pdb2pqr/src/configure.mingw

#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.60 for PDB2PQR 1.3.0.
#
# Report bugs to <todd@ccb.wustl.edu>.
#
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
# 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
# This configure script is free software; the Free Software Foundation
# gives unlimited permission to copy, distribute and modify it.
## --------------------- ##
## M4sh Initialization.  ##
## --------------------- ##

# Be Bourne compatible
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
  emulate sh
  NULLCMD=:
  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '${1+"$@"}'='"$@"'
  setopt NO_GLOB_SUBST
else
  case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
fi
BIN_SH=xpg4; export BIN_SH # for Tru64
DUALCASE=1; export DUALCASE # for MKS sh


# PATH needs CR
# Avoid depending upon Character Ranges.
as_cr_letters='abcdefghijklmnopqrstuvwxyz'
as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
as_cr_Letters=$as_cr_letters$as_cr_LETTERS
as_cr_digits='0123456789'
as_cr_alnum=$as_cr_Letters$as_cr_digits

# The user is always right.
if test "${PATH_SEPARATOR+set}" != set; then
  echo "#! /bin/sh" >conf$$.sh
  echo  "exit 0"   >>conf$$.sh
  chmod +x conf$$.sh
  if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
    PATH_SEPARATOR=';'
  else
    PATH_SEPARATOR=:
  fi
  rm -f conf$$.sh
fi

# Support unset when possible.
if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
  as_unset=unset
else
  as_unset=false
fi


# IFS
# We need space, tab and new line, in precisely that order.  Quoting is
# there to prevent editors from complaining about space-tab.
# (If _AS_PATH_WALK were called with IFS unset, it would disable word
# splitting by setting IFS to empty value.)
as_nl='
'
IFS=" ""        $as_nl"

# Find who we are.  Look in the path if we contain no directory separator.
case $0 in
  *[\\/]* ) as_myself=$0 ;;
  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
done
IFS=$as_save_IFS

     ;;
esac
# We did not find ourselves, most probably we were run as `sh COMMAND'
# in which case we are not to be found in the path.
if test "x$as_myself" = x; then
  as_myself=$0
fi
if test ! -f "$as_myself"; then
  echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
  { (exit 1); exit 1; }
fi

# Work around bugs in pre-3.0 UWIN ksh.
for as_var in ENV MAIL MAILPATH
do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
done
PS1='$ '
PS2='> '
PS4='+ '

# NLS nuisances.
for as_var in \
  LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
  LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
  LC_TELEPHONE LC_TIME
do
  if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
    eval $as_var=C; export $as_var
  else
    ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
  fi
done

# Required to use basename.
if expr a : '\(a\)' >/dev/null 2>&1 &&
   test "X`expr 00001 : '.*\(...\)'`" = X001; then
  as_expr=expr
else
  as_expr=false
fi

if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
  as_basename=basename
else
  as_basename=false
fi


# Name of the executable.
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
         X"$0" : 'X\(//\)$' \| \
         X"$0" : 'X\(/\)' \| . 2>/dev/null ||
echo X/"$0" |
    sed '/^.*\/\([^/][^/]*\)\/*$/{
            s//\1/
            q
          }
          /^X\/\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\/\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`

# CDPATH.
$as_unset CDPATH


if test "x$CONFIG_SHELL" = x; then
  if (eval ":") 2>/dev/null; then
  as_have_required=yes
else
  as_have_required=no
fi

  if test $as_have_required = yes &&     (eval ":
(as_func_return () {
  (exit \$1)
}
as_func_success () {
  as_func_return 0
}
as_func_failure () {
  as_func_return 1
}
as_func_ret_success () {
  return 0
}
as_func_ret_failure () {
  return 1
}

exitcode=0
if as_func_success; then
  :
else
  exitcode=1
  echo as_func_success failed.
fi

if as_func_failure; then
  exitcode=1
  echo as_func_failure succeeded.
fi

if as_func_ret_success; then
  :
else
  exitcode=1
  echo as_func_ret_success failed.
fi

if as_func_ret_failure; then
  exitcode=1
  echo as_func_ret_failure succeeded.
fi

if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
  :
else
  exitcode=1
  echo positional parameters were not saved.
fi

test \$exitcode = 0) || { (exit 1); exit 1; }

(
  as_lineno_1=\$LINENO
  as_lineno_2=\$LINENO
  test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
  test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
") 2> /dev/null; then
  :
else
  as_candidate_shells=
    as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in /usr/bin/posix$PATH_SEPARATOR/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  case $as_dir in
         /*)
           for as_base in sh bash ksh sh5; do
             as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
           done;;
       esac
done
IFS=$as_save_IFS


      for as_shell in $as_candidate_shells $SHELL; do
         # Try only shells that exist, to save several forks.
         if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
                { ("$as_shell") 2> /dev/null <<\_ASEOF
# Be Bourne compatible
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
  emulate sh
  NULLCMD=:
  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '${1+"$@"}'='"$@"'
  setopt NO_GLOB_SUBST
else
  case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
fi
BIN_SH=xpg4; export BIN_SH # for Tru64
DUALCASE=1; export DUALCASE # for MKS sh

:
_ASEOF
}; then
  CONFIG_SHELL=$as_shell
               as_have_required=yes
               if { "$as_shell" 2> /dev/null <<\_ASEOF
# Be Bourne compatible
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
  emulate sh
  NULLCMD=:
  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '${1+"$@"}'='"$@"'
  setopt NO_GLOB_SUBST
else
  case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
fi
BIN_SH=xpg4; export BIN_SH # for Tru64
DUALCASE=1; export DUALCASE # for MKS sh

:
(as_func_return () {
  (exit $1)
}
as_func_success () {
  as_func_return 0
}
as_func_failure () {
  as_func_return 1
}
as_func_ret_success () {
  return 0
}
as_func_ret_failure () {
  return 1
}

exitcode=0
if as_func_success; then
  :
else
  exitcode=1
  echo as_func_success failed.
fi

if as_func_failure; then
  exitcode=1
  echo as_func_failure succeeded.
fi

if as_func_ret_success; then
  :
else
  exitcode=1
  echo as_func_ret_success failed.
fi

if as_func_ret_failure; then
  exitcode=1
  echo as_func_ret_failure succeeded.
fi

if ( set x; as_func_ret_success y && test x = "$1" ); then
  :
else
  exitcode=1
  echo positional parameters were not saved.
fi

test $exitcode = 0) || { (exit 1); exit 1; }

(
  as_lineno_1=$LINENO
  as_lineno_2=$LINENO
  test "x$as_lineno_1" != "x$as_lineno_2" &&
  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }

_ASEOF
}; then
  break
fi

fi

      done

      if test "x$CONFIG_SHELL" != x; then
  for as_var in BASH_ENV ENV
        do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
        done
        export CONFIG_SHELL
        exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
fi


    if test $as_have_required = no; then
  echo This script requires a shell more modern than all the
      echo shells that I found on your system.  Please install a
      echo modern shell, or manually run the script under such a
      echo shell if you do have one.
      { (exit 1); exit 1; }
fi


fi

fi


(eval "as_func_return () {
  (exit \$1)
}
as_func_success () {
  as_func_return 0
}
as_func_failure () {
  as_func_return 1
}
as_func_ret_success () {
  return 0
}
as_func_ret_failure () {
  return 1
}

exitcode=0
if as_func_success; then
  :
else
  exitcode=1
  echo as_func_success failed.
fi

if as_func_failure; then
  exitcode=1
  echo as_func_failure succeeded.
fi

if as_func_ret_success; then
  :
else
  exitcode=1
  echo as_func_ret_success failed.
fi

if as_func_ret_failure; then
  exitcode=1
  echo as_func_ret_failure succeeded.
fi

if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
  :
else
  exitcode=1
  echo positional parameters were not saved.
fi

test \$exitcode = 0") || {
  echo No shell found that supports shell functions.
  echo Please tell autoconf@gnu.org about your system,
  echo including any error possibly output before this
  echo message
}


  as_lineno_1=$LINENO
  as_lineno_2=$LINENO
  test "x$as_lineno_1" != "x$as_lineno_2" &&
  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {

  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
  # uniformly replaced by the line number.  The first 'sed' inserts a
  # line-number line after each line using $LINENO; the second 'sed'
  # does the real work.  The second script uses 'N' to pair each
  # line-number line with the line containing $LINENO, and appends
  # trailing '-' during substitution so that $LINENO is not a special
  # case at line end.
  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
  # scripts with optimization help from Paolo Bonzini.  Blame Lee
  # E. McMahon (1931-1989) for sed's syntax.  :-)
  sed -n '
    p
    /[$]LINENO/=
  ' <$as_myself |
    sed '
      s/[$]LINENO.*/&-/
      t lineno
      b
      :lineno
      N
      :loop
      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
      t loop
      s/-\n.*//
    ' >$as_me.lineno &&
  chmod +x "$as_me.lineno" ||
    { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
   { (exit 1); exit 1; }; }

  # Don't try to exec as it changes $[0], causing all sort of problems
  # (the dirname of $[0] is not the place where we might find the
  # original and so on.  Autoconf is especially sensitive to this).
  . "./$as_me.lineno"
  # Exit status is that of the last command.
  exit
}


if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
  as_dirname=dirname
else
  as_dirname=false
fi

ECHO_C= ECHO_N= ECHO_T=
case `echo -n x` in
-n*)
  case `echo 'x\c'` in
  *c*) ECHO_T=' ';;     # ECHO_T is single tab character.
  *)   ECHO_C='\c';;
  esac;;
*)
  ECHO_N='-n';;
esac

if expr a : '\(a\)' >/dev/null 2>&1 &&
   test "X`expr 00001 : '.*\(...\)'`" = X001; then
  as_expr=expr
else
  as_expr=false
fi

rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
  rm -f conf$$.dir/conf$$.file
else
  rm -f conf$$.dir
  mkdir conf$$.dir
fi
echo >conf$$.file
if ln -s conf$$.file conf$$ 2>/dev/null; then
  as_ln_s='ln -s'
  # ... but there are two gotchas:
  # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
  # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
  # In both cases, we have to default to `cp -p'.
  ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
    as_ln_s='cp -p'
elif ln conf$$.file conf$$ 2>/dev/null; then
  as_ln_s=ln
else
  as_ln_s='cp -p'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null

if mkdir -p . 2>/dev/null; then
  as_mkdir_p=:
else
  test -d ./-p && rmdir ./-p
  as_mkdir_p=false
fi

# Find out whether ``test -x'' works.  Don't use a zero-byte file, as
# systems may use methods other than mode bits to determine executability.
cat >conf$$.file <<_ASEOF
#! /bin/sh
exit 0
_ASEOF
chmod +x conf$$.file
if test -x conf$$.file >/dev/null 2>&1; then
  as_executable_p="test -x"
else
  as_executable_p=:
fi
rm -f conf$$.file

# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"

# Sed expression to map a string onto a valid variable name.
as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"


exec 7<&0 </dev/null 6>&1

# Name of the host.
# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
# so uname gets run too.
ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`

#
# Initializations.
#
ac_default_prefix=/usr/local
ac_clean_files=
ac_config_libobj_dir=.
LIBOBJS=
cross_compiling=no
subdirs=
MFLAGS=
MAKEFLAGS=
SHELL=${CONFIG_SHELL-/bin/sh}

# Identity of this package.
PACKAGE_NAME='PDB2PQR'
PACKAGE_TARNAME='pdb2pqr'
PACKAGE_VERSION='1.3.0'
PACKAGE_STRING='PDB2PQR 1.3.0'
PACKAGE_BUGREPORT='todd@ccb.wustl.edu'

ac_subst_vars='SHELL
PATH_SEPARATOR
PACKAGE_NAME
PACKAGE_TARNAME
PACKAGE_VERSION
PACKAGE_STRING
PACKAGE_BUGREPORT
exec_prefix
prefix
program_transform_name
bindir
sbindir
libexecdir
datarootdir
datadir
sysconfdir
sharedstatedir
localstatedir
includedir
oldincludedir
docdir
infodir
htmldir
dvidir
pdfdir
psdir
libdir
localedir
mandir
DEFS
ECHO_C
ECHO_N
ECHO_T
LIBS
build_alias
host_alias
target_alias
build
build_cpu
build_vendor
build_os
host
host_cpu
host_vendor
host_os
target
target_cpu
target_vendor
target_os
INSTALL_PROGRAM
INSTALL_SCRIPT
INSTALL_DATA
CYGPATH_W
PACKAGE
VERSION
ACLOCAL
AUTOCONF
AUTOMAKE
AUTOHEADER
MAKEINFO
install_sh
STRIP
INSTALL_STRIP_PROGRAM
mkdir_p
AWK
SET_MAKE
am__leading_dot
AMTAR
am__tar
am__untar
PDB2PQR_VERSION
CXX
CXXFLAGS
LDFLAGS
CPPFLAGS
ac_ct_CXX
EXEEXT
OBJEXT
DEPDIR
am__include
am__quote
AMDEP_TRUE
AMDEP_FALSE
AMDEPBACKSLASH
CXXDEPMODE
am__fastdepCXX_TRUE
am__fastdepCXX_FALSE
py_path
PY_SHARED
PY_LDFLAGS
PY_HEADER
PY_FLAGS
PY_CFLAGS
PDB2PQR_SUBDIRS
URL
install_dir_var
website_install_var
action_install_var
with_propka
with_pdb2pka
LIBOBJS
LTLIBOBJS
last_website_install
last_prefix'
ac_subst_files=''
      ac_precious_vars='build_alias
host_alias
target_alias
CXX
CXXFLAGS
LDFLAGS
CPPFLAGS
CCC'


