diff options
Diffstat (limited to 'biology')
-rw-r--r-- | biology/ortep3/Makefile | 54 | ||||
-rw-r--r-- | biology/ortep3/distinfo | 1 | ||||
-rw-r--r-- | biology/ortep3/files/Makefile.ortep3 | 16 | ||||
-rw-r--r-- | biology/ortep3/files/extra-patch-aa | 424 | ||||
-rw-r--r-- | biology/ortep3/pkg-comment | 1 | ||||
-rw-r--r-- | biology/ortep3/pkg-descr | 24 | ||||
-rw-r--r-- | biology/ortep3/pkg-plist | 74 |
7 files changed, 594 insertions, 0 deletions
diff --git a/biology/ortep3/Makefile b/biology/ortep3/Makefile new file mode 100644 index 0000000..be8cd17 --- /dev/null +++ b/biology/ortep3/Makefile @@ -0,0 +1,54 @@ +# New ports collection makefile for: ORTEP-III +# Version required: 1.0 +# Date created: 1999-05-08 +# Whom: Ryo MIYAMOTO +# +# $Id$ +# + +DISTNAME= ortep +PKGNAME= ortep3-1.0 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/ortep/ +EXTRACT_SUFX= .tar.Z + +MAINTAINER= rmiya@cc.hirosaki-u.ac.jp + +LIB_DEPENDS= pgplot.5:${PORTSDIR}/graphics/pgplot + +pre-patch: + ${CP} ${FILESDIR}/Makefile.ortep3 ${WRKDIR}/${DISTNAME}/src/Makefile +.if defined(USEPGPLOT) + ${CP} ${FILESDIR}/patch-aa ${PATCHDIR}/ + ${CP} ${FILESDIR}/patch-ab ${PATCHDIR}/ +.endif + +post-patch: +.if defined(USEPGPLOT) + ${RM} ${PATCHDIR}/patch-aa + ${RM} ${PATCHDIR}/patch-ab +.endif + +do-build: + (cd ${WRKDIR}/${DISTNAME}/src && ${MAKE} all) + +pre-install: + strip ${WRKDIR}/${DISTNAME}/src/ortep3 + ${RM} -rf ${PREFIX}/share/doc/ortep3 + ${MKDIR} ${PREFIX}/share/doc/ortep3 + ${MKDIR} ${PREFIX}/share/doc/ortep3/examples + ${MKDIR} ${PREFIX}/share/doc/ortep3/man + ${MKDIR} ${PREFIX}/share/doc/ortep3/src + +do-install: + ${INSTALL_PROGRAM} ${WRKDIR}/${DISTNAME}/src/ortep3 ${PREFIX}/bin + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/examples/* \ + ${PREFIX}/share/doc/ortep3/examples + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/man/* \ + ${PREFIX}/share/doc/ortep3/man + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/src/000readme.txt \ + ${PREFIX}/share/doc/ortep3/src + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/README.1st \ + ${PREFIX}/share/doc/ortep3 + +.include <bsd.port.mk> diff --git a/biology/ortep3/distinfo b/biology/ortep3/distinfo new file mode 100644 index 0000000..518b17c --- /dev/null +++ b/biology/ortep3/distinfo @@ -0,0 +1 @@ +MD5 (ortep.tar.Z) = c183517406eda8854399287042dac075 diff --git a/biology/ortep3/files/Makefile.ortep3 b/biology/ortep3/files/Makefile.ortep3 new file mode 100644 index 0000000..bd8be39 --- /dev/null +++ b/biology/ortep3/files/Makefile.ortep3 @@ -0,0 +1,16 @@ +# Makefile for the ORTEP-III + +TARGET= ortep3 +SRC= ortep.f +OBJ= ortep.o +FFLAGS= -O2 +LFLAGS= + +all: ${OBJ} + ${FC} ${LFLAGS} -o ${TARGET} ${OBJ} + +ortep.o: ortep.f + ${FC} ${FFLAGS} -c $< + +clean: + rm -f *.o ${TARGET} diff --git a/biology/ortep3/files/extra-patch-aa b/biology/ortep3/files/extra-patch-aa new file mode 100644 index 0000000..05b4427 --- /dev/null +++ b/biology/ortep3/files/extra-patch-aa @@ -0,0 +1,424 @@ +*** src/ortep.f Tue Apr 2 01:34:17 1996 +--- src/ortep.f.pgplot Sat May 8 20:35:22 1999 +*************** +*** 5342,5366 **** + c *** DUMMY SCREEN OUTPUT (MAY BE REPLACED WITH SCREEN DRIVER CODE) + c ***************************************************************** + +! subroutine initsc +! return +! end +! +! subroutine penwsc(penw) +! return +! end +! +! subroutine