diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile index b00a496cad83..1b1129da1393 100644 --- a/biology/tinker/Makefile +++ b/biology/tinker/Makefile @@ -45,46 +45,46 @@ ${PREFIX}/share/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/params/* \ ${PREFIX}/share/tinker/params .if !defined(NOPORTDOCS) - ${MKDIR} ${PREFIX}/share/tinker/doc - ${MKDIR} ${PREFIX}/share/tinker/example + ${MKDIR} ${PREFIX}/share/doc/tinker + ${MKDIR} ${PREFIX}/share/examples/tinker ${MKDIR} ${PREFIX}/share/tinker/bench ${MKDIR} ${PREFIX}/share/tinker/test ${INSTALL_DATA} ${WRKDIR}/tinker/doc/README \ -${PREFIX}/share/tinker/doc +${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.pdf \ -${PREFIX}/share/tinker/doc +${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.ps \ -${PREFIX}/share/tinker/doc +${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.Z \ -${PREFIX}/share/tinker/doc +${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.txt \ -${PREFIX}/share/tinker/doc +${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/README \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/anion.dyn0 \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.in* \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.key \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.log \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/argon.1st \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/crambin.pdb \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.boat \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.chair \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/formamide.cell \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/*.run \ -${PREFIX}/share/tinker/example +${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.input \ ${PREFIX}/share/tinker/bench ${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.key \ diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa index 507e97aae49a..526ce65e518c 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 Sun Aug 29 15:07:57 1999 ++++ ../make/Makefile Wed May 31 16:00:31 2000 @@ -9,8 +9,8 @@ ## ## 1. make all Build all the TINKER executables @@ -62,16 +62,16 @@ +.if ${FC}==f77 +.if !defined(HAVE_G2C) +LIBS = -lU77 -+F77FLAGS = -NL400 -c ++F77FLAGS = -NL400 -c -w +LINKFLAGS = -L${PREFIX}/lib +.else -+LIBS = -lg2c -+F77FLAGS = -Wno-globals -fno-globals -c ++LIBS = ++F77FLAGS = -Wno-globals -fno-globals -c -w +LINKFLAGS = +.endif +.elseif ${FC}==g77 +LIBS= -+F77FLAGS = -Wno-globals -fno-globals -c ++F77FLAGS = -Wno-globals -fno-globals -c -w +LINKFLAGS = +.endif + @@ -143,51 +143,51 @@ - mv xyzint.x $(BINDIR)/xyzint - mv xyzpdb.x $(BINDIR)/xyzpdb - mv xyzsybyl.x $(BINDIR)/xyzsybyl -+ ${INSTALL} -c -s alchemy.x $(BINDIR)/alchemy -+ ${INSTALL} -c -s analyze.x $(BINDIR)/analyze -+ ${INSTALL} -c -s anneal.x $(BINDIR)/anneal -+ ${INSTALL} -c -s archive.x $(BINDIR)/archive -+ ${INSTALL} -c -s correlate.x $(BINDIR)/correlate -+ ${INSTALL} -c -s crystal.x $(BINDIR)/crystal -+ ${INSTALL} -c -s distgeom.x $(BINDIR)/distgeom -+ ${INSTALL} -c -s document.x $(BINDIR)/document -+ ${INSTALL} -c -s dynamic.x $(BINDIR)/dynamic -+ ${INSTALL} -c -s gda.x $(BINDIR)/gda -+ ${INSTALL} -c -s intedit.x $(BINDIR)/intedit -+ ${INSTALL} -c -s intxyz.x $(BINDIR)/intxyz -+ ${INSTALL} -c -s minimize.x $(BINDIR)/minimize -+ ${INSTALL} -c -s minirot.x $(BINDIR)/minirot -+ ${INSTALL} -c -s newton.x $(BINDIR)/newton -+ ${INSTALL} -c -s newtrot.x $(BINDIR)/newtrot -+ ${INSTALL} -c -s optimize.x $(BINDIR)/optimize -+ ${INSTALL} -c -s optirot.x $(BINDIR)/optirot -+ ${INSTALL} -c -s optrigid.x $(BINDIR)/optrigid -+ ${INSTALL} -c -s path.x $(BINDIR)/path -+ ${INSTALL} -c -s pdbxyz.x $(BINDIR)/pdbxyz -+ ${INSTALL} -c -s protein.x $(BINDIR)/protein -+ ${INSTALL} -c -s pss.x $(BINDIR)/pss -+ ${INSTALL} -c -s pssrigid.x $(BINDIR)/pssrigid -+ ${INSTALL} -c -s pssrot.x $(BINDIR)/pssrot -+ ${INSTALL} -c -s saddle.x $(BINDIR)/saddle -+ ${INSTALL} -c -s scan.x $(BINDIR)/scan -+ ${INSTALL} -c -s sniffer.x $(BINDIR)/sniffer -+ ${INSTALL} -c -s spacefill.x $(BINDIR)/spacefill -+ ${INSTALL} -c -s superpose.x $(BINDIR)/superpose -+ ${INSTALL} -c -s sybylxyz.x $(BINDIR)/sybylxyz -+ ${INSTALL} -c -s testgrad.x $(BINDIR)/testgrad -+ ${INSTALL} -c -s testhess.x $(BINDIR)/testhess -+ ${INSTALL} -c -s testlight.x $(BINDIR)/testlight -+ ${INSTALL} -c -s testrot.x $(BINDIR)/testrot -+ ${INSTALL} -c -s timer.x $(BINDIR)/timer -+ ${INSTALL} -c -s timerot.x $(BINDIR)/timerot -+ ${INSTALL} -c -s vibrate.x $(BINDIR)/vibrate -+ ${INSTALL} -c -s vibrot.x $(BINDIR)/vibrot -+ ${INSTALL} -c -s xtalfit.x $(BINDIR)/xtalfit -+ ${INSTALL} -c -s xtalmin.x $(BINDIR)/xtalmin -+ ${INSTALL} -c -s xyzedit.x $(BINDIR)/xyzedit -+ ${INSTALL} -c -s xyzint.x $(BINDIR)/xyzint -+ ${INSTALL} -c -s xyzpdb.x $(BINDIR)/xyzpdb -+ ${INSTALL} -c -s xyzsybyl.x $(BINDIR)/xyzsybyl ++ ${INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy ++ ${INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze ++ ${INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal ++ ${INSTALL_PROGRAM} archive.x $(BINDIR)/archive ++ ${INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate ++ ${INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal ++ ${INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom ++ ${INSTALL_PROGRAM} document.x $(BINDIR)/document ++ ${INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic ++ ${INSTALL_PROGRAM} gda.x $(BINDIR)/gda ++ ${INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit ++ ${INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz ++ ${INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize ++ ${INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot ++ ${INSTALL_PROGRAM} newton.x $(BINDIR)/newton ++ ${INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot ++ ${INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize ++ ${INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot ++ ${INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid ++ ${INSTALL_PROGRAM} path.x $(BINDIR)/path ++ ${INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz ++ ${INSTALL_PROGRAM} protein.x $(BINDIR)/protein ++ ${INSTALL_PROGRAM} pss.x $(BINDIR)/pss ++ ${INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid ++ ${INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot ++ ${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} superpose.x $(BINDIR)/superpose ++ ${INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz ++ ${INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad ++ ${INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess ++ ${INSTALL_PROGRAM} testlight.x $(BINDIR)/testlight ++ ${INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot ++ ${INSTALL_PROGRAM} timer.x $(BINDIR)/timer ++ ${INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot ++ ${INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate ++ ${INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot ++ ${INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit ++ ${INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin ++ ${INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit ++ ${INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint ++ ${INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb ++ ${INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl remove_links: rm -f $(LINKDIR)/alchemy diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist index 2eb5baaddd06..012299f88e88 100644 --- a/biology/tinker/pkg-plist +++ b/biology/tinker/pkg-plist @@ -64,72 +64,72 @@ share/tinker/bench/water.input share/tinker/bench/water.key share/tinker/bench/water.run share/tinker/bench/water.xyz -share/tinker/doc/README -share/tinker/doc/guide.pdf -share/tinker/doc/guide.ps.Z -share/tinker/doc/guide.txt -share/tinker/doc/license.pdf -share/tinker/doc/license.ps.Z -share/tinker/doc/license.txt -share/tinker/doc/logo.ps.Z -share/tinker/doc/spine.ps -share/tinker/doc/summary.pdf -share/tinker/doc/summary.ps -share/tinker/doc/summary.txt -share/tinker/example/README -share/tinker/example/anion.dyn0 -share/tinker/example/anion.in1 -share/tinker/example/anion.in2 -share/tinker/example/anion.key -share/tinker/example/anion.log -share/tinker/example/anion.run -share/tinker/example/anion.xyz -share/tinker/example/argon.1st -share/tinker/example/argon.in1 -share/tinker/example/argon.in2 -share/tinker/example/argon.key -share/tinker/example/argon.log -share/tinker/example/argon.run -share/tinker/example/clean.make -share/tinker/example/cluster.in1 -share/tinker/example/cluster.key -share/tinker/example/cluster.log -share/tinker/example/cluster.run -share/tinker/example/cluster.xyz -share/tinker/example/crambin.in1 -share/tinker/example/crambin.in2 -share/tinker/example/crambin.in3 -share/tinker/example/crambin.key -share/tinker/example/crambin.log -share/tinker/example/crambin.pdb -share/tinker/example/crambin.run -share/tinker/example/cyclohex.boat -share/tinker/example/cyclohex.chair -share/tinker/example/cyclohex.in1 -share/tinker/example/cyclohex.in2 -share/tinker/example/cyclohex.in3 -share/tinker/example/cyclohex.key -share/tinker/example/cyclohex.log -share/tinker/example/cyclohex.run -share/tinker/example/enkephalin.in1 -share/tinker/example/enkephalin.in2 -share/tinker/example/enkephalin.in3 -share/tinker/example/enkephalin.key -share/tinker/example/enkephalin.log -share/tinker/example/enkephalin.run -share/tinker/example/formamide.cell -share/tinker/example/formamide.in1 -share/tinker/example/formamide.in2 -share/tinker/example/formamide.in3 -share/tinker/example/formamide.in4 -share/tinker/example/formamide.key -share/tinker/example/formamide.log -share/tinker/example/formamide.run -share/tinker/example/helix.in1 -share/tinker/example/helix.key -share/tinker/example/helix.log -share/tinker/example/helix.run -share/tinker/example/helix.xyz +share/doc/tinker/README +share/doc/tinker/guide.pdf +share/doc/tinker/guide.ps.Z +share/doc/tinker/guide.txt +share/doc/tinker/license.pdf +share/doc/tinker/license.ps.Z +share/doc/tinker/license.txt +share/doc/tinker/logo.ps.Z +share/doc/tinker/spine.ps +share/doc/tinker/summary.pdf +share/doc/tinker/summary.ps +share/doc/tinker/summary.txt +share/examples/tinker/README +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.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 +share/examples/tinker/cyclohex.in2 +share/examples/tinker/cyclohex.in3 +share/examples/tinker/cyclohex.key +share/examples/tinker/cyclohex.log +share/examples/tinker/cyclohex.run +share/examples/tinker/enkephalin.in1 +share/examples/tinker/enkephalin.in2 +share/examples/tinker/enkephalin.in3 +share/examples/tinker/enkephalin.key +share/examples/tinker/enkephalin.log +share/examples/tinker/enkephalin.run +share/examples/tinker/formamide.cell +share/examples/tinker/formamide.in1 +share/examples/tinker/formamide.in2 +share/examples/tinker/formamide.in3 +share/examples/tinker/formamide.in4 +share/examples/tinker/formamide.key +share/examples/tinker/formamide.log +share/examples/tinker/formamide.run +share/examples/tinker/helix.in1 +share/examples/tinker/helix.key +share/examples/tinker/helix.log +share/examples/tinker/helix.run +share/examples/tinker/helix.xyz share/tinker/params/README share/tinker/params/amber.prm share/tinker/params/charmm.prm @@ -338,8 +338,8 @@ share/tinker/test/white.key share/tinker/test/white.xyz share/tinker/tinker.txt @dirrm share/tinker/bench -@dirrm share/tinker/doc -@dirrm share/tinker/example +@dirrm share/doc/tinker +@dirrm share/examples/tinker @dirrm share/tinker/params @dirrm share/tinker/test @dirrm share/tinker