# Initialize some variables set by options.
ac_init_help=
ac_init_version=false
# The variables have the same names as the options, with
# dashes changed to underlines.
cache_file=/dev/null
exec_prefix=NONE
no_create=
no_recursion=
prefix=NONE
program_prefix=NONE
program_suffix=NONE
program_transform_name=s,x,x,
silent=
site=
srcdir=
verbose=
x_includes=NONE
x_libraries=NONE

# Installation directory options.
# These are left unexpanded so users can "make install exec_prefix=/foo"
# and all the variables that are supposed to be based on exec_prefix
# by default will actually change.
# Use braces instead of parens because sh, perl, etc. also accept them.
# (The list follows the same order as the GNU Coding Standards.)
bindir='${exec_prefix}/bin'
sbindir='${exec_prefix}/sbin'
libexecdir='${exec_prefix}/libexec'
datarootdir='${prefix}/share'
datadir='${datarootdir}'
sysconfdir='${prefix}/etc'
sharedstatedir='${prefix}/com'
localstatedir='${prefix}/var'
includedir='${prefix}/include'
oldincludedir='/usr/include'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
infodir='${datarootdir}/info'
htmldir='${docdir}'
dvidir='${docdir}'
pdfdir='${docdir}'
psdir='${docdir}'
libdir='${exec_prefix}/lib'
localedir='${datarootdir}/locale'
mandir='${datarootdir}/man'

ac_prev=
ac_dashdash=
for ac_option
do
  # If the previous option needs an argument, assign it.
  if test -n "$ac_prev"; then
    eval $ac_prev=\$ac_option
    ac_prev=
    continue
  fi

  case $ac_option in
  *=*)  ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
  *)    ac_optarg=yes ;;
  esac

  # Accept the important Cygnus configure options, so we can diagnose typos.

  case $ac_dashdash$ac_option in
  --)
    ac_dashdash=yes ;;

  -bindir | --bindir | --bindi | --bind | --bin | --bi)
    ac_prev=bindir ;;
  -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
    bindir=$ac_optarg ;;

  -build | --build | --buil | --bui | --bu)
    ac_prev=build_alias ;;
  -build=* | --build=* | --buil=* | --bui=* | --bu=*)
    build_alias=$ac_optarg ;;

  -cache-file | --cache-file | --cache-fil | --cache-fi \
  | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
    ac_prev=cache_file ;;
  -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
  | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
    cache_file=$ac_optarg ;;

  --config-cache | -C)
    cache_file=config.cache ;;

  -datadir | --datadir | --datadi | --datad)
    ac_prev=datadir ;;
  -datadir=* | --datadir=* | --datadi=* | --datad=*)
    datadir=$ac_optarg ;;

  -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
  | --dataroo | --dataro | --datar)
    ac_prev=datarootdir ;;
  -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
  | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
    datarootdir=$ac_optarg ;;

  -disable-* | --disable-*)
    ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null &&
      { echo "$as_me: error: invalid feature name: $ac_feature" >&2
   { (exit 1); exit 1; }; }
    ac_feature=`echo $ac_feature | sed 's/-/_/g'`
    eval enable_$ac_feature=no ;;

  -docdir | --docdir | --docdi | --doc | --do)
    ac_prev=docdir ;;
  -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
    docdir=$ac_optarg ;;

  -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
    ac_prev=dvidir ;;
  -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
    dvidir=$ac_optarg ;;

  -enable-* | --enable-*)
    ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null &&
      { echo "$as_me: error: invalid feature name: $ac_feature" >&2
   { (exit 1); exit 1; }; }
    ac_feature=`echo $ac_feature | sed 's/-/_/g'`
    eval enable_$ac_feature=\$ac_optarg ;;

  -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
  | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
  | --exec | --exe | --ex)
    ac_prev=exec_prefix ;;
  -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
  | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
  | --exec=* | --exe=* | --ex=*)
    exec_prefix=$ac_optarg ;;

  -gas | --gas | --ga | --g)
    # Obsolete; use --with-gas.
    with_gas=yes ;;

  -help | --help | --hel | --he | -h)
    ac_init_help=long ;;
  -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
    ac_init_help=recursive ;;
  -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
    ac_init_help=short ;;

  -host | --host | --hos | --ho)
    ac_prev=host_alias ;;
  -host=* | --host=* | --hos=* | --ho=*)
    host_alias=$ac_optarg ;;

  -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
    ac_prev=htmldir ;;
  -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
  | --ht=*)
    htmldir=$ac_optarg ;;

  -includedir | --includedir | --includedi | --included | --include \
  | --includ | --inclu | --incl | --inc)
    ac_prev=includedir ;;
  -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
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    includedir=$ac_optarg ;;

  -infodir | --infodir | --infodi | --infod | --info | --inf)
    ac_prev=infodir ;;
  -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
    infodir=$ac_optarg ;;

  -libdir | --libdir | --libdi | --libd)
    ac_prev=libdir ;;
  -libdir=* | --libdir=* | --libdi=* | --libd=*)
    libdir=$ac_optarg ;;

  -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
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    ac_prev=libexecdir ;;
  -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
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    libexecdir=$ac_optarg ;;

  -localedir | --localedir | --localedi | --localed | --locale)
    ac_prev=localedir ;;
  -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
    localedir=$ac_optarg ;;

  -localstatedir | --localstatedir | --localstatedi | --localstated \
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    ac_prev=localstatedir ;;
  -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
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    localstatedir=$ac_optarg ;;

  -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
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    mandir=$ac_optarg ;;

  -nfp | --nfp | --nf)
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    with_fp=no ;;

  -no-create | --no-create | --no-creat | --no-crea | --no-cre \
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    no_create=yes ;;

  -no-recursion | --no-recursion | --no-recursio | --no-recursi \
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    no_recursion=yes ;;

  -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
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    ac_prev=oldincludedir ;;
  -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
  | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
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    oldincludedir=$ac_optarg ;;

  -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
    ac_prev=prefix ;;
  -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
    prefix=$ac_optarg ;;

  -program-prefix | --program-prefix | --program-prefi | --program-pref \
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    ac_prev=program_prefix ;;
  -program-prefix=* | --program-prefix=* | --program-prefi=* \
  | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
    program_prefix=$ac_optarg ;;

  -program-suffix | --program-suffix | --program-suffi | --program-suff \
  | --program-suf | --program-su | --program-s)
    ac_prev=program_suffix ;;
  -program-suffix=* | --program-suffix=* | --program-suffi=* \
  | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
    program_suffix=$ac_optarg ;;

  -program-transform-name | --program-transform-name \
  | --program-transform-nam | --program-transform-na \
  | --program-transform-n | --program-transform- \
  | --program-transform | --program-transfor \
  | --program-transfo | --program-transf \
  | --program-trans | --program-tran \
  | --progr-tra | --program-tr | --program-t)
    ac_prev=program_transform_name ;;
  -program-transform-name=* | --program-transform-name=* \
  | --program-transform-nam=* | --program-transform-na=* \
  | --program-transform-n=* | --program-transform-=* \
  | --program-transform=* | --program-transfor=* \
  | --program-transfo=* | --program-transf=* \
  | --program-trans=* | --program-tran=* \
  | --progr-tra=* | --program-tr=* | --program-t=*)
    program_transform_name=$ac_optarg ;;

  -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
    ac_prev=pdfdir ;;
  -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
    pdfdir=$ac_optarg ;;

  -psdir | --psdir | --psdi | --psd | --ps)
    ac_prev=psdir ;;
  -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
    psdir=$ac_optarg ;;

  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
  | -silent | --silent | --silen | --sile | --sil)
    silent=yes ;;

  -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
    ac_prev=sbindir ;;
  -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
  | --sbi=* | --sb=*)
    sbindir=$ac_optarg ;;

  -sharedstatedir | --sharedstatedir | --sharedstatedi \
  | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
  | --sharedst | --shareds | --shared | --share | --shar \
  | --sha | --sh)
    ac_prev=sharedstatedir ;;
  -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
  | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
  | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
  | --sha=* | --sh=*)
    sharedstatedir=$ac_optarg ;;

  -site | --site | --sit)
    ac_prev=site ;;
  -site=* | --site=* | --sit=*)
    site=$ac_optarg ;;

  -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
    ac_prev=srcdir ;;
  -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
    srcdir=$ac_optarg ;;

  -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
  | --syscon | --sysco | --sysc | --sys | --sy)
    ac_prev=sysconfdir ;;
  -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
  | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
    sysconfdir=$ac_optarg ;;

  -target | --target | --targe | --targ | --tar | --ta | --t)
    ac_prev=target_alias ;;
  -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
    target_alias=$ac_optarg ;;

  -v | -verbose | --verbose | --verbos | --verbo | --verb)
    verbose=yes ;;

  -version | --version | --versio | --versi | --vers | -V)
    ac_init_version=: ;;

  -with-* | --with-*)
    ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null &&
      { echo "$as_me: error: invalid package name: $ac_package" >&2
   { (exit 1); exit 1; }; }
    ac_package=`echo $ac_package| sed 's/-/_/g'`
    eval with_$ac_package=\$ac_optarg ;;

  -without-* | --without-*)
    ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null &&
      { echo "$as_me: error: invalid package name: $ac_package" >&2
   { (exit 1); exit 1; }; }
    ac_package=`echo $ac_package | sed 's/-/_/g'`
    eval with_$ac_package=no ;;

  --x)
    # Obsolete; use --with-x.
    with_x=yes ;;

  -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
  | --x-incl | --x-inc | --x-in | --x-i)
    ac_prev=x_includes ;;
  -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
  | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*)
    x_includes=$ac_optarg ;;

  -x-libraries | --x-libraries | --x-librarie | --x-librari \
  | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l)
    ac_prev=x_libraries ;;
  -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
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    x_libraries=$ac_optarg ;;

  -*) { echo "$as_me: error: unrecognized option: $ac_option
Try \`$0 --help' for more information." >&2
   { (exit 1); exit 1; }; }
    ;;

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    ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
    # Reject names that are not valid shell variable names.
    expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
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   { (exit 1); exit 1; }; }
    eval $ac_envvar=\$ac_optarg
    export $ac_envvar ;;

  *)
    # FIXME: should be removed in autoconf 3.0.
    echo "$as_me: WARNING: you should use --build, --host, --target" >&2
    expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
      echo "$as_me: WARNING: invalid host type: $ac_option" >&2
    : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
    ;;

  esac
done

if test -n "$ac_prev"; then
  ac_option=--`echo $ac_prev | sed 's/_/-/g'`
  { echo "$as_me: error: missing argument to $ac_option" >&2
   { (exit 1); exit 1; }; }
fi

# Be sure to have absolute directory names.
for ac_var in   exec_prefix prefix bindir sbindir libexecdir datarootdir \
                datadir sysconfdir sharedstatedir localstatedir includedir \
                oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
                libdir localedir mandir
do
  eval ac_val=\$$ac_var
  case $ac_val in
    [\\/$]* | ?:[\\/]* )  continue;;
    NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
  esac
  { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
   { (exit 1); exit 1; }; }
done

# There might be people who depend on the old broken behavior: `$host'
# used to hold the argument of --host etc.
# FIXME: To remove some day.
build=$build_alias
host=$host_alias
target=$target_alias

# FIXME: To remove some day.
if test "x$host_alias" != x; then
  if test "x$build_alias" = x; then
    cross_compiling=maybe
    echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
    If a cross compiler is detected then cross compile mode will be used." >&2
  elif test "x$build_alias" != "x$host_alias"; then
    cross_compiling=yes
  fi
fi

ac_tool_prefix=
test -n "$host_alias" && ac_tool_prefix=$host_alias-

test "$silent" = yes && exec 6>/dev/null


ac_pwd=`pwd` && test -n "$ac_pwd" &&
ac_ls_di=`ls -di .` &&
ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
  { echo "$as_me: error: Working directory cannot be determined" >&2
   { (exit 1); exit 1; }; }
test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
  { echo "$as_me: error: pwd does not report name of working directory" >&2
   { (exit 1); exit 1; }; }


# Find the source files, if location was not specified.
if test -z "$srcdir"; then
  ac_srcdir_defaulted=yes
  # Try the directory containing this script, then the parent directory.
  ac_confdir=`$as_dirname -- "$0" ||
$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
         X"$0" : 'X\(//\)[^/]' \| \
         X"$0" : 'X\(//\)$' \| \
         X"$0" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$0" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
            s//\1/
            q
          }
          /^X\(\/\/\)[^/].*/{
            s//\1/
            q
          }
          /^X\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`
  srcdir=$ac_confdir
  if test ! -r "$srcdir/$ac_unique_file"; then
    srcdir=..
  fi
else
  ac_srcdir_defaulted=no
fi
if test ! -r "$srcdir/$ac_unique_file"; then
  test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
  { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
   { (exit 1); exit 1; }; }
fi
ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
ac_abs_confdir=`(
        cd "$srcdir" && test -r "./$ac_unique_file" || { echo "$as_me: error: $ac_msg" >&2
   { (exit 1); exit 1; }; }
        pwd)`
# When building in place, set srcdir=.
if test "$ac_abs_confdir" = "$ac_pwd"; then
  srcdir=.
fi
# Remove unnecessary trailing slashes from srcdir.
# Double slashes in file names in object file debugging info
# mess up M-x gdb in Emacs.
case $srcdir in
*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
esac
for ac_var in $ac_precious_vars; do
  eval ac_env_${ac_var}_set=\${${ac_var}+set}
  eval ac_env_${ac_var}_value=\$${ac_var}
  eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
  eval ac_cv_env_${ac_var}_value=\$${ac_var}
done

#
# Report the --help message.
#
if test "$ac_init_help" = "long"; then
  # Omit some internal or obsolete options to make the list less imposing.
  # This message is too long to be a string in the A/UX 3.1 sh.
  cat <<_ACEOF
\`configure' configures PDB2PQR 1.3.0 to adapt to many kinds of systems.

