Changeset e1a46d for util

Timestamp:

Aug 7, 2009, 9:11:56 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

8f9a8e

Parents:

d93bb24

git-author:

Frederik Heber <heber@…> (08/07/09 09:10:43)

git-committer:

Frederik Heber <heber@…> (08/07/09 09:11:56)

Message:

All of my python script put into ESPACK and adapted with @PYTHON@ and so on.

Location:

util

Files:

• configure.ac (modified) (2 diffs)
• depcomp (modified) (2 diffs)
• install-sh (modified) (13 diffs)
• src/AnalysePASFromEllipsoids.py.in (added)
• src/AnalyseStressResults.py.in (added)
• src/Animate.py.in (added)
• src/AnimateStereo.py.in (added)
• src/CalculateDensity.py.in (added)
• src/CalculateDensityfromConfig.sh.in (moved) (moved from util/src/CalculateDensity.sh.in )
• src/CalculatePairCorrelation.py.in (added)
• src/CalculateSurfaceOfCluster.py.in (added)
• src/CalculateXRayFromPDBstep.py.in (added)
• src/CheckMap.py.in (added)
• src/CreateAllVspeShapes.py.in (added)
• src/CreateGaAs.c (modified) (1 prop)
• src/CreateH2.c (modified) (1 prop)
• src/CreateNeighboursForTIP3.py.in (added)
• src/CreateVspeShapes.py.in (added)
• src/CutBlockFromPDB.py.in (added)
• src/FindInnerPointsinBB.py.in (added)
• src/FindNonTriplesTIP3.py.in (added)
• src/GetBondedPairs.py.in (added)
• src/GetBondsFromPDB.py.in (added)
• src/GetIDsOfBorderAtoms.py.in (added)
• src/GetPdb.c (modified) (1 prop)
• src/LinearlyInterpolateBetweenPCPConfigs.py.in (added)
• src/Makefile.am (modified) (2 diffs)
• src/NanoCreator.c (modified) (1 prop)
• src/NanoCreator.h (modified) (1 prop)
• src/OutputRaster3DHeader.py.in (added)
• src/PairCorrelationTIP3toResiduum.py.in (added)
• src/PairCorrelationToCluster.py.in (added)
• src/PairCorrelationToClusterSurface.py.in (added)
• src/PrepareStoneWalesDefects.py.in (added)
• src/ReMapDBondFile.py.in (added)
• src/ReMapDBondFileFromXYZ.py.in (added)
• src/ReadSrcIon.c (modified) (1 prop)
• src/ReduceDBondFiletoSubset.py.in (added)
• src/RemoveConvexPart.py.in (added)
• src/RemoveRandomAtoms.py.in (added)
• src/RestorePDBfromGrape.py.in (added)
• src/ShiftPeriodic.py.in (added)
• src/VibrAlyzer.c (modified) (1 prop)
• src/average.cpp (modified) (1 prop)
• src/convertHessianMPQC2PCP.py.in (added)
• src/convertMPQCout2pcp.py.in (added)
• src/convertPCP2MPQC.py.in (added)
• src/convertXDataToXYData.py.in (added)
• src/diagonalize.c (modified) (1 prop)
• src/mergesort.c (modified) (1 prop)
• src/mergesort.h (modified) (1 prop)
• src/stochastik.cpp (modified) (1 prop)

