diff options
author | ijliao <ijliao@FreeBSD.org> | 2001-01-25 01:58:44 +0800 |
---|---|---|
committer | ijliao <ijliao@FreeBSD.org> | 2001-01-25 01:58:44 +0800 |
commit | 280ec3e7fa1bd61a5d4b9c5802d4fb7835fa16de (patch) | |
tree | 8c3437a7c4ea0b7b7eb1db08e84fd4715767753a /biology | |
parent | 9905c1ce2834b70acbd3fa8f90266f19f8b0755e (diff) | |
download | freebsd-ports-gnome-280ec3e7fa1bd61a5d4b9c5802d4fb7835fa16de.tar.gz freebsd-ports-gnome-280ec3e7fa1bd61a5d4b9c5802d4fb7835fa16de.tar.zst freebsd-ports-gnome-280ec3e7fa1bd61a5d4b9c5802d4fb7835fa16de.zip |
update from 3.7 to 3.8
PR: 24371
Submitted by: MAINTAINER
Diffstat (limited to 'biology')
-rw-r--r-- | biology/tinker/Makefile | 60 | ||||
-rw-r--r-- | biology/tinker/distinfo | 2 | ||||
-rw-r--r-- | biology/tinker/files/patch-aa | 97 | ||||
-rw-r--r-- | biology/tinker/files/patch-ab | 12 | ||||
-rw-r--r-- | biology/tinker/files/patch-ac | 13 | ||||
-rw-r--r-- | biology/tinker/files/patch-ad | 7 | ||||
-rw-r--r-- | biology/tinker/files/patch-ae | 7 | ||||
-rw-r--r-- | biology/tinker/files/patch-af | 11 | ||||
-rw-r--r-- | biology/tinker/files/patch-ag | 11 | ||||
-rw-r--r-- | biology/tinker/files/patch-ah | 5 | ||||
-rw-r--r-- | biology/tinker/files/patch-ai | 5 | ||||
-rw-r--r-- | biology/tinker/files/patch-aj | 5 | ||||
-rw-r--r-- | biology/tinker/files/patch-ak | 7 | ||||
-rw-r--r-- | biology/tinker/files/patch-al | 7 | ||||
-rw-r--r-- | biology/tinker/pkg-descr | 15 | ||||
-rw-r--r-- | biology/tinker/pkg-plist | 163 | ||||
-rw-r--r-- | biology/tinker/pkg-plist.viewer | 399 | ||||
-rw-r--r-- | biology/tinker/scripts/build_viewer | 47 |
18 files changed, 706 insertions, 167 deletions
diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile index 1b1129da1393..9436e26f402b 100644 --- a/biology/tinker/Makefile +++ b/biology/tinker/Makefile @@ -6,7 +6,7 @@ # PORTNAME= tinker -PORTVERSION= 3.7 +PORTVERSION= 3.8 CATEGORIES= biology MASTER_SITES= ftp://dasher.wustl.edu/pub/ DISTNAME= ${PORTNAME} @@ -37,6 +37,25 @@ INSTALL_TARGET= rename RESTRICTED= author requests no distribution except from his FTP site + +.if defined(WANT_VIEWER) +.if ${XFREE86_VERSION} == 3 +BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake +.elif ${XFREE86_VERSION} == 4 +BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake-4 +.endif +PLIST= ${PKGDIR}/pkg-plist.viewer +USE_XLIB= yes +post-build: + ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer +.else +pre-extract: + @${ECHO} "" + @${ECHO} If you would like to also build + @${ECHO} the molecular viewer, define WANT_VIEWER. + @${ECHO} "" +.endif + post-install: ${MKDIR} ${PREFIX}/share/tinker ${MKDIR} ${PREFIX}/share/tinker/params @@ -44,6 +63,7 @@ post-install: ${PREFIX}/share/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/params/* \ ${PREFIX}/share/tinker/params + .if !defined(NOPORTDOCS) ${MKDIR} ${PREFIX}/share/doc/tinker ${MKDIR} ${PREFIX}/share/examples/tinker @@ -51,54 +71,62 @@ ${PREFIX}/share/tinker/params ${MKDIR} ${PREFIX}/share/tinker/test ${INSTALL_DATA} ${WRKDIR}/tinker/doc/README \ ${PREFIX}/share/doc/tinker + ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.gz \ +${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.pdf \ ${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.ps \ ${PREFIX}/share/doc/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.Z \ -${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.txt \ ${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/README \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/anion.dyn0 \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.1st \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.in* \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.boat \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.key \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.cell \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.log \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.chair \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.dat \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/argon.1st \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.dyn0 \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/crambin.pdb \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.key \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.boat \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.log \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.chair \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.pdb \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/example/formamide.cell \ + ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \ ${PREFIX}/share/examples/tinker ${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \ ${PREFIX}/share/examples/tinker ${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/*.run \ ${PREFIX}/share/examples/tinker - ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.input \ + ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.dyn0 \ +${PREFIX}/share/tinker/bench + ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.log \ ${PREFIX}/share/tinker/bench ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.key \ ${PREFIX}/share/tinker/bench ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.xyz \ ${PREFIX}/share/tinker/bench - ${INSTALL_DATA} ${WRKDIR}/tinker/bench/water.dyn0 \ -${PREFIX}/share/tinker/bench ${INSTALL_DATA} ${WRKDIR}/tinker/bench/results* \ ${PREFIX}/share/tinker/bench ${INSTALL_SCRIPT} ${WRKDIR}/tinker/bench/*.run \ ${PREFIX}/share/tinker/bench ${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${PREFIX}/share/tinker/test .endif + +.if defined(WANT_VIEWER) + ${MKDIR} ${PREFIX}/share/tinker/rasmol + ${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin + ${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp ${PREFIX}/share/tinker/rasmol + +.endif + @${ECHO} "" @${ECHO} " **********************************************************" @${ECHO} " The author requests that you return a license form " diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo index 3f6df0ec8b72..673edd1ec5f2 100644 --- a/biology/tinker/distinfo +++ b/biology/tinker/distinfo @@ -1 +1 @@ -MD5 (tinker.tar.gz) = 057d58a10c3b35370b04f3239fbdce1d +MD5 (tinker.tar.gz) = e3784b524b5e8acf80b592657c457602 diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa index 526ce65e518c..0d3f17e2ce38 100644 --- a/biology/tinker/files/patch-aa +++ b/biology/tinker/files/patch-aa @@ -1,5 +1,5 @@ ---- ../make/Makefile.orig Mon Jul 12 10:56:36 1999 -+++ ../make/Makefile Wed May 31 16:00:31 2000 +--- ../make/Makefile.orig Mon Jan 15 12:39:52 2001 ++++ ../make/Makefile Mon Jan 15 15:48:37 2001 @@ -9,8 +9,8 @@ ## ## 1. make all Build all the TINKER executables @@ -24,41 +24,36 @@ #################################################################### ## Known Machine Types; Uncomment One of the Following Sections ## -@@ -45,13 +45,13 @@ - ## Compiler: DEC