Usage: $0 [OPTION]... [VAR=VALUE]...

To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE.  See below for descriptions of some of the useful variables.

Defaults for the options are specified in brackets.

Configuration:
  -h, --help              display this help and exit
      --help=short        display options specific to this package
      --help=recursive    display the short help of all the included packages
  -V, --version           display version information and exit
  -q, --quiet, --silent   do not print \`checking...' messages
      --cache-file=FILE   cache test results in FILE [disabled]
  -C, --config-cache      alias for \`--cache-file=config.cache'
  -n, --no-create         do not create output files
      --srcdir=DIR        find the sources in DIR [configure dir or \`..']

Installation directories:
  --prefix=PREFIX         install architecture-independent files in PREFIX
                          [$ac_default_prefix]
  --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX
                          [PREFIX]

By default, \`make install' will install all the files in
\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc.  You can specify
an installation prefix other than \`$ac_default_prefix' using \`--prefix',
for instance \`--prefix=\$HOME'.

For better control, use the options below.

Fine tuning of the installation directories:
  --bindir=DIR           user executables [EPREFIX/bin]
  --sbindir=DIR          system admin executables [EPREFIX/sbin]
  --libexecdir=DIR       program executables [EPREFIX/libexec]
  --sysconfdir=DIR       read-only single-machine data [PREFIX/etc]
  --sharedstatedir=DIR   modifiable architecture-independent data [PREFIX/com]
  --localstatedir=DIR    modifiable single-machine data [PREFIX/var]
  --libdir=DIR           object code libraries [EPREFIX/lib]
  --includedir=DIR       C header files [PREFIX/include]
  --oldincludedir=DIR    C header files for non-gcc [/usr/include]
  --datarootdir=DIR      read-only arch.-independent data root [PREFIX/share]
  --datadir=DIR          read-only architecture-independent data [DATAROOTDIR]
  --infodir=DIR          info documentation [DATAROOTDIR/info]
  --localedir=DIR        locale-dependent data [DATAROOTDIR/locale]
  --mandir=DIR           man documentation [DATAROOTDIR/man]
  --docdir=DIR           documentation root [DATAROOTDIR/doc/pdb2pqr]
  --htmldir=DIR          html documentation [DOCDIR]
  --dvidir=DIR           dvi documentation [DOCDIR]
  --pdfdir=DIR           pdf documentation [DOCDIR]
  --psdir=DIR            ps documentation [DOCDIR]
_ACEOF

  cat <<\_ACEOF

Program names:
  --program-prefix=PREFIX            prepend PREFIX to installed program names
  --program-suffix=SUFFIX            append SUFFIX to installed program names
  --program-transform-name=PROGRAM   run sed PROGRAM on installed program names

System types:
  --build=BUILD     configure for building on BUILD [guessed]
  --host=HOST       cross-compile to build programs to run on HOST [BUILD]
  --target=TARGET   configure for building compilers for TARGET [HOST]
_ACEOF
fi

if test -n "$ac_init_help"; then
  case $ac_init_help in
     short | recursive ) echo "Configuration of PDB2PQR 1.3.0:";;
   esac
  cat <<\_ACEOF

Optional Features:
  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
  --disable-dependency-tracking  speeds up one-time build
  --enable-dependency-tracking   do not reject slow dependency extractors
  --disable-propka        Disable propka compilation
  --disable-pdb2pka       Disable pdb2pka compilation

Optional Packages:
  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
  --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
  --with-python=PYTHONPATH           Specify Python location.
  --with-url=URL           Set url for the website.  Default http://fully_qualified_domain/pdb2pqr.
  --with-max-atoms=MAX_ATOMS    Sets the maximum number of atoms in a protein for non-Opal job submission.  Default is 10000
  --with-opal=OPALURL                   Set url for the Opal service.  Default is http://ws.nbcr.net:8080/axis-1.2.1/services/Pdb2pqrOpalService.

Some influential environment variables:
  CXX         C++ compiler command
  CXXFLAGS    C++ compiler flags
  LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
              nonstandard directory <lib dir>
  CPPFLAGS    C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
              you have headers in a nonstandard directory <include dir>

Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.

Report bugs to <todd@ccb.wustl.edu>.
_ACEOF
ac_status=$?
fi

if test "$ac_init_help" = "recursive"; then
  # If there are subdirs, report their specific --help.
  for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
    test -d "$ac_dir" || continue
    ac_builddir=.

case "$ac_dir" in
.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
*)
  ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
  # A ".." for each directory in $ac_dir_suffix.
  ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
  case $ac_top_builddir_sub in
  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
  esac ;;
esac
ac_abs_top_builddir=$ac_pwd
ac_abs_builddir=$ac_pwd$ac_dir_suffix
# for backward compatibility:
ac_top_builddir=$ac_top_build_prefix

case $srcdir in
  .)  # We are building in place.
    ac_srcdir=.
    ac_top_srcdir=$ac_top_builddir_sub
    ac_abs_top_srcdir=$ac_pwd ;;
  [\\/]* | ?:[\\/]* )  # Absolute name.
    ac_srcdir=$srcdir$ac_dir_suffix;
    ac_top_srcdir=$srcdir
    ac_abs_top_srcdir=$srcdir ;;
  *) # Relative name.
    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
    ac_top_srcdir=$ac_top_build_prefix$srcdir
    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
esac
ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix

    cd "$ac_dir" || { ac_status=$?; continue; }
    # Check for guested configure.
    if test -f "$ac_srcdir/configure.gnu"; then
      echo &&
      $SHELL "$ac_srcdir/configure.gnu" --help=recursive
    elif test -f "$ac_srcdir/configure"; then
      echo &&
      $SHELL "$ac_srcdir/configure" --help=recursive
    else
      echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
    fi || ac_status=$?
    cd "$ac_pwd" || { ac_status=$?; break; }
  done
fi

test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
  cat <<\_ACEOF
PDB2PQR configure 1.3.0
generated by GNU Autoconf 2.60

Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.
_ACEOF
  exit
fi
cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by PDB2PQR $as_me 1.3.0, which was
generated by GNU Autoconf 2.60.  Invocation command line was

  $ $0 $@

_ACEOF
exec 5>>config.log
{
cat <<_ASUNAME
## --------- ##
## Platform. ##
## --------- ##

hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
uname -m = `(uname -m) 2>/dev/null || echo unknown`
uname -r = `(uname -r) 2>/dev/null || echo unknown`
uname -s = `(uname -s) 2>/dev/null || echo unknown`
uname -v = `(uname -v) 2>/dev/null || echo unknown`

/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
/bin/uname -X     = `(/bin/uname -X) 2>/dev/null     || echo unknown`

/bin/arch              = `(/bin/arch) 2>/dev/null              || echo unknown`
/usr/bin/arch -k       = `(/usr/bin/arch -k) 2>/dev/null       || echo unknown`
/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
/usr/bin/hostinfo      = `(/usr/bin/hostinfo) 2>/dev/null      || echo unknown`
/bin/machine           = `(/bin/machine) 2>/dev/null           || echo unknown`
/usr/bin/oslevel       = `(/usr/bin/oslevel) 2>/dev/null       || echo unknown`
/bin/universe          = `(/bin/universe) 2>/dev/null          || echo unknown`

_ASUNAME

as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  echo "PATH: $as_dir"
done
IFS=$as_save_IFS

} >&5

cat >&5 <<_ACEOF


## ----------- ##
## Core tests. ##
## ----------- ##

_ACEOF


# Keep a trace of the command line.
# Strip out --no-create and --no-recursion so they do not pile up.
# Strip out --silent because we don't want to record it for future runs.
# Also quote any args containing shell meta-characters.
# Make two passes to allow for proper duplicate-argument suppression.
ac_configure_args=
ac_configure_args0=
ac_configure_args1=
ac_must_keep_next=false
for ac_pass in 1 2
do
  for ac_arg
  do
    case $ac_arg in
    -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
    -q | -quiet | --quiet | --quie | --qui | --qu | --q \
    | -silent | --silent | --silen | --sile | --sil)
      continue ;;
    *\'*)
      ac_arg=`echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
    esac
    case $ac_pass in
    1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
    2)
      ac_configure_args1="$ac_configure_args1 '$ac_arg'"
      if test $ac_must_keep_next = true; then
        ac_must_keep_next=false # Got value, back to normal.
      else
        case $ac_arg in
          *=* | --config-cache | -C | -disable-* | --disable-* \
          | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
          | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
          | -with-* | --with-* | -without-* | --without-* | --x)
            case "$ac_configure_args0 " in
              "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
            esac
            ;;
          -* ) ac_must_keep_next=true ;;
        esac
      fi
      ac_configure_args="$ac_configure_args '$ac_arg'"
      ;;
    esac
  done
done
$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }

# When interrupted or exit'd, cleanup temporary files, and complete
# config.log.  We remove comments because anyway the quotes in there
# would cause problems or look ugly.
# WARNING: Use '\'' to represent an apostrophe within the trap.
# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
trap 'exit_status=$?
  # Save into config.log some information that might help in debugging.
  {
    echo

    cat <<\_ASBOX
## ---------------- ##
## Cache variables. ##
## ---------------- ##
_ASBOX
    echo
    # The following way of writing the cache mishandles newlines in values,
(
  for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
    eval ac_val=\$$ac_var
    case $ac_val in #(
    *${as_nl}*)
      case $ac_var in #(
      *_cv_*) { echo "$as_me:$LINENO: WARNING: Cache variable $ac_var contains a newline." >&5
echo "$as_me: WARNING: Cache variable $ac_var contains a newline." >&2;} ;;
      esac
      case $ac_var in #(
      _ | IFS | as_nl) ;; #(
      *) $as_unset $ac_var ;;
      esac ;;
    esac
  done
  (set) 2>&1 |
    case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
    *${as_nl}ac_space=\ *)
      sed -n \
        "s/'\''/'\''\\\\'\'''\''/g;
          s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
      ;; #(
    *)
      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
      ;;
    esac |
    sort
)
    echo

    cat <<\_ASBOX
## ----------------- ##
## Output variables. ##
## ----------------- ##
_ASBOX
    echo
    for ac_var in $ac_subst_vars
    do
      eval ac_val=\$$ac_var
      case $ac_val in
      *\'\''*) ac_val=`echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
      esac
      echo "$ac_var='\''$ac_val'\''"
    done | sort
    echo

    if test -n "$ac_subst_files"; then
      cat <<\_ASBOX
## ------------------- ##
## File substitutions. ##
## ------------------- ##
_ASBOX
      echo
      for ac_var in $ac_subst_files
      do
        eval ac_val=\$$ac_var
        case $ac_val in
        *\'\''*) ac_val=`echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
        esac
        echo "$ac_var='\''$ac_val'\''"
      done | sort
      echo
    fi

    if test -s confdefs.h; then
      cat <<\_ASBOX
## ----------- ##
## confdefs.h. ##
## ----------- ##
_ASBOX
      echo
      cat confdefs.h
      echo
    fi
    test "$ac_signal" != 0 &&
      echo "$as_me: caught signal $ac_signal"
    echo "$as_me: exit $exit_status"
  } >&5
  rm -f core *.core core.conftest.* &&
    rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
    exit $exit_status
' 0
for ac_signal in 1 2 13 15; do
  trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
done
ac_signal=0