util/configure.ac

@@ -13 +13 @@
 AC_PROG_CXX
 AC_PATH_PROG([PERL],[perl])
+AC_PATH_PROG([PYTHON],[python])
 AC_PATH_PROG([SHELL],[sh])
 AC_PROG_AWK
@@ -45 +46 @@
 AC_CHECK_FUNCS([pow sqrt strchr strrchr strstr])
 AC_CONFIG_FILES([Makefile doc/Makefile src/Makefile])
-AC_CONFIG_FILES([src/Nanotubes.pl src/ReSequenceDX.pl src/BOSSMatcher.pl])
-AC_CONFIG_FILES([src/average_result.sh src/CalculateDensity.sh src/CalculateMass.sh src/config2xyz.sh src/convert2old.sh src/convertpdb.sh src/gather_all_results.sh src/gather_averaged_results.sh src/gather_result.sh src/grep_shielding.sh src/meas2pdb.sh src/AdaptiveANOVA.sh src/CreateFromXYZ.sh src/dynamicANOVA.sh src/SortByRings.sh])
+AC_CONFIG_FILES([src/AnalysePASFromEllipsoids.py \
+                src/AnalyseStressResults.py
+                src/Animate.py \
+                src/AnimateStereo.py \
+                src/CalculateDensity.py \
+                src/CalculatePairCorrelation.py \
+                src/CalculateSurfaceOfCluster.py \
+                src/CalculateXRayFromPDBstep.py \
+                src/CreateNeighboursForTIP3.py \
+                src/convertHessianMPQC2PCP.py \
+                src/convertMPQCout2pcp.py \
+                src/convertPCP2MPQC.py \
+                src/convertXDataToXYData.py \
+                src/CreateAllVspeShapes.py \
+                src/CreateVspeShapes.py \
+                src/CutBlockFromPDB.py \
+                src/FindInnerPointsinBB.py \
+                src/FindNonTriplesTIP3.py \
+                src/GetBondedPairs.py \
+                src/GetBondsFromPDB.py \
+                src/GetIDsOfBorderAtoms.py \
+                src/LinearlyInterpolateBetweenPCPConfigs.py \
+                src/OutputRaster3DHeader.py \
+                src/PairCorrelationTIP3toResiduum.py \
+                src/PairCorrelationToCluster.py \
+                src/PairCorrelationToClusterSurface.py \
+                src/PrepareStoneWalesDefects.py \
+                src/ReduceDBondFiletoSubset.py \
+                src/ReMapDBondFileFromXYZ.py \
+                src/ReMapDBondFile.py \
+                src/RemoveConvexPart.py \
+                src/RemoveRandomAtoms.py \
+                src/RestorePDBfromGrape.py \
+                src/ShiftPeriodic.py \
+                ])
+AC_CONFIG_FILES([src/Nanotubes.pl \
+                src/ReSequenceDX.pl \
+                src/BOSSMatcher.pl \
+                ])
+AC_CONFIG_FILES([src/average_result.sh \
+                src/AdaptiveANOVA.sh \
+                src/CalculateDensityfromConfig.sh \
+                src/CalculateMass.sh \
+                src/CreateFromXYZ.sh \
+                src/config2xyz.sh \
+                src/convert2old.sh \
+                src/convertpdb.sh \
+                src/dynamicANOVA.sh \
+                src/gather_all_results.sh \
+                src/gather_averaged_results.sh \
+                src/gather_result.sh \
+                src/grep_shielding.sh \
+                src/meas2pdb.sh \
+                src/SortByRings.sh])
 AC_OUTPUT
 

util/depcomp

@@ -2 +2 @@
 # depcomp - compile a program generating dependencies as side-effects
 
-scriptversion=2006-10-15.18
-
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006 Free Software
+scriptversion=2007-03-29.01
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software
 # Foundation, Inc.
 
@@ -216 +216 @@
   # start of each line; $object doesn't have directory information.
   # Version 6 uses the directory in both cases.
-  stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
-  tmpdepfile="$stripped.u"
+  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+  test "x$dir" = "x$object" && dir=
+  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
   if test "$libtool" = yes; then
+    tmpdepfile1=$dir$base.u
+    tmpdepfile2=$base.u
+    tmpdepfile3=$dir.libs/$base.u
     "$@" -Wc,-M
   else
+    tmpdepfile1=$dir$base.u
+    tmpdepfile2=$dir$base.u
+    tmpdepfile3=$dir$base.u
     "$@" -M
   fi
   stat=$?
 