colrsc(icolor) +! return +! end +! +! subroutine pensc(x,y,ipen) +! return +! end +! +! subroutine endsc +! return +! end + + c *** end of dummy screen output + c **************************************************************** +--- 5342,5366 ---- + c *** DUMMY SCREEN OUTPUT (MAY BE REPLACED WITH SCREEN DRIVER CODE) + c ***************************************************************** + +! c subroutine initsc +! c return +! c end +! +! c subroutine penwsc(penw) +! c return +! c end +! +! c subroutine colrsc(icolor) +! c return +! c end +! +! c subroutine pensc(x,y,ipen) +! c return +! c end +! +! c subroutine endsc +! c return +! c end + + c *** end of dummy screen output + c **************************************************************** +*************** +*** 5376,5558 **** + c or via e-mail to tjp@astro.caltech.edu. + c **************************************************************** + +! c subroutine initsc +! c character*10 outdev +! c common /ns/ npf,ndraw,norient,nvar +! c integer pgbeg + c +! c xwid=11. +! c yhgt=8.5 + c + c *** The following is for PGPLOT on an X-windows system. +! c outdev = '/XWINDOW' + c *** The following is for PGPLOT on an MS-DOS system. + c outdev = '/MS' + c *** The following is for PGPLOT on a Macintosh system. + c outdev = '/MAC' + +! c open(npf,status='scratch') + +! c if (pgbeg(0,' ',1,1) .ne. 1) call exitng(8) + + c switch black and white +! c call pgscr(0,1.,1.,1.) +! c call pgscr(1,0.,0.,0.) + + c set up drawing window +! c call pgpage +! c call pgqch(osize) +! c call pgsch(0.) +! c call pgvstd +! c call pgwnad(0.,xwid,0.,yhgt) +! c call pgsch(osize) +! c call pgbox('BCT',1.,0,'BCT',1.,0) +! c call pgsci(1) +! c call pgsfs(2) +! c call pgrect(10.4,11.,8.2,8.5) +! c call pgtext(10.5,8.3,'EXIT') + +! c return +! c end + +! c subroutine colrsc(icolor) + c *** set plot color + c *** in ORTEP icolor=0 => black + c *** PGPLOT is set up for 1=black +! c common /ns/ npf,ndraw,norient,nvar +! c icol=icolor +! c if (icol.eq.0) icol=1 +! c nvar=icol +! c if (ndraw.eq.1) call pgsci(icol) +! c if (ndraw.eq.9) write (npf,111) icol +! c 111 format('COL',1x,i2) +! c return +! c end + +! c subroutine penwsc(penw) + c *** change pen width + c *** PGPLOT measures pen width in 200ths of an inch +! c common /ns/ npf,ndraw,norient,nvar +! c ipenw=nint(.001*penw*200.) +! c if (ipenw.le.0) ipenw=1 +! c if (ipenw.gt.200) ipenw=200 +! c if (ndraw.eq.1) call pgslw(ipenw) +! c if (ndraw.eq.9) write (npf,111) ipenw +! c 111 format('WID',1x,i3) +! c return +! c end + +! c subroutine pensc(x,y,ipen) + c *** move the pen +! c common /trfac/ xtrans,ytrans +! c common /ns/ npf,ndraw,norient,nvar + +! c if (ipen.eq.2) then +! c if (ndraw.eq.1) call pgdraw(x+xtrans,y+ytrans) +! c if (ndraw.eq.9) write (npf,111) x+xtrans,y+ytrans +! c 111 format('LIN',2(1x,f10.6)) +! c end if +! c if (ipen.eq.3) then +! c if (ndraw.eq.1) call pgmove(x+xtrans,y+ytrans) +! c if (ndraw.eq.9) write (npf,112) x+xtrans,y+ytrans +! c 112 format('MOV',2(1x,f10.6)) +! c end if + +! c return +! c end + +! c subroutine endsc +! c common /ns/ npf,ndraw,norient,nvar + +! c call curssc +! c close(npf) + + c *** tell user to hit <enter> key +! c call pgsci(0) +! c call pgsfs(1) +! c call pgrect(7.5,11.,8.2,8.5) +! c call pgsci(1) +! c call pgsfs(2) +! c call pgrect(7.5,11.,8.2,8.5) +! c call pgsci(1) +! c call