Fortran 77/90, V4.1 +@@ -87,12 +87,12 @@ + ## Compiler: GNU g77 ## --F77 = /usr/bin/f77 --RM = /sbin/rm +-F77 = /usr/bin/g77 -LIBS = -F77FLAGS = -c --OPTFLAGS = -fast -tune host --LIBFLAGS = -rlv --LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched -+#F77 = /usr/bin/f77 -+#RM = /sbin/rm +-OPTFLAGS = -O3 -ffast-math +-LIBFLAGS = -crusv +-LINKFLAGS = ++#F77 = /usr/bin/g77 +#LIBS = +#F77FLAGS = -c -+#OPTFLAGS = -fast -tune host -+#LIBFLAGS = -rlv -+#LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched ++#OPTFLAGS = -O3 -ffast-math ++#LIBFLAGS = -crusv ++#LINKFLAGS = ## - ## Machine: Silicon Graphics -@@ -104,6 +104,40 @@ - #diagq.o: - # ${F77} ${F77FLAGS} -ffast-math diagq.f + ## Machine: IntelPC / Linux +@@ -108,6 +108,35 @@ + #LIBFLAGS = -crusv + #LINKFLAGS = +## -+## Machine: IntelPC -+## CPU Type: Pentium Pro -+## Oper Sys: FreeBSD 3.0 -+## Compiler: f77(f2c/gcc version 2.7.2.1) || egcs g77 -+## ++## Machine: IntelPC / FreeBSD ++## CPU Type: Intel, AMD, Cyrix ++## Oper Sys: FreeBSD 4.2 ++## Compiler: f77 , aka g77 + +F77 = ${FC} -+RM = /bin/rm -+ +.if ${FC}==f77 +.if !defined(HAVE_G2C) +LIBS = -lU77 @@ -70,32 +65,38 @@ +LINKFLAGS = +.endif +.elseif ${FC}==g77 -+LIBS= ++LIBS = +F77FLAGS = -Wno-globals -fno-globals -c -w +LINKFLAGS = +.endif + +OPTFLAGS = ${FFLAGS} -ffast-math +.if ${MACHINE_ARCH} == "i386" -+OPTFLAGS+= -malign-double ++OPTFLAGS += -malign-double +.endif +LIBFLAGS = -rcuv -+diagq.o: -+ ${F77} ${F77FLAGS} -ffast-math diagq.f + ################################################################# ## Should not be Necessary to Change Things Below this Point ## ################################################################# -@@ -775,6 +809,7 @@ - volume2.o \ - writeout.o \ - xyzatm.o -+ ranlib libtinker.a +@@ -486,11 +515,13 @@ + xyzpdb.x \ + xyzsybyl.x + ++.SUFFIXES: .x ++ + .f.o: + ${F77} ${F77FLAGS} ${OPTFLAGS} $*.f + +-%.x: %.o libtinker.a +- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS} ++.o.x: libtinker.a ++ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} + + all: ${EXEFILES} - alchemy.x: - ${F77} ${LINKFLAGS} -o alchemy.x alchemy.o libtinker.a ${LIBS} -@@ -868,51 +903,51 @@ - ${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS} +@@ -501,56 +532,56 @@ + cat *.i *.f > tinker.txt rename: - mv alchemy.x $(BINDIR)/alchemy @@ -104,6 +105,7 @@ - mv archive.x $(BINDIR)/archive - mv correlate.x $(BINDIR)/correlate - mv crystal.x $(BINDIR)/crystal +- mv diffuse.x $(BINDIR)/diffuse - mv distgeom.x $(BINDIR)/distgeom - mv document.x $(BINDIR)/document - mv dynamic.x $(BINDIR)/dynamic @@ -112,8 +114,10 @@ - mv intxyz.x $(BINDIR)/intxyz - mv minimize.x $(BINDIR)/minimize - mv minirot.x $(BINDIR)/minirot +- mv minrigid.x $(BINDIR)/minrigid - mv newton.x $(BINDIR)/newton - mv newtrot.x $(BINDIR)/newtrot +- mv nucleic.x $(BINDIR)/nucleic - mv optimize.x $(BINDIR)/optimize - mv optirot.x $(BINDIR)/optirot - mv optrigid.x $(BINDIR)/optrigid @@ -123,10 +127,12 @@ - mv pss.x $(BINDIR)/pss - mv pssrigid.x $(BINDIR)/pssrigid - mv pssrot.x $(BINDIR)/pssrot +- mv radial.x $(BINDIR)/radial - mv saddle.x $(BINDIR)/saddle - mv scan.x $(BINDIR)/scan - mv sniffer.x $(BINDIR)/sniffer - mv spacefill.x $(BINDIR)/spacefill +- mv spectrum.x $(BINDIR)/spectrum - mv superpose.x $(BINDIR)/superpose - mv sybylxyz.x $(BINDIR)/sybylxyz - mv testgrad.x $(BINDIR)/testgrad @@ -149,6 +155,7 @@ + ${INSTALL_PROGRAM} archive.x $(BINDIR)/archive + ${INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate + ${INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal ++ ${INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse + ${INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom + ${INSTALL_PROGRAM} document.x $(BINDIR)/document + ${INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic @@ -157,8 +164,10 @@ + ${INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz + ${INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize + ${INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot ++ ${INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid + ${INSTALL_PROGRAM} newton.x $(BINDIR)/newton + ${INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot ++ ${INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic + ${INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize + ${INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot + ${INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid @@ -168,10 +177,12 @@ + ${INSTALL_PROGRAM} pss.x $(BINDIR)/pss + ${INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid + ${INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot ++ ${INSTALL_PROGRAM} radial.x $(BINDIR)/radial + ${INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle + ${INSTALL_PROGRAM} scan.x $(BINDIR)/scan + ${INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer + ${INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill ++ ${INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum + ${INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose + ${INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz + ${INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad @@ -191,3 +202,13 @@ remove_links: rm -f $(LINKDIR)/alchemy +@@ -671,8 +702,8 @@ + bspline.o \ + calendar.o \ + center.o \ +- chkxyz.o \ + cholesky.o \ ++ chkxyz.o \ + clock.o \ + cluster.o \ + column.o \ diff --git a/biology/tinker/files/patch-ab b/biology/tinker/files/patch-ab deleted file mode 100644 index 5fbcd518580c..000000000000 --- a/biology/tinker/files/patch-ab +++ /dev/null @@ -1,12 +0,0 @@ ---- ../doc/license.txt.orig Wed Jun 16 13:54:43 1999 -+++ ../doc/license.txt Sat Jun 19 14:19:18 1999 -@@ -1,7 +1,7 @@ -- TINKER Software Tools for Molecular Design -+ TINKER - Software Tools for Molecular Design - - Version 3.7 June 1999 -- Copyright © 1990-1999 Jay William Ponder -+ Copyright (c) 1990-1999 Jay William Ponder - - TINKER is a modular program package for molecular mechanics- - based potential energy calculations, molecular dynamics diff --git a/biology/tinker/files/patch-ac b/biology/tinker/files/patch-ac deleted file mode 100644 index e21d420dce16..000000000000 --- a/biology/tinker/files/patch-ac +++ /dev/null @@ -1,13 +0,0 @@ -*** ../doc/summary.txt.orig Fri Aug 28 23:50:17 1998 ---- ../doc/summary.txt Fri Aug 28 23:50:33 1998 -*************** -*** 1,4 **** -! TINKER Software Tools for Molecular Design - - Jay Ponder Lab, Dept. of Biochemistry & Molecular - Biophysics, ---- 1,4 ---- -! TINKER - Software Tools for Molecular Design - - Jay Ponder Lab, Dept. of Biochemistry & Molecular - Biophysics, diff --git a/biology/tinker/files/patch-ad b/biology/tinker/files/patch-ad deleted file mode 100644 index 7171c8290043..000000000000 --- a/biology/tinker/files/patch-ad +++ /dev/null @@ -1,7 +0,0 @@ -*** ../bench/crambin.run.orig Sat Aug 29 21:54:06 1998 ---- ../bench/crambin.run Sat Aug 29 21:54:20 1998 -*************** -*** 1 **** -! ../bin/timer < crambin.input ---- 1 ---- -! timer < crambin.input diff --git a/biology/tinker/files/patch-ae b/biology/tinker/files/patch-ae deleted file mode 100644 index d8d1efdaf941..000000000000 --- a/biology/tinker/files/patch-ae +++ /dev/null @@ -1,7 +0,0 @@ -*** ../bench/crystal.run.orig Sat Aug 29 21:56:20 1998 ---- ../bench/crystal.run Sat Aug 29 21:56:30 1998 -*************** -*** 1 **** -! ../bin/timer < crystal.input ---- 1 ---- -! timer < crystal.input diff --git a/biology/tinker/files/patch-af b/biology/tinker/files/patch-af deleted file mode 100644 index a1fa92a8963a..000000000000 --- a/biology/tinker/files/patch-af +++ /dev/null @@ -1,11 +0,0 @@ -*** ../bench/water.run.orig Sat Aug 29 21:56:44 1998 ---- ../bench/water.run Sat Aug 29 21:56:58 1998 -*************** -*** 1,3 **** - cp water.dyn0 water.dyn -! time ../bin/dynamic < water.input - rm water.dyn ---- 1,3 ---- - cp water.dyn0 water.dyn -! time dynamic < water.input - rm water.dyn diff --git a/biology/tinker/files/patch-ag b/biology/tinker/files/patch-ag new file mode 100644 index 000000000000..a1084876fe7d --- /dev/null +++ b/biology/tinker/files/patch-ag @@ -0,0 +1,11 @@ +--- sizes.i.orig Fri Jan 12 11:43:06 2001 ++++ sizes.i Fri Jan 12 11:43:38 2001 +@@ -52,7 +52,7 @@ + integer maxvar,maxopt,maxhess,maxlight,maxvib,maxgeo,maxcell + integer maxring,maxfix,maxbio,maxres,maxamino,maxnuc,maxbnd + integer maxang,maxtors,maxpi,maxpib,maxpit +- parameter (maxatm=10000) ++ parameter (maxatm=2500) + parameter (maxval=4) + parameter (maxgrp=100) + parameter (maxtyp=1000) diff --git a/biology/tinker/files/patch-ah b/biology/tinker/files/patch-ah new file mode 100644 index 000000000000..c3f23dd2e057 --- /dev/null +++ b/biology/tinker/files/patch-ah @@ -0,0 +1,5 @@ +--- ../bench/bench-1.run.orig Tue Jan 9 14:28:53 2001 ++++ ../bench/bench-1.run Tue Jan 9 14:29:19 2001 +@@ -1 +1 @@ +-../bin/timer bench-1 1 y ++timer bench-1 1 y diff --git a/biology/tinker/files/patch-ai b/biology/tinker/files/patch-ai new file mode 100644 index 000000000000..643cc82de1ed --- /dev/null +++ b/biology/tinker/files/patch-ai @@ -0,0 +1,5 @@ +--- ../bench/bench-2.run.orig Tue Jan 9 14:29:26 2001 ++++ ../bench/bench-2.run Tue Jan 9 14:29:33 2001 +@@ -1 +1 @@ +-../bin/timer bench-2 1 y ++timer bench-2 1 y diff --git a/biology/tinker/files/patch-aj b/biology/tinker/files/patch-aj new file mode 100644 index 000000000000..1f36c30fe172 --- /dev/null +++ b/biology/tinker/files/patch-aj @@ -0,0 +1,5 @@ +--- ../bench/bench-3.run.orig Tue Jan 9 14:29:40 2001 ++++ ../bench/bench-3.run Tue Jan 9 14:29:53 2001 +@@ -1 +1 @@ +-time ../bin/vibrate bench-3 0 ++time vibrate bench-3 0 diff --git a/biology/tinker/files/patch-ak b/biology/tinker/files/patch-ak new file mode 100644 index 000000000000..d0549d42829d --- /dev/null +++ b/biology/tinker/files/patch-ak @@ -0,0 +1,7 @@ +--- ../bench/bench-4.run.orig Tue Jan 9 14:29:59 2001 ++++ ../bench/bench-4.run Tue Jan 9 14:30:14 2001 +@@ -1,3 +1,3 @@ + cp bench-4.dyn0 bench-4.dyn +-time ../bin/dynamic bench-4 1000 1.0 10.0 2 298.0 ++time dynamic bench-4 1000 1.0 10.0 2 298.0 + rm bench-4.dyn diff --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-al new file mode 100644 index 000000000000..8127254d2daa --- /dev/null +++ b/biology/tinker/files/patch-al @@ -0,0 +1,7 @@ +--- ../bench/bench-5.run.orig Tue Jan 9 14:30:18 2001 ++++ ../bench/bench-5.run Tue Jan 9 14:30:29 2001 +@@ -1,3 +1,3 @@ + cp bench-5.dyn0 bench-5.dyn +-time ../bin/dynamic bench-5 