-  if test -f "$tmpdepfile"; then :
-  else
-    stripped=`echo "$stripped" | sed 's,^.*/,,'`
-    tmpdepfile="$stripped.u"
-  fi
-
   if test $stat -eq 0; then :
   else
-    rm -f "$tmpdepfile"
+    rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
     exit $stat
   fi
 
+  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+  do
+    test -f "$tmpdepfile" && break
+  done
   if test -f "$tmpdepfile"; then
-    outname="$stripped.o"
     # Each line is of the form `foo.o: dependent.h'.
     # Do two passes, one to just change these to
     # `$object: dependent.h' and one to simply `dependent.h:'.
-    sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
-    sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
+    sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+    # That's a tab and a space in the [].
+    sed -e 's,^.*\.[a-z]*:[      ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
   else
     # The sourcefile does not contain any dependencies, so just

util/install-sh

@@ -2 +2 @@
 # install - install a program, script, or datafile
 
-scriptversion=2006-10-14.15
+scriptversion=2006-12-25.00
 
 # This originates from X11R5 (mit/util/scripts/install.sh), which was
@@ -49 +49 @@
 
 # Don't use :- since 4.3BSD and earlier shells don't like it.
-doit="${DOITPROG-}"
+doit=${DOITPROG-}
 if test -z "$doit"; then
   doit_exec=exec
@@ -59 +59 @@
 # or use environment vars.
 
-mvprog="${MVPROG-mv}"
-cpprog="${CPPROG-cp}"
-chmodprog="${CHMODPROG-chmod}"
-chownprog="${CHOWNPROG-chown}"
-chgrpprog="${CHGRPPROG-chgrp}"
-stripprog="${STRIPPROG-strip}"
-rmprog="${RMPROG-rm}"
-mkdirprog="${MKDIRPROG-mkdir}"
-
-posix_glob=
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+  test "$posix_glob" != "?" || {
+    if (set -f) 2>/dev/null; then
+      posix_glob=
+    else
+      posix_glob=:
+    fi
+  }
+'
+
 posix_mkdir=
 
@@ -74 +85 @@
 mode=0755
 
+chgrpcmd=
 chmodcmd=$chmodprog
 chowncmd=
-chgrpcmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
 stripcmd=
-rmcmd="$rmprog -f"
-mvcmd="$mvprog"
+
 src=
 dst=
 dir_arg=
-dstarg=
+dst_arg=
+
+copy_on_change=false
 no_target_directory=
 
-usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
    or: $0 [OPTION]... SRCFILES... DIRECTORY
    or: $0 [OPTION]... -t DIRECTORY SRCFILES...
@@ -96 +111 @@
 
 Options:
--c         (ignored)
--d         create directories instead of installing files.
--g GROUP   $chgrpprog installed files to GROUP.
--m MODE    $chmodprog installed files to MODE.
--o USER    $chownprog installed files to USER.
--s         $stripprog installed files.
--t DIRECTORY  install into DIRECTORY.
--T         report an error if DSTFILE is a directory.
---help     display this help and exit.
---version  display version info and exit.
+     --help     display this help and exit.
+     --version  display version info and exit.
+
+  -c            (ignored)
+  -C            install only if different (preserve the last data modification time)
+  -d            create directories instead of installing files.
+  -g GROUP      $chgrpprog installed files to GROUP.
+  -m MODE       $chmodprog installed files to MODE.
+  -o USER       $chownprog installed files to USER.
+  -s            $stripprog installed files.
+  -t DIRECTORY  install into DIRECTORY.
+  -T            report an error if DSTFILE is a directory.
 
 Environment variables override the default commands:
-  CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
+  CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+  RMPROG STRIPPROG
 "
 
 while test $# -ne 0; do
   case $1 in
-    -c) shift
-        continue;;
-
-    -d) dir_arg=true
-        shift
-        continue;;
+    -c) ;;
+
+    -C) copy_on_change=true;;
+
+    -d) dir_arg=true;;
 
     -g) chgrpcmd="$chgrpprog $2"
-        shift
-        shift
-        continue;;
+        shift;;
 
     --help) echo "$usage"; exit $?;;
 
     -m) mode=$2
-        shift
-        shift
         case $mode in
           *' '* | *'    '* | *'
@@ -136 +149 @@
             exit 1;;
         esac
-        continue;;
+        shift;;
 
