) then
write(output,211)
1 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),radius,
2 SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),radius,
3 1.0, 1.0, 1.0
call U2RGB( SPAM(4,IATM), Umin, Umax, RED1, GREEN1, BLUE1 )
call U2RGB( SPAM(4,JATM), Umin, Umax, RED2, GREEN2, BLUE2 )
write(output,212)
1 RED1,GREEN1,BLUE1, RED2,GREEN2,BLUE2, 0., 0., 0.
c Same color atoms
elseif (RGB(1,ICOL) .EQ. RGB(1,JCOL) .AND.
1 RGB(2,ICOL) .EQ. RGB(2,JCOL) .AND.
2 RGB(3,ICOL) .EQ. RGB(3,JCOL)) THEN
WRITE(OUTPUT,211)
1 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),radius,
2 SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),radius,
3 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
ELSE
DO K=1,3
center(K) = (SPAM(K,IATM)+SPAM(K,JATM))/2
ENDDO
WRITE(OUTPUT,211)
1 SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),radius,
2 center(1),center(2),center(3),radius,
3 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
WRITE(OUTPUT,211)
1 center(1),center(2),center(3),radius,
2 SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),radius,
3 RGB(1,JCOL),RGB(2,JCOL),RGB(3,JCOL)
ENDIF
201 CONTINUE
202 CONTINUE
210 CONTINUE
C211 FORMAT(1H3,/,11(f8.3))
211 FORMAT(1H3,/,3(1x,f8.3),f7.3,3(1x,f8.3),f7.3,3(f6.3))
212 FORMAT(2H17,/,9f8.3)
c
if (suvflag) then
if (suvbad.eq.0) write (suvlun,*) '... None!'
call exit(0)
endif
c
write (noise,'(/)')
write (noise,156) 'X min max center-of-mass:', XMIN, XMAX, xcom
write (noise,156) 'Y min max center-of-mass:', YMIN, YMAX, ycom
write (noise,156) 'Z min max center-of-mass:', ZMIN, ZMAX, zcom
write (noise,156) ' scale:', SCALE
156 format(1x,a,2f8.2,f10.3)
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
C Dummy routine to make linker happy (called by QINP in quadric.f)
SUBROUTINE TRANSF (X,Y,Z)
RETURN
END
SUBROUTINE ASSERT (LOGIC, DAMMIT)
LOGICAL LOGIC
CHARACTER*(*) DAMMIT
COMMON /ASSOUT/ NOISE
IF (LOGIC) RETURN
WRITE (NOISE,*) 'ERROR >>>>>> ',DAMMIT
C STOP 1234
CALL EXIT(-1)
END
CCC Return RGB triple that runs from dark blue at Bmin
CC to light red at Bmax
C
subroutine U2rgb( Uiso, Umin, Umax, r, g, b )
real Uiso, Umin, Umax, r, g, b
c
real fraction, h, s, v
c
fraction = (Uiso-Umin) / (Umax-Umin)
if (fraction.lt.0.) fraction = 0.
if (fraction.gt.1.) fraction = 1.
h = 240. * (1.-fraction)
s = 0.95
v = 0.75 + fraction/4.
call hsv2rgb( h, s, v, r, g, b )
return
end
CCC Return RGB triple that runs from
CC red for A=0.0 -> white for A=0.5 -> green for A=1.0
C
subroutine A2rgb( A, r, g, b )
real A, r, g, b
c
real fraction, h, s, v
c
if (A .lt. 0.5) h = 0.0
if (A .ge. 0.5) h = 120.
fraction = abs( (A-0.5)*2.0 )
c s = fraction**2
s = fraction
v = 1.0 - s/2.0
if (A .le. 0.0) then
h = 300.
v = 1.0
endif
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
CCC This subroutine is not strictly necessary.
CC It smooths the histogram/curve of Anisotropy by
C distance from center of mass
subroutine hisclean( value, number, shells, nanis )
c
integer shells
real value(shells)
integer number(shells)
integer nanis
c
integer minshell, maxshell, min10, max10
integer nsum
real vsum
c
if (nanis .lt. 1200) then
shells = shells / 2
do i = 1, shells
number(i) = number(2*i-1) + number(2*i)
value(i) = value(2*i-1) + value(2*i)
enddo
endif
c
do i = shells, 1, -1
if (number(i).gt.0) minshell = i
enddo
do i = 1, shells
if (number(i).gt.0) maxshell = i
enddo
nsum = 0
min10 = minshell
do i = minshell, shells
if (nsum + number(i) .gt. 10) then
goto 101
else
nsum = nsum + number(i)
min10 = i
endif
enddo
101 continue
nsum = 0
max10 = maxshell
do i = maxshell, 1, -1
if (nsum + number(i) .gt. 10) then
goto 102
else
nsum = nsum + number(i)
max10 = i
endif
enddo
102 continue
c
nsum = 0
vsum = 0.0
do i = minshell, min10
nsum = nsum + number(i)
vsum = vsum + value(i)
number(i) = 0
value(i) = 0.0
enddo
i = (minshell + min10) / 2
number(i) = nsum
value(i) = vsum
c
nsum = 0
vsum = 0.0
do i = maxshell, max10, -1
nsum = nsum + number(i)
vsum = vsum + value(i)
number(i) = 0
value(i) = 0.0
enddo
i = (maxshell + max10) / 2
number(i) = nsum
value(i) = vsum
c
return
end
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