100 1.0 10.0 2 298.0 ++time dynamic bench-5 100 1.0 10.0 2 298.0 + rm bench-5.dyn diff --git a/biology/tinker/pkg-descr b/biology/tinker/pkg-descr index eee99649421d..a34d7f69fd53 100644 --- a/biology/tinker/pkg-descr +++ b/biology/tinker/pkg-descr @@ -1,10 +1,15 @@ Tinker is a set of small programs for doing general purpose molecular -modeling. Tools are included for energy minimizations, geometry -calculations, and molecular analysis calculations. Tools for converting -coordinate sets are also provided. +modeling calculations. Tools are included for energy minimizations, +geometry calculations, simulated annealing, molecular dynamics, and +molecular analysis calculations. Tools for converting coordinate sets +are also provided. Tinker employs several force fields and minimization +techniques. -Tinker employs several force fields and minimizaation techniques. -Simulated annealing and molecular dynamics can be performed with Tinker. +This port sets the maxatm value to 2500 atoms. This should be +sufficient for most molecular systems. Should you need to work with +larger systems you can set the maxatm parameter in the sizes.i file +located in the tinker/source directory and recompile. Note that if it +is set too large that tinker programs will abort and core dump. For more information about Tinker see: diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist index 012299f88e88..880a1d1110ce 100644 --- a/biology/tinker/pkg-plist +++ b/biology/tinker/pkg-plist @@ -4,6 +4,7 @@ bin/anneal bin/archive bin/correlate bin/crystal +bin/diffuse bin/distgeom bin/document bin/dynamic @@ -12,8 +13,10 @@ bin/intedit bin/intxyz bin/minimize bin/minirot +bin/minrigid bin/newton bin/newtrot +bin/nucleic bin/optimize bin/optirot bin/optrigid @@ -23,10 +26,12 @@ bin/protein bin/pss bin/pssrigid bin/pssrot +bin/radial bin/saddle bin/scan bin/sniffer bin/spacefill +bin/spectrum bin/superpose bin/sybylxyz bin/testgrad @@ -43,95 +48,92 @@ bin/xyzedit bin/xyzint bin/xyzpdb bin/xyzsybyl -share/tinker/bench/crambin.input -share/tinker/bench/crambin.key -share/tinker/bench/crambin.run -share/tinker/bench/crambin.xyz -share/tinker/bench/crystal.input -share/tinker/bench/crystal.key -share/tinker/bench/crystal.run -share/tinker/bench/crystal.xyz -share/tinker/bench/results-2.3 -share/tinker/bench/results-2.4 -share/tinker/bench/results-2.9 -share/tinker/bench/results-3.1 -share/tinker/bench/results-3.2 -share/tinker/bench/results-3.4 -share/tinker/bench/results-3.5 -share/tinker/bench/results-3.7 -share/tinker/bench/water.dyn0 -share/tinker/bench/water.input -share/tinker/bench/water.key -share/tinker/bench/water.run -share/tinker/bench/water.xyz share/doc/tinker/README +share/doc/tinker/announce.txt share/doc/tinker/guide.pdf -share/doc/tinker/guide.ps.Z +share/doc/tinker/guide.ps.gz share/doc/tinker/guide.txt share/doc/tinker/license.pdf -share/doc/tinker/license.ps.Z +share/doc/tinker/license.ps share/doc/tinker/license.txt -share/doc/tinker/logo.ps.Z -share/doc/tinker/spine.ps +share/doc/tinker/logo.pdf +share/doc/tinker/logo.ps.gz share/doc/tinker/summary.pdf share/doc/tinker/summary.ps share/doc/tinker/summary.txt share/examples/tinker/README +share/examples/tinker/anion.dat share/examples/tinker/anion.dyn0 -share/examples/tinker/anion.in1 -share/examples/tinker/anion.in2 share/examples/tinker/anion.key share/examples/tinker/anion.log share/examples/tinker/anion.run share/examples/tinker/anion.xyz share/examples/tinker/argon.1st -share/examples/tinker/argon.in1 -share/examples/tinker/argon.in2 share/examples/tinker/argon.key share/examples/tinker/argon.log share/examples/tinker/argon.run share/examples/tinker/clean.make -share/examples/tinker/cluster.in1 +share/examples/tinker/cluster.dat share/examples/tinker/cluster.key share/examples/tinker/cluster.log share/examples/tinker/cluster.run share/examples/tinker/cluster.xyz -share/examples/tinker/crambin.in1 -share/examples/tinker/crambin.in2 -share/examples/tinker/crambin.in3 share/examples/tinker/crambin.key share/examples/tinker/crambin.log share/examples/tinker/crambin.pdb share/examples/tinker/crambin.run share/examples/tinker/cyclohex.boat share/examples/tinker/cyclohex.chair -share/examples/tinker/cyclohex.in1 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share/tinker/params/amber.prm +share/tinker/params/amberN.prm share/tinker/params/charmm.prm share/tinker/params/emr.prm share/tinker/params/hoch.prm @@ -147,19 +149,18 @@ share/tinker/params/water.prm share/tinker/test/README share/tinker/test/ala20.key share/tinker/test/ala20.xyz -share/tinker/test/annulene.int -share/tinker/test/annulene.key -share/tinker/test/annulene.xyz -share/tinker/test/annulene2.key -share/tinker/test/annulene2.xyz -share/tinker/test/annulene3.key -share/tinker/test/annulene3.xyz +share/tinker/test/alkane.key +share/tinker/test/alkane.xyz share/tinker/test/arach.int share/tinker/test/arach.key share/tinker/test/arach.xyz share/tinker/test/azulene.int share/tinker/test/azulene.key share/tinker/test/azulene.xyz +share/tinker/test/bdna.int +share/tinker/test/bdna.key +share/tinker/test/bdna.seq +share/tinker/test/bdna.xyz share/tinker/test/bearing.key share/tinker/test/bearing.pdb share/tinker/test/bearing.xyz @@ -169,6 +170,13 @@ share/tinker/test/bearing2.xyz share/tinker/test/benzene.int share/tinker/test/benzene.key share/tinker/test/benzene.xyz +share/tinker/test/bowl.int +share/tinker/test/bowl.key +share/tinker/test/bowl.xyz +share/tinker/test/bowl2.key +share/tinker/test/bowl2.xyz +share/tinker/test/bowl3.key +share/tinker/test/bowl3.xyz share/tinker/test/butane.int share/tinker/test/butane.key share/tinker/test/butane.xyz @@ -195,13 +203,20 @@ share/tinker/test/c7ax.xyz share/tinker/test/c7eq.key share/tinker/test/c7eq.seq share/tinker/test/c7eq.xyz +share/tinker/test/calmodulin.key +share/tinker/test/calmodulin.pdb +share/tinker/test/calmodulin.seq +share/tinker/test/calmodulin.xyz share/tinker/test/cpentene.key share/tinker/test/cpentene.xyz share/tinker/test/crambin.key +share/tinker/test/crambin.min share/tinker/test/crambin.pdb share/tinker/test/crambin.seq +share/tinker/test/crambin.super share/tinker/test/crambin.xyz share/tinker/test/crambinx.key +share/tinker/test/crambinx.ray share/tinker/test/crambinx.xyz share/tinker/test/crown.int share/tinker/test/crown.key @@ -221,12 +236,12 @@ share/tinker/test/diene.xyz share/tinker/test/dimethane.key share/tinker/test/dimethane.xyz share/tinker/test/diwater.key +share/tinker/test/diwater.lin +share/tinker/test/diwater.min share/tinker/test/diwater.xyz share/tinker/test/enkephalin.int share/tinker/test/enkephalin.key share/tinker/test/enkephalin.make -share/tinker/test/enkephalin.pdb -share/tinker/test/enkephalin.run share/tinker/test/enkephalin.seq share/tinker/test/enkephalin.xyz share/tinker/test/ermer.int @@ -237,14 +252,21 @@ share/tinker/test/ester.xyz share/tinker/test/ethane.int share/tinker/test/ethane.key