     -o) chowncmd="$chownprog $2"
-        shift
-        shift
-        continue;;
-
-    -s) stripcmd=$stripprog
-        shift
-        continue;;
-
-    -t) dstarg=$2
-        shift
-        shift
-        continue;;
-
-    -T) no_target_directory=true
-        shift
-        continue;;
+        shift;;
+
+    -s) stripcmd=$stripprog;;
+
+    -t) dst_arg=$2
+        shift;;
+
+    -T) no_target_directory=true;;
 
     --version) echo "$0 $scriptversion"; exit $?;;
@@ -166 +171 @@
     *)  break;;
   esac
+  shift
 done
 
-if test $# -ne 0 && test -z "$dir_arg$dstarg"; then
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
   # When -d is used, all remaining arguments are directories to create.
   # When -t is used, the destination is already specified.
@@ -174 +180 @@
   for arg
   do
-    if test -n "$dstarg"; then
+    if test -n "$dst_arg"; then
       # $@ is not empty: it contains at least $arg.
-      set fnord "$@" "$dstarg"
+      set fnord "$@" "$dst_arg"
       shift # fnord
     fi
     shift # arg
-    dstarg=$arg
+    dst_arg=$arg
   done
 fi
@@ -225 +231 @@
   # Protect names starting with `-'.
   case $src in
-    -*) src=./$src ;;
+    -*) src=./$src;;
   esac
 
@@ -243 +249 @@
     fi
 
-    if test -z "$dstarg"; then
+    if test -z "$dst_arg"; then
       echo "$0: no destination specified." >&2
       exit 1
     fi
 
-    dst=$dstarg
+    dst=$dst_arg
     # Protect names starting with `-'.
     case $dst in
-      -*) dst=./$dst ;;
+      -*) dst=./$dst;;
     esac
 
@@ -258 +264 @@
     if test -d "$dst"; then
       if test -n "$no_target_directory"; then
-        echo "$0: $dstarg: Is a directory" >&2
+        echo "$0: $dst_arg: Is a directory" >&2
         exit 1
       fi
@@ -379 +385 @@
 
       case $dstdir in
-        /*) prefix=/ ;;
-        -*) prefix=./ ;;
-        *)  prefix= ;;
+        /*) prefix='/';;
+        -*) prefix='./';;
+        *)  prefix='';;
       esac
 
-      case $posix_glob in
-        '')
-          if (set -f) 2>/dev/null; then
-            posix_glob=true
-          else
-            posix_glob=false
-          fi ;;
-      esac
+      eval "$initialize_posix_glob"
 
       oIFS=$IFS
       IFS=/
-      $posix_glob && set -f
+      $posix_glob set -f
       set fnord $dstdir
       shift
-      $posix_glob && set +f
+      $posix_glob set +f
       IFS=$oIFS
 