# confdefs.h avoids OS command line length limits that DEFS can exceed.
rm -f -r conftest* confdefs.h

# Predefined preprocessor variables.

cat >>confdefs.h <<_ACEOF
#define PACKAGE_NAME "$PACKAGE_NAME"
_ACEOF


cat >>confdefs.h <<_ACEOF
#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
_ACEOF


cat >>confdefs.h <<_ACEOF
#define PACKAGE_VERSION "$PACKAGE_VERSION"
_ACEOF


cat >>confdefs.h <<_ACEOF
#define PACKAGE_STRING "$PACKAGE_STRING"
_ACEOF


cat >>confdefs.h <<_ACEOF
#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
_ACEOF


# Let the site file select an alternate cache file if it wants to.
# Prefer explicitly selected file to automatically selected ones.
if test -n "$CONFIG_SITE"; then
  set x "$CONFIG_SITE"
elif test "x$prefix" != xNONE; then
  set x "$prefix/share/config.site" "$prefix/etc/config.site"
else
  set x "$ac_default_prefix/share/config.site" \
        "$ac_default_prefix/etc/config.site"
fi
shift
for ac_site_file
do
  if test -r "$ac_site_file"; then
    { echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
echo "$as_me: loading site script $ac_site_file" >&6;}
    sed 's/^/| /' "$ac_site_file" >&5
    . "$ac_site_file"
  fi
done

if test -r "$cache_file"; then
  # Some versions of bash will fail to source /dev/null (special
  # files actually), so we avoid doing that.
  if test -f "$cache_file"; then
    { echo "$as_me:$LINENO: loading cache $cache_file" >&5
echo "$as_me: loading cache $cache_file" >&6;}
    case $cache_file in
      [\\/]* | ?:[\\/]* ) . "$cache_file";;
      *)                      . "./$cache_file";;
    esac
  fi
else
  { echo "$as_me:$LINENO: creating cache $cache_file" >&5
echo "$as_me: creating cache $cache_file" >&6;}
  >$cache_file
fi

# Check that the precious variables saved in the cache have kept the same
# value.
ac_cache_corrupted=false
for ac_var in $ac_precious_vars; do
  eval ac_old_set=\$ac_cv_env_${ac_var}_set
  eval ac_new_set=\$ac_env_${ac_var}_set
  eval ac_old_val=\$ac_cv_env_${ac_var}_value
  eval ac_new_val=\$ac_env_${ac_var}_value
  case $ac_old_set,$ac_new_set in
    set,)
      { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
      ac_cache_corrupted=: ;;
    ,set)
      { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
      ac_cache_corrupted=: ;;
    ,);;
    *)
      if test "x$ac_old_val" != "x$ac_new_val"; then
        { echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
        { echo "$as_me:$LINENO:   former value:  $ac_old_val" >&5
echo "$as_me:   former value:  $ac_old_val" >&2;}
        { echo "$as_me:$LINENO:   current value: $ac_new_val" >&5
echo "$as_me:   current value: $ac_new_val" >&2;}
        ac_cache_corrupted=:
      fi;;
  esac
  # Pass precious variables to config.status.
  if test "$ac_new_set" = set; then
    case $ac_new_val in
    *\'*) ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
    *) ac_arg=$ac_var=$ac_new_val ;;
    esac
    case " $ac_configure_args " in
      *" '$ac_arg' "*) ;; # Avoid dups.  Use of quotes ensures accuracy.
      *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
    esac
  fi
done
if $ac_cache_corrupted; then
  { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
echo "$as_me: error: changes in the environment can compromise the build" >&2;}
  { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
   { (exit 1); exit 1; }; }
fi


ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu


ac_aux_dir=
for ac_dir in config "$srcdir"/config; do
  if test -f "$ac_dir/install-sh"; then
    ac_aux_dir=$ac_dir
    ac_install_sh="$ac_aux_dir/install-sh -c"
    break
  elif test -f "$ac_dir/install.sh"; then
    ac_aux_dir=$ac_dir
    ac_install_sh="$ac_aux_dir/install.sh -c"
    break
  elif test -f "$ac_dir/shtool"; then
    ac_aux_dir=$ac_dir
    ac_install_sh="$ac_aux_dir/shtool install -c"
    break
  fi
done
if test -z "$ac_aux_dir"; then
  { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in config \"$srcdir\"/config" >&5
echo "$as_me: error: cannot find install-sh or install.sh in config \"$srcdir\"/config" >&2;}
   { (exit 1); exit 1; }; }
fi

# These three variables are undocumented and unsupported,
# and are intended to be withdrawn in a future Autoconf release.
# They can cause serious problems if a builder's source tree is in a directory
# whose full name contains unusual characters.
ac_config_guess="$SHELL $ac_aux_dir/config.guess"  # Please don't use this var.
ac_config_sub="$SHELL $ac_aux_dir/config.sub"  # Please don't use this var.
ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.


# Make sure we can run config.sub.
$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
  { { echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5
echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
   { (exit 1); exit 1; }; }

{ echo "$as_me:$LINENO: checking build system type" >&5
echo $ECHO_N "checking build system type... $ECHO_C" >&6; }
if test "${ac_cv_build+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  ac_build_alias=$build_alias
test "x$ac_build_alias" = x &&
  ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
test "x$ac_build_alias" = x &&
  { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
   { (exit 1); exit 1; }; }
ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
  { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
   { (exit 1); exit 1; }; }

fi
{ echo "$as_me:$LINENO: result: $ac_cv_build" >&5
echo "${ECHO_T}$ac_cv_build" >&6; }
case $ac_cv_build in
*-*-*) ;;
*) { { echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
echo "$as_me: error: invalid value of canonical build" >&2;}
   { (exit 1); exit 1; }; };;
esac
build=$ac_cv_build
ac_save_IFS=$IFS; IFS='-'
set x $ac_cv_build
shift
build_cpu=$1
build_vendor=$2
shift; shift
# Remember, the first character of IFS is used to create $*,
# except with old shells:
build_os=$*
IFS=$ac_save_IFS
case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac


{ echo "$as_me:$LINENO: checking host system type" >&5
echo $ECHO_N "checking host system type... $ECHO_C" >&6; }
if test "${ac_cv_host+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test "x$host_alias" = x; then
  ac_cv_host=$ac_cv_build
else
  ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
    { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
   { (exit 1); exit 1; }; }
fi

fi
{ echo "$as_me:$LINENO: result: $ac_cv_host" >&5
echo "${ECHO_T}$ac_cv_host" >&6; }
case $ac_cv_host in
*-*-*) ;;
*) { { echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
echo "$as_me: error: invalid value of canonical host" >&2;}
   { (exit 1); exit 1; }; };;
esac
host=$ac_cv_host
ac_save_IFS=$IFS; IFS='-'
set x $ac_cv_host
shift
host_cpu=$1
host_vendor=$2
shift; shift
# Remember, the first character of IFS is used to create $*,
# except with old shells:
host_os=$*
IFS=$ac_save_IFS
case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac


{ echo "$as_me:$LINENO: checking target system type" >&5
echo $ECHO_N "checking target system type... $ECHO_C" >&6; }
if test "${ac_cv_target+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test "x$target_alias" = x; then
  ac_cv_target=$ac_cv_host
else
  ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` ||
    { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5
echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;}
   { (exit 1); exit 1; }; }
fi

fi
{ echo "$as_me:$LINENO: result: $ac_cv_target" >&5
echo "${ECHO_T}$ac_cv_target" >&6; }
case $ac_cv_target in
*-*-*) ;;
*) { { echo "$as_me:$LINENO: error: invalid value of canonical target" >&5
echo "$as_me: error: invalid value of canonical target" >&2;}
   { (exit 1); exit 1; }; };;
esac
target=$ac_cv_target
ac_save_IFS=$IFS; IFS='-'
set x $ac_cv_target
shift
target_cpu=$1
target_vendor=$2
shift; shift
# Remember, the first character of IFS is used to create $*,
# except with old shells:
target_os=$*
IFS=$ac_save_IFS
case $target_os in *\ *) target_os=`echo "$target_os" | sed 's/ /-/g'`;; esac


# The aliases save the names the user supplied, while $host etc.
# will get canonicalized.
test -n "$target_alias" &&
  test "$program_prefix$program_suffix$program_transform_name" = \
    NONENONEs,x,x, &&
  program_prefix=${target_alias}-

# Added by J.Ren

chmod 755 .

pwd > cwdfile
cwd=`awk -F"/" '{ print $NF }' cwdfile`
rm cwdfile

if test ${prefix} == "NONE" ; then
  if test `whoami` = "root" ; then
    if test -d "/var/www/html/pdb2pqr" ; then
      echo "*** Warning: As root, your default --prefix is set to /var/www/html/pdb2pqr."
      echo "    However, we have detected that /var/www/html/pdb2pqr already exists."
      echo "    You may run configure again and specify a different --prefix"
      echo "    Do you want to overwrite this directory? (Y/N)"
      read choice
      while test $choice != "Y" && test $choice != "y" && test $choice != "N" && test $choice != "n"
        do
        echo You have entered $choice. Please enter Y or N:
        read choice
      done
      if test $choice = "N" || test $choice = "n" ; then
        echo Please run configure again and specify a different --prefix
        exit 0
      fi
    fi
    prefix=/var/www/html/pdb2pqr
  else
    if test -d ${HOME}/pdb2pqr ; then
      echo "*** Warning: As a regular user, your default --prefix is set to ${HOME}/pdb2pqr."
      echo "    However, we have detected that ${HOME}/pdb2pqr already exists."
      echo "    You may run configure again and specify --prefix"
      echo "    You may run configure again and specify a different --prefix"
      echo "    Do you want to overwrite this directory? (Y/N)"
      read choice
      while test $choice != "Y" && test $choice != "y" && test $choice != "N" && test $choice != "n"
        do
        echo You have entered $choice. Please enter Y or N:
        read choice
      done
      if test $choice = "N" || test $choice = "n" ; then
        echo Please run configure again and specify a different --prefix
        exit 0
      fi
    fi
    prefix=${HOME}/pdb2pqr
  fi
  default_prefix_used="true"
fi

echo ${prefix} > prefix_test
isslash=`awk -F"/" '{print $NF}' prefix_test`
rm -f prefix_test

if ! test -z $isslash ; then
  prefix=${prefix}/
fi


# Find a good install program.  We prefer a C program (faster),
# so one script is as good as another.  But avoid the broken or
# incompatible versions:
# SysV /etc/install, /usr/sbin/install
# SunOS /usr/etc/install
# IRIX /sbin/install
# AIX /bin/install
# AmigaOS /C/install, which installs bootblocks on floppy discs
# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
# AFS /usr/afsws/bin/install, which mishandles nonexistent args
# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
# OS/2's system install, which has a completely different semantic
# ./install, which can be erroneously created by make from ./install.sh.
{ echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6; }
if test -z "$INSTALL"; then
if test "${ac_cv_path_install+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  # Account for people who put trailing slashes in PATH elements.
case $as_dir/ in
  ./ | .// | /cC/* | \
  /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
  ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
  /usr/ucb/* ) ;;
  *)
    # OSF1 and SCO ODT 3.0 have their own names for install.
    # Don't use installbsd from OSF since it installs stuff as root
    # by default.
    for ac_prog in ginstall scoinst install; do
      for ac_exec_ext in '' $ac_executable_extensions; do
        if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; }; then
          if test $ac_prog = install &&
            grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
            # AIX install.  It has an incompatible calling convention.
            :
          elif test $ac_prog = install &&
            grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
            # program-specific install script used by HP pwplus--don't use.
            :
          else
            ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
            break 3
          fi
        fi
      done
    done
    ;;
esac
done
IFS=$as_save_IFS


fi
  if test "${ac_cv_path_install+set}" = set; then
    INSTALL=$ac_cv_path_install
  else
    # As a last resort, use the slow shell script.  Don't cache a
    # value for INSTALL within a source directory, because that will
    # break other packages using the cache if that directory is
    # removed, or if the value is a relative name.
    INSTALL=$ac_install_sh
  fi
fi
{ echo "$as_me:$LINENO: result: $INSTALL" >&5
echo "${ECHO_T}$INSTALL" >&6; }

# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
# It thinks the first close brace ends the variable substitution.
test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'

test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'

test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'


am__api_version="1.9"
{ echo "$as_me:$LINENO: checking whether build environment is sane" >&5
echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6; }
# Just in case
sleep 1
echo timestamp > conftest.file
# Do `set' in a subshell so we don't clobber the current shell's
# arguments.  Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
   set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
   if test "$*" = "X"; then
      # -L didn't work.
      set X `ls -t $srcdir/configure conftest.file`
   fi
   rm -f conftest.file
   if test "$*" != "X $srcdir/configure conftest.file" \
      && test "$*" != "X conftest.file $srcdir/configure"; then

      # If neither matched, then we have a broken ls.  This can happen
      # if, for instance, CONFIG_SHELL is bash and it inherits a
      # broken ls alias from the environment.  This has actually
      # happened.  Such a system could not be considered "sane".
      { { echo "$as_me:$LINENO: error: ls -t appears to fail.  Make sure there is not a broken
alias in your environment" >&5
echo "$as_me: error: ls -t appears to fail.  Make sure there is not a broken
alias in your environment" >&2;}
   { (exit 1); exit 1; }; }
   fi

   test "$2" = conftest.file
   )
then
   # Ok.
   :
else
   { { echo "$as_me:$LINENO: error: newly created file is older than distributed files!
Check your system clock" >&5
echo "$as_me: error: newly created file is older than distributed files!
Check your system clock" >&2;}
   { (exit 1); exit 1; }; }
fi
{ echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }
test "$program_prefix" != NONE &&
  program_transform_name="s&^&$program_prefix&;$program_transform_name"
# Use a double $ so make ignores it.
test "$program_suffix" != NONE &&
  program_transform_name="s&\$&$program_suffix&;$program_transform_name"
# Double any \ or $.  echo might interpret backslashes.
# By default was `s,x,x', remove it if useless.
cat <<\_ACEOF >conftest.sed
s/[\\$]/&&/g;s/;s,x,x,$//
_ACEOF
program_transform_name=`echo $program_transform_name | sed -f conftest.sed`
rm -f conftest.sed

# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`

test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
# Use eval to expand $SHELL
if eval "$MISSING --run true"; then
  am_missing_run="$MISSING --run "
else
  am_missing_run=
  { echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
fi

if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
  # We used to keeping the `.' as first argument, in order to
  # allow $(mkdir_p) to be used without argument.  As in
  #   $(mkdir_p) $(somedir)
  # where $(somedir) is conditionally defined.  However this is wrong
  # for two reasons:
  #  1. if the package is installed by a user who cannot write `.'
  #     make install will fail,
  #  2. the above comment should most certainly read
  #     $(mkdir_p) $(DESTDIR)$(somedir)
  #     so it does not work when $(somedir) is undefined and
  #     $(DESTDIR) is not.
  #  To support the latter case, we have to write
  #     test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
  #  so the `.' trick is pointless.
  mkdir_p='mkdir -p --'
else
  # On NextStep and OpenStep, the `mkdir' command does not
  # recognize any option.  It will interpret all options as
  # directories to create, and then abort because `.' already
  # exists.
  for d in ./-p ./--version;
  do
    test -d $d && rmdir $d
  done
  # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
  if test -f "$ac_aux_dir/mkinstalldirs"; then
    mkdir_p='$(mkinstalldirs)'
  else
    mkdir_p='$(install_sh) -d'
  fi
fi

for ac_prog in gawk mawk nawk awk
do
  # Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
if test "${ac_cv_prog_AWK+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test -n "$AWK"; then
  ac_cv_prog_AWK="$AWK" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  for ac_exec_ext in '' $ac_executable_extensions; do
  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
    ac_cv_prog_AWK="$ac_prog"
    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
done
IFS=$as_save_IFS

fi
fi
AWK=$ac_cv_prog_AWK
if test -n "$AWK"; then
  { echo "$as_me:$LINENO: result: $AWK" >&5
echo "${ECHO_T}$AWK" >&6; }
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi


  test -n "$AWK" && break
done

{ echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6; }
set x ${MAKE-make}; ac_make=`echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  cat >conftest.make <<\_ACEOF
SHELL = /bin/sh
all:
        @echo '@@@%%%=$(MAKE)=@@@%%%'
_ACEOF
# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
case `${MAKE-make} -f conftest.make 2>/dev/null` in
  *@@@%%%=?*=@@@%%%*)
    eval ac_cv_prog_make_${ac_make}_set=yes;;
  *)
    eval ac_cv_prog_make_${ac_make}_set=no;;
esac
rm -f conftest.make
fi
if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
  { echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }
  SET_MAKE=
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
  SET_MAKE="MAKE=${MAKE-make}"
fi

rm -rf .tst 2>/dev/null
mkdir .tst 2>/dev/null
if test -d .tst; then
  am__leading_dot=.
else
  am__leading_dot=_
fi
rmdir .tst 2>/dev/null

# test to see if srcdir already configured
if test "`cd $srcdir && pwd`" != "`pwd`" &&
   test -f $srcdir/config.status; then
  { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
   { (exit 1); exit 1; }; }
fi

# test whether we have cygpath
if test -z "$CYGPATH_W"; then
  if (cygpath --version) >/dev/null 2>/dev/null; then
    CYGPATH_W='cygpath -w'
  else
    CYGPATH_W=echo
  fi
fi


# Define the identity of the package.
 PACKAGE=PDB2PQR
 VERSION=1.3.0


cat >>confdefs.h <<_ACEOF
#define PACKAGE "$PACKAGE"
_ACEOF


cat >>confdefs.h <<_ACEOF
#define VERSION "$VERSION"
_ACEOF

# Some tools Automake needs.

ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}


AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}


AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}


AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}


MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}

install_sh=${install_sh-"$am_aux_dir/install-sh"}

# Installed binaries are usually stripped using `strip' when the user
# run `make install-strip'.  However `strip' might not be the right
# tool to use in cross-compilation environments, therefore Automake
# will honor the `STRIP' environment variable to overrule this program.
if test "$cross_compiling" != no; then
  if test -n "$ac_tool_prefix"; then
  # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
set dummy ${ac_tool_prefix}strip; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
if test "${ac_cv_prog_STRIP+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test -n "$STRIP"; then
  ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  for ac_exec_ext in '' $ac_executable_extensions; do
  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
    ac_cv_prog_STRIP="${ac_tool_prefix}strip"
    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
done
IFS=$as_save_IFS

fi
fi
STRIP=$ac_cv_prog_STRIP
if test -n "$STRIP"; then
  { echo "$as_me:$LINENO: result: $STRIP" >&5
echo "${ECHO_T}$STRIP" >&6; }
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi


fi
if test -z "$ac_cv_prog_STRIP"; then
  ac_ct_STRIP=$STRIP
  # Extract the first word of "strip", so it can be a program name with args.
set dummy strip; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test -n "$ac_ct_STRIP"; then
  ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  for ac_exec_ext in '' $ac_executable_extensions; do
  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
    ac_cv_prog_ac_ct_STRIP="strip"
    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
done
IFS=$as_save_IFS

fi
fi
ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
if test -n "$ac_ct_STRIP"; then
  { echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
echo "${ECHO_T}$ac_ct_STRIP" >&6; }
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi

  if test "x$ac_ct_STRIP" = x; then
    STRIP=":"
  else
    case $cross_compiling:$ac_tool_warned in
yes:)
{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
whose name does not start with the host triplet.  If you think this
configuration is useful to you, please write to autoconf@gnu.org." >&5
echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
whose name does not start with the host triplet.  If you think this
configuration is useful to you, please write to autoconf@gnu.org." >&2;}
ac_tool_warned=yes ;;
esac
    STRIP=$ac_ct_STRIP
  fi
else
  STRIP="$ac_cv_prog_STRIP"
fi

fi
INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s"

# We need awk for the "check" target.  The system "awk" is bad on
# some platforms.
# Always define AMTAR for backward compatibility.

AMTAR=${AMTAR-"${am_missing_run}tar"}

am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'


PDB2PQR_VERSION="1:3:0"

ACLOCAL=":";
AUTOCONF=":";
AUTOMAKE=":";
AUTOHEADER=":";


ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
if test -z "$CXX"; then
  if test -n "$CCC"; then
    CXX=$CCC
  else
    if test -n "$ac_tool_prefix"; then
  for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
  do
    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
set dummy $ac_tool_prefix$ac_prog; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
if test "${ac_cv_prog_CXX+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test -n "$CXX"; then
  ac_cv_prog_CXX="$CXX" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  for ac_exec_ext in '' $ac_executable_extensions; do
  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
    ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
done
IFS=$as_save_IFS

fi
fi
CXX=$ac_cv_prog_CXX
if test -n "$CXX"; then
  { echo "$as_me:$LINENO: result: $CXX" >&5
echo "${ECHO_T}$CXX" >&6; }
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi


    test -n "$CXX" && break
  done
fi
if test -z "$CXX"; then
  ac_ct_CXX=$CXX
  for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
do
  # Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test -n "$ac_ct_CXX"; then
  ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  for ac_exec_ext in '' $ac_executable_extensions; do
  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
    ac_cv_prog_ac_ct_CXX="$ac_prog"
    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
done
IFS=$as_save_IFS

fi
fi
ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
if test -n "$ac_ct_CXX"; then
  { echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
echo "${ECHO_T}$ac_ct_CXX" >&6; }
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi


  test -n "$ac_ct_CXX" && break
done

  if test "x$ac_ct_CXX" = x; then
    CXX="g++"
  else
    case $cross_compiling:$ac_tool_warned in
yes:)
{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
whose name does not start with the host triplet.  If you think this
configuration is useful to you, please write to autoconf@gnu.org." >&5
echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
whose name does not start with the host triplet.  If you think this
configuration is useful to you, please write to autoconf@gnu.org." >&2;}
ac_tool_warned=yes ;;
esac
    CXX=$ac_ct_CXX
  fi
fi

  fi
fi
# Provide some information about the compiler.
echo "$as_me:$LINENO: checking for C++ compiler version" >&5
ac_compiler=`set X $ac_compile; echo $2`
{ (ac_try="$ac_compiler --version >&5"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compiler --version >&5") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }
{ (ac_try="$ac_compiler -v >&5"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compiler -v >&5") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }
{ (ac_try="$ac_compiler -V >&5"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compiler -V >&5") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }

cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

int
main ()
{

  ;
  return 0;
}
_ACEOF
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files a.out a.exe b.out"
# Try to create an executable without -o first, disregard a.out.
# It will help us diagnose broken compilers, and finding out an intuition
# of exeext.
{ echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5
echo $ECHO_N "checking for C++ compiler default output file name... $ECHO_C" >&6; }
ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
#
# List of possible output files, starting from the most likely.
# The algorithm is not robust to junk in `.', hence go to wildcards (a.*)
# only as a last resort.  b.out is created by i960 compilers.
ac_files='a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out'
#
# The IRIX 6 linker writes into existing files which may not be
# executable, retaining their permissions.  Remove them first so a
# subsequent execution test works.
ac_rmfiles=
for ac_file in $ac_files
do
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj ) ;;
    * ) ac_rmfiles="$ac_rmfiles $ac_file";;
  esac
done
rm -f $ac_rmfiles

if { (ac_try="$ac_link_default"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_link_default") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; then
  # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
# in a Makefile.  We should not override ac_cv_exeext if it was cached,
# so that the user can short-circuit this test for compilers unknown to
# Autoconf.
for ac_file in $ac_files
do
  test -f "$ac_file" || continue
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj )
        ;;
    [ab].out )
        # We found the default executable, but exeext='' is most
        # certainly right.
        break;;
    *.* )
        if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
        then :; else
           ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
        fi
        # We set ac_cv_exeext here because the later test for it is not
        # safe: cross compilers may not add the suffix if given an `-o'
        # argument, so we may need to know it at that point already.
        # Even if this section looks crufty: it has the advantage of
        # actually working.
        break;;
    * )
        break;;
  esac
done
test "$ac_cv_exeext" = no && ac_cv_exeext=

else
  echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

{ { echo "$as_me:$LINENO: error: C++ compiler cannot create executables
See \`config.log' for more details." >&5
echo "$as_me: error: C++ compiler cannot create executables
See \`config.log' for more details." >&2;}
   { (exit 77); exit 77; }; }
fi

ac_exeext=$ac_cv_exeext
{ echo "$as_me:$LINENO: result: $ac_file" >&5
echo "${ECHO_T}$ac_file" >&6; }

# Check that the compiler produces executables we can run.  If not, either
# the compiler is broken, or we cross compile.
{ echo "$as_me:$LINENO: checking whether the C++ compiler works" >&5
echo $ECHO_N "checking whether the C++ compiler works... $ECHO_C" >&6; }
# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
# If not cross compiling, check that we can run a simple program.
if test "$cross_compiling" != yes; then
  if { ac_try='./$ac_file'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; }; then
    cross_compiling=no
  else
    if test "$cross_compiling" = maybe; then
        cross_compiling=yes
    else
        { { echo "$as_me:$LINENO: error: cannot run C++ compiled programs.
If you meant to cross compile, use \`--host'.
See \`config.log' for more details." >&5
echo "$as_me: error: cannot run C++ compiled programs.
If you meant to cross compile, use \`--host'.
See \`config.log' for more details." >&2;}
   { (exit 1); exit 1; }; }
    fi
  fi
fi
{ echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }

rm -f a.out a.exe conftest$ac_cv_exeext b.out
ac_clean_files=$ac_clean_files_save
# Check that the compiler produces executables we can run.  If not, either
# the compiler is broken, or we cross compile.
{ echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6; }
{ echo "$as_me:$LINENO: result: $cross_compiling" >&5
echo "${ECHO_T}$cross_compiling" >&6; }