share/tinker/test/ethane.xyz +share/tinker/test/ethanol.int +share/tinker/test/ethanol.key +share/tinker/test/ethanol.xyz share/tinker/test/ethylene.int share/tinker/test/ethylene.key share/tinker/test/ethylene.xyz share/tinker/test/flane.int share/tinker/test/flane.key share/tinker/test/flane.xyz -share/tinker/test/formamide.key -share/tinker/test/formamide.xyz +share/tinker/test/form.key +share/tinker/test/form.xyz +share/tinker/test/formbig.key +share/tinker/test/formbig.xyz +share/tinker/test/formbox.key +share/tinker/test/formbox.xyz share/tinker/test/furan.int share/tinker/test/furan.key share/tinker/test/furan.xyz @@ -252,6 +274,13 @@ share/tinker/test/glucose.key share/tinker/test/glucose.xyz share/tinker/test/helix.key share/tinker/test/helix.xyz +share/tinker/test/hexane.int +share/tinker/test/hexane.key +share/tinker/test/hexane.xyz +share/tinker/test/hexanes.dyn +share/tinker/test/hexanes.key +share/tinker/test/hexanes.run +share/tinker/test/hexanes.xyz share/tinker/test/imidazole.int share/tinker/test/imidazole.key share/tinker/test/imidazole.xyz @@ -260,11 +289,19 @@ share/tinker/test/imine.key share/tinker/test/imine.xyz share/tinker/test/lactam.key share/tinker/test/lactam.xyz +share/tinker/test/melittin.key +share/tinker/test/melittin.pdb +share/tinker/test/melittin.seq 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+share/tinker/test/waterhuge.key +share/tinker/test/waterhuge.xyz +share/tinker/test/wateroct.dyn +share/tinker/test/wateroct.key +share/tinker/test/wateroct.xyz +share/tinker/test/watersmall.dyn +share/tinker/test/watersmall.key +share/tinker/test/watersmall.xyz +share/tinker/test/white.int +share/tinker/test/white.key +share/tinker/test/white.xyz +share/tinker/tinker.txt +@dirrm share/doc/tinker +@dirrm share/examples/tinker +@dirrm share/tinker/bench +@dirrm share/tinker/params +@dirrm share/tinker/rasmol +@dirrm share/tinker/test +@dirrm share/tinker diff --git a/biology/tinker/scripts/build_viewer b/biology/tinker/scripts/build_viewer new file mode 100644 index 000000000000..24fb838c4fd0 --- /dev/null +++ b/biology/tinker/scripts/build_viewer @@ -0,0 +1,47 @@ +#!/bin/sh + +# This builds the molecular viewer for tinker files. It is a modified +# version of rasmol. One of the problems with rasmol is that is only +# works at one color depth. This script will build three viewers at +# different color depths, 8-bit, 16-bit, and 32-bit. The binaries are +# called tview-8, tview-16, and tview-32 respectively. + +cd ${WRKSRC}/../rasmol + +cp Imakefile Imakefile.orig + +sed s@/user/ponder@${PREFIX}/share@ Imakefile > Imakefile.temp + +sed s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-32)'@ \ + Imakefile.temp > Imakefile + +xmkmf -a + +make clean && make + +sed -e s@'DEPTHDEF = -DTHIRTYTWOBIT'@'# DEPTHDEF = -DTHIRTYTWOBIT'@ \ + -e s@'# DEPTHDEF = -DSIXTEENBIT'@'DEPTHDEF = -DSIXTEENBIT'@ \ + -e s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-16)'@ \ + Imakefile.temp > Imakefile + +xmkmf -a + +make clean && make + +sed -e s@'DEPTHDEF = -DTHIRTYTWOBIT'@'# DEPTHDEF = -DTHIRTYTWOBIT'@ \ + -e s@'# DEPTHDEF = -DEIGHTBIT'@'DEPTHDEF = -DEIGHTBIT'@ \ + -e s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-8)'@ \ + Imakefile.temp > Imakefile + +xmkmf -a + +make clean && make + +# Restore Imakefile to original state so that rerunning this script does +# the right thing. +rm Imakefile.temp +mv Imakefile.orig Imakefile +xmkmf -a +make clean + +exit 0 |