@@ -460 +459 @@
     # errors from the above "$doit $cpprog $src $dsttmp" command.
     #
-    { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
-      && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
-      && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
-      && { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
-
-    # Now rename the file to the real destination.
-    { $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null \
-      || {
-           # The rename failed, perhaps because mv can't rename something else
-           # to itself, or perhaps because mv is so ancient that it does not
-           # support -f.
-
-           # Now remove or move aside any old file at destination location.
-           # We try this two ways since rm can't unlink itself on some
-           # systems and the destination file might be busy for other
-           # reasons.  In this case, the final cleanup might fail but the new
-           # file should still install successfully.
-           {
-             if test -f "$dst"; then
-               $doit $rmcmd -f "$dst" 2>/dev/null \
-               || { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null \
-                     && { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }; }\
-               || {
-                 echo "$0: cannot unlink or rename $dst" >&2
-                 (exit 1); exit 1
-               }
-             else
-               :
-             fi
-           } &&
-
-           # Now rename the file to the real destination.
-           $doit $mvcmd "$dsttmp" "$dst"
-         }
-    } || exit 1
+    { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+    { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+    { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+    # If -C, don't bother to copy if it wouldn't change the file.
+    if $copy_on_change &&
+       old=`LC_ALL=C ls -dlL "$dst"     2>/dev/null` &&
+       new=`LC_ALL=C ls -dlL "$dsttmp"  2>/dev/null` &&
+
+       eval "$initialize_posix_glob" &&
+       $posix_glob set -f &&
+       set X $old && old=:$2:$4:$5:$6 &&
+       set X $new && new=:$2:$4:$5:$6 &&
+       $posix_glob set +f &&
+
+       test "$old" = "$new" &&
+       $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+    then
+      rm -f "$dsttmp"
+    else
+      # Rename the file to the real destination.
+      $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+      # The rename failed, perhaps because mv can't rename something else
+      # to itself, or perhaps because mv is so ancient that it does not
+      # support -f.
+      {
+        # Now remove or move aside any old file at destination location.
+        # We try this two ways since rm can't unlink itself on some
+        # systems and the destination file might be busy for other
+        # reasons.  In this case, the final cleanup might fail but the new
+        # file should still install successfully.
+        {
+          test ! -f "$dst" ||
+          $doit $rmcmd -f "$dst" 2>/dev/null ||
+          { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+            { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+          } ||
+          { echo "$0: cannot unlink or rename $dst" >&2
+            (exit 1); exit 1
+          }
+        } &&
+
+        # Now rename the file to the real destination.
+        $doit $mvcmd "$dsttmp" "$dst"
+      }
+    fi || exit 1
 
     trap '' 0

util/src/Makefile.am

@@ -21 +21 @@
 VibrAlyzer_SOURCES = VibrAlyzer.c
 
-scripts = \
+bashscripts = \
         AdaptiveANOVA.sh \
         average_result.sh \
         CreateFromXYZ.sh \
-        CalculateDensity.sh \
+        CalculateDensityfromConfig.sh \
         CalculateMass.sh \
         config2xyz.sh \
@@ -36 +36 @@
         gather_averaged_results.sh \
         meas2pdb.sh \
+        SortByRings.sh
+
+perlscripts = \
         BOSSMatcher.pl \
         Nanotubes.pl \
-        ReSequenceDX.pl \
-        SortByRings.sh
+        ReSequenceDX.pl
 
-bin_SCRIPTS = ${scripts}
+pythonscripts = \
+        AnalysePASFromEllipsoids.py \
+        AnalyseStressResults.py \
+        Animate.py \
+        AnimateStereo.py \
+        CalculateDensity.py \
+        CalculatePairCorrelation.py \
+        CalculateSurfaceOfCluster.py \
+        CalculateXRayFromPDBstep.py \
+        CreateNeighboursForTIP3.py \
+        convertHessianMPQC2PCP.py \
+        convertMPQCout2pcp.py \
+        convertPCP2MPQC.py \
+        convertXDataToXYData.py \
+        CreateAllVspeShapes.py \
+        CreateVspeShapes.py \
+        CutBlockFromPDB.py \
+        FindInnerPointsinBB.py \
+        FindNonTriplesTIP3.py \
+        GetBondedPairs.py \
+        GetBondsFromPDB.py \
+        GetIDsOfBorderAtoms.py \
+        LinearlyInterpolateBetweenPCPConfigs.py \
+        OutputRaster3DHeader.py \
+        LinearlyInterpolateBetweenPCPConfigs.py \
+        PairCorrelationTIP3toResiduum.py \
+        PairCorrelationToCluster.py \
+        PairCorrelationToClusterSurface.py \
+        PrepareStoneWalesDefects.py \
+        ReduceDBondFiletoSubset.py \
+        ReMapDBondFileFromXYZ.py \
+        ReMapDBondFile.py \
+        RemoveConvexPart.py \
+        RemoveRandomAtoms.py \
+        RemoveConvexPart.py \
+        RemoveRandomAtoms.py \
+        RestorePDBfromGrape.py \
+        ShiftPeriodic.py
 
+
+bin_SCRIPTS = ${bashscripts} ${perlscripts} ${pythonscripts}
+