pgtext(7.6,8.3,'Hit <RETURN> or <ENTER> key') + +! c call pgend + +! c return +! c end + +! c subroutine curssc + c *** correlate screen cursor position with atom positions and display results +! c character ch +! c character*21 str +! c integer pgcurs +! c character*6 label,alabel +! c character*9 tomid,atomid +! c common /trfac/ xtrans,ytrans +! c common /ns/ npf,ndraw,norient,nvar +! +! c call pgsfs(1) +! c call pgscf(1) +! c call pgsch(1.) + + c *** get cursor position +! c 1 junk = pgcurs(x,y,ch) + +! c if (ch.eq.'x' .or. ch.eq.'X') return +! c if (ch.eq.'d' .or. ch.eq.'D') return +! c if (x.ge.10.4 .and. x.le.11. .and. y.ge.8.2 .and. y.le.8.5) return +! c if (ichar(ch).eq.13) return + + c *** initial values for variables +! c xpt = x +! c ypt = y +! c adiffx = .0625 +! c adiffy = .0625 +! c odiffx = adiffx +! c odiffy = adiffy +! c atomid = ' ' +! c alabel = ' ' +! c iflag = 0 +! c nflag = 0 +! +! c rewind(npf) +! +! c 2 read(npf,3,end=4) label,tomid,xx,yy +! c 3 format(11x,a6,3x,a9,4x,2f8.0) +! c diffx = abs(xx-xpt) +! c diffy = abs(yy-ypt) +! c if (diffx.le.adiffx .and. diffy.le.adiffy) nflag=nflag+1 +! c if (diffx.le.odiffx .and. diffy.le.odiffy) then +! c atomid = tomid +! c alabel = label +! c odiffx = diffx +! c odiffy = diffy +! c end if +! c go to 2 +! +! c 4 if (nflag.eq.0) write(str,5) +! c if (nflag.eq.1) write(str,6) alabel,atomid +! c if (nflag.gt.1) write(str,7) alabel,atomid +! c 5 format('Not near atom center') +! c 6 format(a6,1x,a9) +! c 7 format(a6,1x,a9,' + ??') + + c *** erase rectangle +! c call pgsci(0) +! c call pgsfs(1) +! c call pgrect(0.,2.8,8.2,8.5) + c *** redraw empty rectangle +! c call pgsci(1) +! c call pgsfs(2) +! c call pgrect(0.,2.8,8.2,8.5) + + c *** print atom information in rectangle +! c call pgtext(0.1,8.3,str) + +! c go to 1 + +! c end + + c *** end of PGPLOT specific routines + c **************************************************************** +--- 5376,5558 ---- + c or via e-mail to tjp@astro.caltech.edu. + c **************************************************************** + +! subroutine initsc +! character*10 outdev +! common /ns/ npf,ndraw,norient,nvar +! integer pgbeg + c +! xwid=11. +! yhgt=8.5 + c + c *** The following is for PGPLOT on an X-windows system. +! outdev = '/XWINDOW' + c *** The following is for PGPLOT on an MS-DOS system. + c outdev = '/MS' + c *** The following is for PGPLOT on a Macintosh system. + c outdev = '/MAC' + +! open(npf,status='scratch') + +! if (pgbeg(0,' ',1,1) .ne. 1) call exitng(8) + + c switch black and white +! call pgscr(0,1.,1.,1.) +! call pgscr(1,0.,0.,0.) + + c set up drawing window +! call pgpage +! call pgqch(osize) +! call pgsch(0.) +! call pgvstd +! call pgwnad(0.,xwid,0.,yhgt) +! call pgsch(osize) +! call pgbox('BCT',1.,0,'BCT',1.,0) +! call pgsci(1) +! call pgsfs(2) +! call pgrect(10.4,11.,8.2,8.5) +! call pgtext(10.5,8.3,'EXIT') + +! return +! end + +! subroutine colrsc(icolor) + c *** set plot color + c *** in ORTEP icolor=0 => black + c *** PGPLOT is set up for 1=black +! common /ns/ npf,ndraw,norient,nvar +! icol=icolor +! if (icol.eq.0) icol=1 +! nvar=icol +! if (ndraw.eq.1) call pgsci(icol) +! if (ndraw.eq.9) write (npf,111) icol +! 