{ echo "$as_me:$LINENO: checking for suffix of executables" >&5
echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6; }
if { (ac_try="$ac_link"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_link") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; then
  # If both `conftest.exe' and `conftest' are `present' (well, observable)
# catch `conftest.exe'.  For instance with Cygwin, `ls conftest' will
# work properly (i.e., refer to `conftest.exe'), while it won't with
# `rm'.
for ac_file in conftest.exe conftest conftest.*; do
  test -f "$ac_file" || continue
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj ) ;;
    *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
          break;;
    * ) break;;
  esac
done
else
  { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
See \`config.log' for more details." >&5
echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
See \`config.log' for more details." >&2;}
   { (exit 1); exit 1; }; }
fi

rm -f conftest$ac_cv_exeext
{ echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
echo "${ECHO_T}$ac_cv_exeext" >&6; }

rm -f conftest.$ac_ext
EXEEXT=$ac_cv_exeext
ac_exeext=$EXEEXT
{ echo "$as_me:$LINENO: checking for suffix of object files" >&5
echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6; }
if test "${ac_cv_objext+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

int
main ()
{

  ;
  return 0;
}
_ACEOF
rm -f conftest.o conftest.obj
if { (ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compile") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; then
  for ac_file in conftest.o conftest.obj conftest.*; do
  test -f "$ac_file" || continue;
  case $ac_file in
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    *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
       break;;
  esac
done
else
  echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
See \`config.log' for more details." >&5
echo "$as_me: error: cannot compute suffix of object files: cannot compile
See \`config.log' for more details." >&2;}
   { (exit 1); exit 1; }; }
fi

rm -f conftest.$ac_cv_objext conftest.$ac_ext
fi
{ echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
echo "${ECHO_T}$ac_cv_objext" >&6; }
OBJEXT=$ac_cv_objext
ac_objext=$OBJEXT
{ echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6; }
if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

int
main ()
{
#ifndef __GNUC__
       choke me
#endif

  ;
  return 0;
}
_ACEOF
rm -f conftest.$ac_objext
if { (ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compile") 2>conftest.er1
  ac_status=$?
  grep -v '^ *+' conftest.er1 >conftest.err
  rm -f conftest.er1
  cat conftest.err >&5
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); } &&
         { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; } &&
         { ac_try='test -s conftest.$ac_objext'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; }; then
  ac_compiler_gnu=yes
else
  echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

        ac_compiler_gnu=no
fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_cv_cxx_compiler_gnu=$ac_compiler_gnu

fi
{ echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6; }
GXX=`test $ac_compiler_gnu = yes && echo yes`
ac_test_CXXFLAGS=${CXXFLAGS+set}
ac_save_CXXFLAGS=$CXXFLAGS
{ echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6; }
if test "${ac_cv_prog_cxx_g+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  ac_save_cxx_werror_flag=$ac_cxx_werror_flag
   ac_cxx_werror_flag=yes
   ac_cv_prog_cxx_g=no
   CXXFLAGS="-g"
   cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

int
main ()
{

  ;
  return 0;
}
_ACEOF
rm -f conftest.$ac_objext
if { (ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compile") 2>conftest.er1
  ac_status=$?
  grep -v '^ *+' conftest.er1 >conftest.err
  rm -f conftest.er1
  cat conftest.err >&5
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); } &&
         { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; } &&
         { ac_try='test -s conftest.$ac_objext'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; }; then
  ac_cv_prog_cxx_g=yes
else
  echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

        CXXFLAGS=""
      cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

int
main ()
{

  ;
  return 0;
}
_ACEOF
rm -f conftest.$ac_objext
if { (ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compile") 2>conftest.er1
  ac_status=$?
  grep -v '^ *+' conftest.er1 >conftest.err
  rm -f conftest.er1
  cat conftest.err >&5
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); } &&
         { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; } &&
         { ac_try='test -s conftest.$ac_objext'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; }; then
  :
else
  echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

        ac_cxx_werror_flag=$ac_save_cxx_werror_flag
         CXXFLAGS="-g"
         cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

int
main ()
{

  ;
  return 0;
}
_ACEOF
rm -f conftest.$ac_objext
if { (ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_compile") 2>conftest.er1
  ac_status=$?
  grep -v '^ *+' conftest.er1 >conftest.err
  rm -f conftest.er1
  cat conftest.err >&5
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); } &&
         { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; } &&
         { ac_try='test -s conftest.$ac_objext'
  { (case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  echo "$as_me:$LINENO: \$? = $ac_status" >&5
  (exit $ac_status); }; }; then
  ac_cv_prog_cxx_g=yes
else
  echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5


fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
   ac_cxx_werror_flag=$ac_save_cxx_werror_flag
fi
{ echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6; }
if test "$ac_test_CXXFLAGS" = set; then
  CXXFLAGS=$ac_save_CXXFLAGS
elif test $ac_cv_prog_cxx_g = yes; then
  if test "$GXX" = yes; then
    CXXFLAGS="-g -O2"
  else
    CXXFLAGS="-g"
  fi
else
  if test "$GXX" = yes; then
    CXXFLAGS="-O2"
  else
    CXXFLAGS=
  fi
fi
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
DEPDIR="${am__leading_dot}deps"

ac_config_commands="$ac_config_commands depfiles"


am_make=${MAKE-make}
cat > confinc << 'END'
am__doit:
        @echo done
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
{ echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
echo $ECHO_N "checking for style of include used by $am_make... $ECHO_C" >&6; }
am__include="#"
am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
# We grep out `Entering directory' and `Leaving directory'
# messages which can occur if `w' ends up in MAKEFLAGS.
# In particular we don't look at `^make:' because GNU make might
# be invoked under some other name (usually "gmake"), in which
# case it prints its new name instead of `make'.
if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
   am__include=include
   am__quote=
   _am_result=GNU
fi
# Now try BSD make style include.
if test "$am__include" = "#"; then
   echo '.include "confinc"' > confmf
   if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
      am__include=.include
      am__quote="\""
      _am_result=BSD
   fi
fi


{ echo "$as_me:$LINENO: result: $_am_result" >&5
echo "${ECHO_T}$_am_result" >&6; }
rm -f confinc confmf

# Check whether --enable-dependency-tracking was given.
if test "${enable_dependency_tracking+set}" = set; then
  enableval=$enable_dependency_tracking;
fi

if test "x$enable_dependency_tracking" != xno; then
  am_depcomp="$ac_aux_dir/depcomp"
  AMDEPBACKSLASH='\'
fi


if test "x$enable_dependency_tracking" != xno; then
  AMDEP_TRUE=
  AMDEP_FALSE='#'
else
  AMDEP_TRUE='#'
  AMDEP_FALSE=
fi


depcc="$CXX"  am_compiler_list=

{ echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6; }
if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
  # We make a subdir and do the tests there.  Otherwise we can end up
  # making bogus files that we don't know about and never remove.  For
  # instance it was reported that on HP-UX the gcc test will end up
  # making a dummy file named `D' -- because `-MD' means `put the output
  # in D'.
  mkdir conftest.dir
  # Copy depcomp to subdir because otherwise we won't find it if we're
  # using a relative directory.
  cp "$am_depcomp" conftest.dir
  cd conftest.dir
  # We will build objects and dependencies in a subdirectory because
  # it helps to detect inapplicable dependency modes.  For instance
  # both Tru64's cc and ICC support -MD to output dependencies as a
  # side effect of compilation, but ICC will put the dependencies in
  # the current directory while Tru64 will put them in the object
  # directory.
  mkdir sub

  am_cv_CXX_dependencies_compiler_type=none
  if test "$am_compiler_list" = ""; then
     am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
  fi
  for depmode in $am_compiler_list; do
    # Setup a source with many dependencies, because some compilers
    # like to wrap large dependency lists on column 80 (with \), and
    # we should not choose a depcomp mode which is confused by this.
    #
    # We need to recreate these files for each test, as the compiler may
    # overwrite some of them when testing with obscure command lines.
    # This happens at least with the AIX C compiler.
    : > sub/conftest.c
    for i in 1 2 3 4 5 6; do
      echo '#include "conftst'$i'.h"' >> sub/conftest.c
      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
      # Solaris 8's {/usr,}/bin/sh.
      touch sub/conftst$i.h
    done
    echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf

    case $depmode in
    nosideeffect)
      # after this tag, mechanisms are not by side-effect, so they'll
      # only be used when explicitly requested
      if test "x$enable_dependency_tracking" = xyes; then
        continue
      else
        break
      fi
      ;;
    none) break ;;
    esac
    # We check with `-c' and `-o' for the sake of the "dashmstdout"
    # mode.  It turns out that the SunPro C++ compiler does not properly
    # handle `-M -o', and we need to detect this.
    if depmode=$depmode \
       source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
       depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
       $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
         >/dev/null 2>conftest.err &&
       grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
       grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
       ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
      # icc doesn't choke on unknown options, it will just issue warnings
      # or remarks (even with -Werror).  So we grep stderr for any message
      # that says an option was ignored or not supported.
      # When given -MP, icc 7.0 and 7.1 complain thusly:
      #   icc: Command line warning: ignoring option '-M'; no argument required
      # The diagnosis changed in icc 8.0:
      #   icc: Command line remark: option '-MP' not supported
      if (grep 'ignoring option' conftest.err ||
          grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
        am_cv_CXX_dependencies_compiler_type=$depmode
        break
      fi
    fi
  done

  cd ..
  rm -rf conftest.dir
else
  am_cv_CXX_dependencies_compiler_type=none
fi

fi
{ echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
echo "${ECHO_T}$am_cv_CXX_dependencies_compiler_type" >&6; }
CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type


if
  test "x$enable_dependency_tracking" != xno \
  && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
  am__fastdepCXX_TRUE=
  am__fastdepCXX_FALSE='#'
else
  am__fastdepCXX_TRUE='#'
  am__fastdepCXX_FALSE=
fi


# Check whether --with-python was given.
if test "${with_python+set}" = set; then
  withval=$with_python; PYTHONPATH=$withval
else
  PYTHONPATH=""
fi


if test "$PYTHONPATH" = "" ; then
  # Extract the first word of "python", so it can be a program name with args.
set dummy python; ac_word=$2
{ echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
if test "${ac_cv_path_py_path+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  case $py_path in
  [\\/]* | ?:[\\/]*)
  ac_cv_path_py_path="$py_path" # Let the user override the test with a path.
  ;;
  *)
  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  for ac_exec_ext in '' $ac_executable_extensions; do
  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then
    ac_cv_path_py_path="$as_dir/$ac_word$ac_exec_ext"
    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
done
IFS=$as_save_IFS

  ;;
esac
fi
py_path=$ac_cv_path_py_path
if test -n "$py_path"; then
  { echo "$as_me:$LINENO: result: $py_path" >&5
echo "${ECHO_T}$py_path" >&6; }
else
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
fi


  if test -z "${py_path}"; then
     { { echo "$as_me:$LINENO: error: Unable to find python!  Python location can be specified with --with-python" >&5
echo "$as_me: error: Unable to find python!  Python location can be specified with --with-python" >&2;}
   { (exit 1); exit 1; }; }
  fi
else
  py_path=$PYTHONPATH
fi

srcpath=`pwd`

sed -e 's%@srcdir@%'${srcpath}'%' tests/test/test.cpp.in > tests/test/test.cpp
sed -e 's%@srcdir@%'${srcpath}'%' tests/adv-test/test.cpp.in > tests/adv-test/test.cpp
sed -e 's%@py_path@%'${py_path}'%' tests/test/test.sh.in > tests/test/test.sh.tmp.1
sed -e 's%@py_path@%'${py_path}'%' tests/adv-test/test.sh.in > tests/adv-test/test.sh.tmp.1
sed -e 's%@srcdir@%'${srcpath}'%' tests/test/test.sh.tmp.1 > tests/test/test.sh
sed -e 's%@srcdir@%'${srcpath}'%' tests/adv-test/test.sh.tmp.1 > tests/adv-test/test.sh
rm -f tests/test/test.sh.tmp.*
rm -f tests/adv-test/test.sh.tmp.*