111 format('COL',1x,i2) +! return +! end + +! subroutine penwsc(penw) + c *** change pen width + c *** PGPLOT measures pen width in 200ths of an inch +! common /ns/ npf,ndraw,norient,nvar +! ipenw=nint(.001*penw*200.) +! if (ipenw.le.0) ipenw=1 +! if (ipenw.gt.200) ipenw=200 +! if (ndraw.eq.1) call pgslw(ipenw) +! if (ndraw.eq.9) write (npf,111) ipenw +! 111 format('WID',1x,i3) +! return +! end + +! subroutine pensc(x,y,ipen) + c *** move the pen +! common /trfac/ xtrans,ytrans +! common /ns/ npf,ndraw,norient,nvar + +! if (ipen.eq.2) then +! if (ndraw.eq.1) call pgdraw(x+xtrans,y+ytrans) +! if (ndraw.eq.9) write (npf,111) x+xtrans,y+ytrans +! 111 format('LIN',2(1x,f10.6)) +! end if +! if (ipen.eq.3) then +! if (ndraw.eq.1) call pgmove(x+xtrans,y+ytrans) +! if (ndraw.eq.9) write (npf,112) x+xtrans,y+ytrans +! 112 format('MOV',2(1x,f10.6)) +! end if + +! return +! end + +! subroutine endsc +! common /ns/ npf,ndraw,norient,nvar + +! call curssc +! close(npf) + + c *** tell user to hit <enter> key +! call pgsci(0) +! call pgsfs(1) +! call pgrect(7.5,11.,8.2,8.5) +! call pgsci(1) +! call pgsfs(2) +! call pgrect(7.5,11.,8.2,8.5) +! call pgsci(1) +! call pgtext(7.6,8.3,'Hit <RETURN> or <ENTER> key') + +! call pgend + +! return +! end + +! subroutine curssc + c *** correlate screen cursor position with atom positions and display results +! character ch +! character*21 str +! integer pgcurs +! character*6 label,alabel +! character*9 tomid,atomid +! common /trfac/ xtrans,ytrans +! common /ns/ npf,ndraw,norient,nvar +! +! call pgsfs(1) +! call pgscf(1) +! call pgsch(1.) + + c *** get cursor position +! 1 junk = pgcurs(x,y,ch) + +! if (ch.eq.'x' .or. ch.eq.'X') return +! if (ch.eq.'d' .or. ch.eq.'D') return +! if (x.ge.10.4 .and. x.le.11. .and. y.ge.8.2 .and. y.le.8.5) return +! if (ichar(ch).eq.13) return + + c *** initial values for variables +! xpt = x +! ypt = y +! adiffx = .0625 +! adiffy = .0625 +! odiffx = adiffx +! odiffy = adiffy +! atomid = ' ' +! alabel = ' ' +! iflag = 0 +! nflag = 0 +! +! rewind(npf) +! +! 2 read(npf,3,end=4) label,tomid,xx,yy +! 3 format(11x,a6,3x,a9,4x,2f8.0) +! diffx = abs(xx-xpt) +! diffy = abs(yy-ypt) +! if (diffx.le.adiffx .and. diffy.le.adiffy) nflag=nflag+1 +! if (diffx.le.odiffx .and. diffy.le.odiffy) then +! atomid = tomid +! alabel = label +! odiffx = diffx +! odiffy = diffy +! end if +! go to 2 +! +! 4 if (nflag.eq.0) write(str,5) +! if (nflag.eq.1) write(str,6) alabel,atomid +! if (nflag.gt.1) write(str,7) alabel,atomid +! 5 format('Not near atom center') +! 6 format(a6,1x,a9) +! 7 format(a6,1x,a9,' + ??') + + c *** erase rectangle +! call pgsci(0) +! call pgsfs(1) +! call pgrect(0.,2.8,8.2,8.5) + c *** redraw empty rectangle +! call pgsci(1) +! call pgsfs(2) +! call pgrect(0.,2.8,8.2,8.5) + + c *** print atom information in rectangle +! call pgtext(0.1,8.3,str) + +! go to 1 + +! end + + c *** end of PGPLOT specific routines + c **************************************************************** diff --git a/biology/ortep3/pkg-comment b/biology/ortep3/pkg-comment new file mode 100644 index 0000000..243dd03 --- /dev/null +++ b/biology/ortep3/pkg-comment @@ -0,0 +1 @@ +The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure diff --git a/biology/ortep3/pkg-descr b/biology/ortep3/pkg-descr new file mode 100644 index 0000000..29efc8d --- /dev/null +++ b/biology/ortep3/pkg-descr @@ -0,0 +1,24 @@ +ORTEP-III, the Oak Ridge Thermal Ellipsoid Plot Program for Crystal +Structure Illustrations is this one. + +(1) The program, examples, and