{ echo "$as_me:$LINENO: checking for python include directory" >&5
echo $ECHO_N "checking for python include directory... $ECHO_C" >&6; }
PY_VERSION=`$py_path -c 'import sys; print sys.version[:3]'`
PY_PREFIX=`$py_path -c 'import sys; print sys.prefix'`
if test -f $PY_PREFIX/include/python$PY_VERSION/Python.h; then
   PY_HEADER="-I$PY_PREFIX/include/python$PY_VERSION"
   { echo "$as_me:$LINENO: result: $PY_HEADER" >&5
echo "${ECHO_T}$PY_HEADER" >&6; }
elif test -f $PY_PREFIX/include/Python.h; then
   PY_HEADER="-I$PY_PREFIX/include"
   { echo "$as_me:$LINENO: result: $PY_HEADER" >&5
echo "${ECHO_T}$PY_HEADER" >&6; }
else
   { { echo "$as_me:$LINENO: error: Unable to find Python.h!" >&5
echo "$as_me: error: Unable to find Python.h!" >&2;}
   { (exit 1); exit 1; }; }
fi


PY_LDFLAGS=""
PY_SHARED=""
PY_FLAGS=""
case $host_os in
   linux*)
      PY_SHARED="-shared";;
   irix*)
      PY_SHARED="-shared"
      PY_LDFLAGS="-lftn -lm";;
   sun|solaris**)
      PY_SHARED="-G"
      PY_LDFLAGS="-lF77 -lm -lM77 -lsunmath";;
   darwin*)
      PY_LDFLAGS="-Wl,-framework -Wl,Python -bundle";;
esac

case $host_cpu in
   x86_64*)
      PY_FLAGS="-fPIC";;
esac

PY_SHARED=$PY_SHARED

PY_LDFLAGS=$PY_LDFLAGS

PY_HEADER=$PY_HEADER

PY_FLAGS=$PY_FLAGS


PDB2PQR_SUBDIRS=""

# A.  propka

{ echo "$as_me:$LINENO: checking for --disable-propka" >&5
echo $ECHO_N "checking for --disable-propka... $ECHO_C" >&6; }
# Check whether --enable-propka was given.
if test "${enable_propka+set}" = set; then
  enableval=$enable_propka;  with_propka="$enableval"
else
   with_propka="enable"

fi


if test "$with_propka" = "yes" ; then
  with_propka="enable"
elif test "$with_propka" = "no"; then
  with_propka="disable"
fi

if test "${with_propka}" = "enable"; then
     PDB2PQR_SUBDIRS="propka"
     { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
     { echo "$as_me:$LINENO: result: " >&5
echo "${ECHO_T}" >&6; }
     { echo "$as_me:$LINENO: result: ------------- Begin Processing PropKa Configure Options -----------" >&5
echo "${ECHO_T}------------- Begin Processing PropKa Configure Options -----------" >&6; }
     cd propka
     ./configure py_path=$py_path
     cd ..
     { echo "$as_me:$LINENO: result: ------------- End Processing PropKa Configure Options -----------" >&5
echo "${ECHO_T}------------- End Processing PropKa Configure Options -----------" >&6; }
     { echo "$as_me:$LINENO: result: " >&5
echo "${ECHO_T}" >&6; }
else
     { echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }
     PDB2PQR_SUBDIRS=""
fi

# B. pdb2pka

{ echo "$as_me:$LINENO: checking for--disable-pdb2pka" >&5
echo $ECHO_N "checking for--disable-pdb2pka... $ECHO_C" >&6; }
# Check whether --enable-pdb2pka was given.
if test "${enable_pdb2pka+set}" = set; then
  enableval=$enable_pdb2pka;  with_pdb2pka="$enableval"
else
   with_pdb2pka="enable"

fi


if test "$with_pdb2pka" = "yes" ; then
  with_pdb2pka="enable"
elif test "$with_pdb2pka" = "no"; then
  with_pdb2pka="disable"
fi

if test "$with_pdb2pka" = "enable" ; then
  PY_CFLAGS="$PY_HEADER"
  PACKAGE_PATH=""
  PDB2PQR_SUBDIRS="$PDB2PQR_SUBDIRS pdb2pka"
  { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }

  { echo "$as_me:$LINENO: result: " >&5
echo "${ECHO_T}" >&6; }
  { echo "$as_me:$LINENO: result: ------------- Begin Processing pdb2pka Configure Options -----------" >&5
echo "${ECHO_T}------------- Begin Processing pdb2pka Configure Options -----------" >&6; }

  # Test for Numeric install
  { echo "$as_me:$LINENO: checking whether you defined Numeric or Numpy" >&5
echo $ECHO_N "checking whether you defined Numeric or Numpy... $ECHO_C" >&6; }
  if (test -n "${NUMERIC}") ; then
    { echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }
    NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1`
    if test "$NUMERIC_INC" = ""; then
      { { echo "$as_me:$LINENO: error: Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}" >&5
echo "$as_me: error: Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}" >&2;}
   { (exit 1); exit 1; }; }
    fi
    NUMERIC_INC=`dirname ${NUMERIC_INC}`
    NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1`
    if test "${NUMERIC_LIB}" = ""; then
      { { echo "$as_me:$LINENO: error: Please check your NUMERIC path.  Numpy.pth cannot be found in ${NUMERIC}" >&5
echo "$as_me: error: Please check your NUMERIC path.  Numpy.pth cannot be found in ${NUMERIC}" >&2;}
   { (exit 1); exit 1; }; }
    fi
    NUMERIC_NAME=`cat ${NUMERIC_LIB}`
    NUMERIC_LIB=`dirname ${NUMERIC_LIB}`
    NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME}
    if test "${PACKAGE_PATH}" = ""; then
      PACKAGE_PATH=${NUMERIC_LIB}
    else
      PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}"
    fi
    PY_NUMERIC="-I${NUMERIC_INC} "
    PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
  else
    { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
    { echo "$as_me:$LINENO: checking for Numeric include files" >&5
echo $ECHO_N "checking for Numeric include files... $ECHO_C" >&6; }
    if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then
      PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric"
      { echo "$as_me:$LINENO: result: $PY_NUMERIC" >&5
echo "${ECHO_T}$PY_NUMERIC" >&6; }
      PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
    else
      { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
    fi
  fi

  # If failed, test for numpy
  { echo "$as_me:$LINENO: checking whether you defined numpy" >&5
echo $ECHO_N "checking whether you defined numpy... $ECHO_C" >&6; }
  if (test -n "${NUMPY}") ; then
    { echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }
    { echo "$as_me:$LINENO: WARNING: Integration with Numpy is incomplete" >&5
echo "$as_me: WARNING: Integration with Numpy is incomplete" >&2;}
    NUMPY_INC=`find ${NUMPY} -iname "arrayobject.h" | tail -n1`
    if test "$NUMPY_INC" = ""; then
        { { echo "$as_me:$LINENO: error: Please check your NUMPY path.  arrayobject.h cannot be found in ${NUMPY}" >&5
echo "$as_me: error: Please check your NUMPY path.  arrayobject.h cannot be found in ${NUMPY}" >&2;}
   { (exit 1); exit 1; }; }
    fi
    NUMPY_INC=`dirname ${NUMPY_INC}`
    NUMPY_LIB=`find ${NUMPY} -iname "Numpy.pth" | tail -n1`
    if test "${NUMPY_LIB}" = ""; then
        { { echo "$as_me:$LINENO: error: Please check your NUMPY path.  Numpy.pth cannot be found in ${NUMPY}" >&5
echo "$as_me: error: Please check your NUMPY path.  Numpy.pth cannot be found in ${NUMPY}" >&2;}
   { (exit 1); exit 1; }; }
    fi
    NUMPY_NAME=`cat ${NUMPY_LIB}`
    NUMPY_LIB=`dirname ${NUMPY_LIB}`
    NUMPY_LIB=${NUMPY_LIB}/${NUMPY_NAME}
    if test "${PACKAGE_PATH}" = ""; then
      PACKAGE_PATH=${NUMPY_LIB}
    else
      PACKAGE_PATH="${PACKAGE_PATH}:${NUMPY_LIB}"
    fi
    PY_NUMPY="-I${NUMPY_INC}"
    PY_CFLAGS="$PY_CFLAGS $PY_NUMPY"
  else
    { echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6; }
    if test "$PY_NUMERIC" = "" ; then
      { echo "$as_me:$LINENO: checking for numpy includes files" >&5
echo $ECHO_N "checking for numpy includes files... $ECHO_C" >&6; }
      if test -f $PY_PREFIX/lib/python$PY_VERSION/site-packages/numpy/core/include/numpy/arrayobject.h; then
        PY_NUMERIC="-I$PY_PREFIX/lib/python$PY_VERSION/site-packages/numpy/core/include/numpy"
        { echo "$as_me:$LINENO: result: $PY_NUMERIC" >&5
echo "${ECHO_T}$PY_NUMERIC" >&6; }
        PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
      elif test -f /opt/rocks/lib/python$PY_VERSION/site-packages/numpy/core/include/numpy/arrayobject.h; then
        { echo "$as_me:$LINENO: result: $PY_NUMERIC" >&5
echo "${ECHO_T}$PY_NUMERIC" >&6; }
        PY_FLAGS="$PY_HEADER -I/opt/rocks/lib/python$PY_VERSION/site-packages/numpy/core/include/numpy"
      else
        { { echo "$as_me:$LINENO: error: Unable to find Numeric or Numpy!  Please install Numeric or Numpy or specify the location with ./configure NUMPY=path_to_numpy or NUMERIC=path_to_numeric or disable PDB2PKA during configuration with --disable-pdb2pka" >&5
echo "$as_me: error: Unable to find Numeric or Numpy!  Please install Numeric or Numpy or specify the location with ./configure NUMPY=path_to_numpy or NUMERIC=path_to_numeric or disable PDB2PKA during configuration with --disable-pdb2pka" >&2;}
   { (exit 1); exit 1; }; }
      fi
    fi
  fi

  # Test for APBS Python wrappers
  #AC_MSG_CHECKING([if --with-apbsdir was used])
  #AC_ARG_WITH(apbsdir,
  #   [AC_HELP_STRING([--with-apbsdir=PATH], [full path to top-level APBS directory])],
  #   [apbsdir="$with_apbsdir/tools/python"; AC_MSG_RESULT([yes])],
  #   [apbsdir=""; AC_MSG_RESULT([no])]
  #)

  #if test "$apbsdir" = ""; then
  #   AC_MSG_CHECKING([for APBSDIR environment variable])
  #   if test "$APBSDIR" != ""; then
  #       apbsdir="$APBSDIR/tools/python"
  #       AC_MSG_RESULT([yes])
  #   else
  #       AC_MSG_RESULT([no])
  #       apbsdir="./pdb2pka"
  #   fi
  #fi

  #AC_MSG_CHECKING([for compiled APBS Python wrappers])
  #apbserror=0
  #if test -f "$apbsdir/apbslib.py"; then
  #    if test -f "$apbsdir/_apbslib.so"; then
  #        AC_MSG_RESULT([$apbsdir])
  #    else
  #        AC_MSG_RESULT([no])
  #        apbserror=1
  #    fi
  #else
  #    AC_MSG_RESULT([no])
  #    apbserror=1
  #fi

  #if test "$apbserror" -eq 1; then
  #    echo ""
  #    echo "Unable to find apbslib.py and _apbslib.so in $apbsdir!"
  #    echo "Compiled APBS Python wrappers are needed to use the pdb2pka functions"
  #    echo "Please recompile APBS with the '--enable-python' flag."
  #    echo ""
  #    AC_MSG_ERROR(["APBS Python wrappers not found!"])
  #fi


  #AC_SUBST(APBS_PYDIR,[$apbsdir])
  { echo "$as_me:$LINENO: result: ------------- End Processing pdb2ka Configure Options -----------" >&5
echo "${ECHO_T}------------- End Processing pdb2ka Configure Options -----------" >&6; }
  { echo "$as_me:$LINENO: result: " >&5
echo "${ECHO_T}" >&6; }


else
  PY_CFLAGS="$PY_HEADER"
  { echo "$as_me:$LINENO: result: yes" >&5
echo "${ECHO_T}yes" >&6; }
fi

#PY_CFLAGS="$PY_CFLAGS -I$PY_PREFIX/lib/python$PY_VERSION "

PY_CFLAGS=$PY_CFLAGS

PDB2PQR_SUBDIRS=$PDB2PQR_SUBDIRS


# Check whether --with-url was given.
if test "${with_url+set}" = set; then
  withval=$with_url; URL=$withval
else
  URL="http://`uname -n`/pdb2pqr"
fi


echo ${URL} > url_test
isslash=`awk -F"/" '{print $NF}' url_test`
hashttp=`awk -F"http://" '{print $2}' url_test`
rm -f url_test

if ! test -z $isslash ; then
  URL=${URL}/
fi

if test -z $hashttp ; then
  URL=http://${URL}
fi


# Check whether --with-max-atoms was given.
if test "${with_max_atoms+set}" = set; then
  withval=$with_max_atoms; MAX_ATOMS=$withval
else
  MAX_ATOMS=10000
fi