online documentation are + available on the WWW site at + + http://www.ornl.gov/ortep/ortep.html + +(2) If you can use `pgplot' as screen drawing routine, type + + % make USEPGPLOT=yes + +(3) If you are not familier to `pgplot', note the followings: + + Before you use ortep3 with pgplot library, + run pgdisp server and setenv PGPLOT_DEV as + + % pgdisp & + % setenv PGPLOT_DEV /xdisp + + then you can see the ortep-drawing on a pgplot window. + +-- +rmiya diff --git a/biology/ortep3/pkg-plist b/biology/ortep3/pkg-plist new file mode 100644 index 0000000..6544d0f --- /dev/null +++ b/biology/ortep3/pkg-plist @@ -0,0 +1,74 @@ +bin/ortep3 +share/doc/ortep3/README.1st +share/doc/ortep3/examples/000index.txt +share/doc/ortep3/examples/ATOMS.DAT +share/doc/ortep3/examples/READIN.F +share/doc/ortep3/examples/README.LYSO +share/doc/ortep3/examples/ahelix.dat +share/doc/ortep3/examples/ahelix.hp +share/doc/ortep3/examples/ahelix.ps +share/doc/ortep3/examples/amylose.dat +share/doc/ortep3/examples/amylose.hp +share/doc/ortep3/examples/amylose.ps +share/doc/ortep3/examples/b12.dat +share/doc/ortep3/examples/b12.hp +share/doc/ortep3/examples/b12.ps +share/doc/ortep3/examples/bcc.dat +share/doc/ortep3/examples/bcc.hp +share/doc/ortep3/examples/bcc.ps +share/doc/ortep3/examples/benzofuran.dat +share/doc/ortep3/examples/benzofuran.hp +share/doc/ortep3/examples/benzofuran.ps +share/doc/ortep3/examples/cubane.dat +share/doc/ortep3/examples/cubane.hp +share/doc/ortep3/examples/cubane.ps +share/doc/ortep3/examples/cyclobutane.dat +share/doc/ortep3/examples/cyclobutane.hp +share/doc/ortep3/examples/cyclobutane.ps +share/doc/ortep3/examples/diamond.dat +share/doc/ortep3/examples/diamond.hp +share/doc/ortep3/examples/diamond.ps +share/doc/ortep3/examples/fcc.dat +share/doc/ortep3/examples/fcc.hp +share/doc/ortep3/examples/fcc.ps +share/doc/ortep3/examples/graphite.dat +share/doc/ortep3/examples/graphite.hp +share/doc/ortep3/examples/graphite.ps +share/doc/ortep3/examples/hcp.dat +share/doc/ortep3/examples/hcp.hp +share/doc/ortep3/examples/hcp.ps +share/doc/ortep3/examples/hyox3h.dat +share/doc/ortep3/examples/hyox3h.hp +share/doc/ortep3/examples/hyox3h.ps +share/doc/ortep3/examples/lyso.dat +share/doc/ortep3/examples/lyso1.hp +share/doc/ortep3/examples/lyso1.ps +share/doc/ortep3/examples/lyso2.hp +share/doc/ortep3/examples/lyso2.ps +share/doc/ortep3/examples/lyso3.hp +share/doc/ortep3/examples/lyso3.ps +share/doc/ortep3/examples/mgpyrin.dat +share/doc/ortep3/examples/mgpyrin.hp +share/doc/ortep3/examples/mgpyrin.ps +share/doc/ortep3/examples/nacl.dat +share/doc/ortep3/examples/nacl.hp +share/doc/ortep3/examples/nacl.ps +share/doc/ortep3/examples/norbornanone.dat +share/doc/ortep3/examples/norbornanone.hp +share/doc/ortep3/examples/norbornanone.ps +share/doc/ortep3/examples/thiourea.dat +share/doc/ortep3/examples/thiourea.hp +share/doc/ortep3/examples/thiourea.ps +share/doc/ortep3/examples/thornitrate.dat +share/doc/ortep3/examples/thornitrate.hp +share/doc/ortep3/examples/thornitrate.ps +share/doc/ortep3/examples/xenate.dat +share/doc/ortep3/examples/xenate.hp +share/doc/ortep3/examples/xenate.ps +@dirrm share/doc/ortep3/examples +share/doc/ortep3/man/000readme.txt +share/doc/ortep3/man/instrsum.ps +@dirrm share/doc/ortep3/man +share/doc/ortep3/src/000readme.txt +@dirrm share/doc/ortep3/src +@dirrm share/doc/ortep3 |