# Check whether --with-opal was given.
if test "${with_opal+set}" = set; then
  withval=$with_opal; OPALURL=$withval
else
  OPALURL=""
fi


if test "$OPALURL" = "yes"; then
  OPALURL="http://ws.nbcr.net:8080/axis-1.2.1/services/Pdb2pqrOpalService"
fi

if test "$OPALURL" != ""; then
  if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
    echo ZSI is installed
  else
    #  need to install ZSI
    echo Installing ZSI.  This might take a while...
    tar zxvf ZSI-1.7.tar.gz
    cd ZSI-1.7
    if test `whoami` = "root"; then
      $py_path setup.py install
    else
      zsi_pyxml_install="true"
      $py_path setup.py install --prefix=${prefix}
    fi
    cd ..
  fi

  if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/_xmlplus ; then
    echo PyXML is installed
  else
    #  need to install ZSI
    echo Installing PyXML.  This might take a while...
    tar zxvf PyXML-0.8.4.tar.gz
    cd PyXML-0.8.4
    if test `whoami` = "root"; then
      $py_path setup.py build
      $py_path setup.py install
    else
      zsi_pyxml_install="true"
      $py_path setup.py build
      $py_path setup.py install --prefix=${prefix}
    fi
    cd ..
  fi
fi

# Add tmp/ if it doesn't already exist

{ echo "$as_me:$LINENO: checking for tmp/" >&5
echo $ECHO_N "checking for tmp/... $ECHO_C" >&6; }
if test "${ac_cv_file_tmp_+set}" = set; then
  echo $ECHO_N "(cached) $ECHO_C" >&6
else
  test "$cross_compiling" = yes &&
  { { echo "$as_me:$LINENO: error: cannot check for file existence when cross compiling" >&5
echo "$as_me: error: cannot check for file existence when cross compiling" >&2;}
   { (exit 1); exit 1; }; }
if test -r "tmp/"; then
  ac_cv_file_tmp_=yes
else
  ac_cv_file_tmp_=no
fi
fi
{ echo "$as_me:$LINENO: result: $ac_cv_file_tmp_" >&5
echo "${ECHO_T}$ac_cv_file_tmp_" >&6; }
if test $ac_cv_file_tmp_ = yes; then
  hastmp="yes"
else
  hastmp="no"
fi


if test "${hastmp}" = "no"; then
  mkdir tmp
fi

chmod 777 tmp

chmod o+x tests/test/test.sh
chmod u+x tests/test/test.sh
chmod o+x tests/adv-test/test.sh
chmod u+x tests/adv-test/test.sh

if test "${prefix}" != `pwd` ; then
  website_install=${URL}
  pdb2pqr_cgi_install=${URL}pdb2pqr.cgi

  echo ${website_install} > website_install_file
  echo ${prefix} > prefix_file
  last_website_install=`awk -F"/" '{print $(NF-1)}' website_install_file`
  last_prefix=`awk -F"/" '{print $(NF-1)}' prefix_file`
  rm -f website_install_file prefix_file
fi

#if test "${prefix}" != `pwd` ; then
#  if test "${default_prefix_used}" = "true" ; then
#    website_install=${URL}
#    pdb2pqr_cgi_install=${URL}pdb2pqr.cgi
#  else
#    echo ${prefix} > install_dir_file
#    lastdir=`awk -F"/" '{print $NF}' install_dir_file`

#    if test -z $lastdir; then
#      last=`awk -F"/" '{print NF-1}' install_dir_file`
#      lastdir=`awk -F"/" '{print $(NF-1)}' install_dir_file`
#    fi

#    rm -f install_dir_file

#    website_install=${URL}$lastdir
#    pdb2pqr_cgi_install=${URL}$lastdir/pdb2pqr.cgi
#  fi
#fi

# Set the max number of atoms in a protein when not using Opal for job submission
#  Also move pdb2pqr.py to pdb2pqr.cgi
sed -e 's%@MAXATOMS@%'${MAX_ATOMS}'%' -e 's%@PACKAGE_PATH@%'${PACKAGE_PATH}'%' -e 's%@WHICHPYTHON@%'${py_path}'%' pdb2pqr.py.in > pdb2pqr.py
chmod 755 pdb2pqr.py
cp pdb2pqr.py pdb2pqr.cgi

#echo ${srcpath} > srcpathtemp1
#sed 's/\//\\\//g' srcpathtemp1 > srcpathtemp2
#srcpathvar=`cat srcpathtemp2`
#rm srcpathtemp1 srcpathtemp2
#sed -e 's/\@srcpath\@/'${srcpathvar}'/g' src/server.py.in > src/server.py.in.tmp.1

#if test "${prefix}" != `pwd` ; then
  #echo ${prefix} > install_dir_temp1
  #sed 's/\//\\\//g' install_dir_temp1 > install_dir_temp2
  #install_dir_var=`cat install_dir_temp2`
  #rm install_dir_temp1 install_dir_temp2
  #  sed -e 's/\@srcpath\@/'${install_dir_var}'/g' src/server.py.in > src/server.py.install.tmp.1
#fi

echo ${prefix} > install_dir_temp1
sed 's/\//\\\//g' install_dir_temp1 > install_dir_temp2
install_dir_var=`cat install_dir_temp2`
rm install_dir_temp1 install_dir_temp2
sed -e 's/\@srcpath\@/'${install_dir_var}'/g' src/server.py.in > src/server.py.in.tmp.1


website=${URL}
echo $website > websitetemp1
sed 's/\//\\\//g' websitetemp1 > websitetemp2
websitevar=`cat websitetemp2`
rm websitetemp1 websitetemp2
sed -e 's/\@website\@/'${websitevar}'/g' src/server.py.in.tmp.1 > src/server.py.in.tmp.2
mv src/server.py.in.tmp.2 src/server.py
rm -rf src/server.py.in.tmp.*

#if test "${prefix}" != `pwd` ; then
#  echo ${website_install} > website_install_temp1
#  sed 's/\//\\\//g' website_install_temp1 > website_install_temp2
#  website_install_var=`cat website_install_temp2`
#  rm website_install_temp1 website_install_temp2
  # sed -e 's/\@website\@/'${website_install_var}'/g' src/server.py.install.tmp.1 > src/server.py.install.tmp.2
  # cp src/server.py.install.tmp.2 src/server.py.install
  # rm -rf src/server.py.install.tmp.*
#fi


if test -z "${OPALURL}" ; then
  pdb2pqr_cgi=${URL}pdb2pqr.cgi
else
  pdb2pqr_cgi=${URL}pdb2pqr-opal.cgi
fi
echo $pdb2pqr_cgi > actiontemp1
sed 's/\//\\\//g' actiontemp1 > actiontemp2
actionvar=`cat actiontemp2`
rm actiontemp1 actiontemp2
if test -z "${OPALURL}" ; then
  sed -e 's/\@action\@/'${actionvar}'/g' \
      -e '/@WITHOPAL@/d' \
      -e 's%@MAXATOMS@%'${MAX_ATOMS}'%' \
      -e '/@WITHOUTOPAL@/,/@WITHOUTOPAL@/d' html/server.html.in > html/server.html.tmp
  sed -e 's/\@website\@/'${websitevar}'/g' html/server.html.tmp > html/server.html.tmp.2
  cp html/server.html.tmp.2 html/server.html
  rm html/server.html.tmp*
else
  sed -e 's/\@action\@/'${actionvar}'/g' \
      -e '/@WITHOPAL@/,/@WITHOPAL@/d' \
      -e 's/\@website\@/'${websitevar}'/g' \
      -e '/@WITHOUTOPAL@/d' html/server.html.in > html/server.html
fi
cp html/server.html index.html

if test "${prefix}" != `pwd` ; then
  if test -z "${OPALURL}" ; then
    pdb2pqr_cgi_install=${URL}pdb2pqr.cgi
  else
    pdb2pqr_cgi_install=${URL}pdb2pqr-opal.cgi
  fi
  echo $pdb2pqr_cgi_install > action_install_temp1
  sed 's/\//\\\//g' action_install_temp1 > action_install_temp2
  action_install_var=`cat action_install_temp2`
  rm action_install_temp1 action_install_temp2
  #  sed -e 's/\@action\@/'${action_install_var}'/g' html/server.html.in > html/server.html.install.tmp
  #  sed -e 's/\@website\@/'${website_install_var}'/g' html/server.html.install.tmp > html/server.html.install.tmp.2
  #  cp html/server.html.install.tmp.2 html/server.html.install
  #  rm html/server.html.install.tmp*
fi


sed -e 's%@OPALURL@%'${OPALURL}'%' -e 's%@WHICHPYTHON@%'${py_path}'%' pdb2pqr-opal.py > pdb2pqr-opal.cgi
sed -e 's%@OPALURL@%'${OPALURL}'%' -e 's%@WHICHPYTHON@%'${py_path}'%' querystatus.py > querystatus.cgi
chmod 755 pdb2pqr-opal.cgi
chmod 755 querystatus.cgi


PDB2PQR_SUBDIRS="${PDB2PQR_SUBDIRS} tests"


{ echo "$as_me:$LINENO: result: ------------- End Processing PDB2PQR Configure Options -----------" >&5
echo "${ECHO_T}------------- End Processing PDB2PQR Configure Options -----------" >&6; }
{ echo "$as_me:$LINENO: result: " >&5
echo "${ECHO_T}" >&6; }
if test -n "${PDB2PQR_SUBDIRS}"; then
   ac_config_files="$ac_config_files Makefile pdb2pka/Makefile pdb2pka/substruct/Makefile tests/Makefile tests/test/Makefile tests/adv-test/Makefile"

cat >confcache <<\_ACEOF
# This file is a shell script that caches the results of configure
# tests run on this system so they can be shared between configure
# scripts and configure runs, see configure's option --config-cache.
# It is not useful on other systems.  If it contains results you don't
# want to keep, you may remove or edit it.
#
# config.status only pays attention to the cache file if you give it
# the --recheck option to rerun configure.
#
# `ac_cv_env_foo' variables (set or unset) will be overridden when
# loading this file, other *unset* `ac_cv_foo' will be assigned the
# following values.

_ACEOF

# The following way of writing the cache mishandles newlines in values,
# but we know of no workaround that is simple, portable, and efficient.
# So, we kill variables containing newlines.
# Ultrix sh set writes to stderr and can't be redirected directly,
# and sets the high bit in the cache file unless we assign to the vars.
(
  for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
    eval ac_val=\$$ac_var
    case $ac_val in #(
    *${as_nl}*)
      case $ac_var in #(
      *_cv_*) { echo "$as_me:$LINENO: WARNING: Cache variable $ac_var contains a newline." >&5
echo "$as_me: WARNING: Cache variable $ac_var contains a newline." >&2;} ;;
      esac
      case $ac_var in #(
      _ | IFS | as_nl) ;; #(
      *) $as_unset $ac_var ;;
      esac ;;
    esac
  done

  (set) 2>&1 |
    case $as_nl`(ac_space=' '; set) 2>&1` in #(
    *${as_nl}ac_space=\ *)
      # `set' does not quote correctly, so add quotes (double-quote
      # substitution turns \\\\ into \\, and sed turns \\ into \).
      sed -n \
        "s/'/'\\\\''/g;
          s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
      ;; #(
    *)
      # `set' quotes correctly as required by POSIX, so do not add quotes.
      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
      ;;
    esac |
    sort
) |
  sed '
     /^ac_cv_env_/b end
     t clear
     :clear
     s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
     t end
     s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
     :end' >>confcache
if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
  if test -w "$cache_file"; then
    test "x$cache_file" != "x/dev/null" &&
      { echo "$as_me:$LINENO: updating cache $cache_file" >&5
echo "$as_me: updating cache $cache_file" >&6;}
    cat confcache >$cache_file
  else
    { echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
echo "$as_me: not updating unwritable cache $cache_file" >&6;}
  fi
fi
rm -f confcache

test "x$prefix" = xNONE && prefix=$ac_default_prefix
# Let make expand exec_prefix.
test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'

# Transform confdefs.h into DEFS.
# Protect against shell expansion while executing Makefile rules.
# Protect against Makefile macro expansion.
#
# If the first sed substitution is executed (which looks for macros that
# take arguments), then branch to the quote section.  Otherwise,
# look for a macro that doesn't take arguments.
ac_script='
t clear
:clear
s/^[     ]*#[    ]*define[       ][      ]*\([^  (][^    (]*([^)]*)\)[   ]*\(.*\)/-D\1=\2/g
t quote
s/^[     ]*#[    ]*define[       ][      ]*\([^  ][^     ]*\)[   ]*\(.*\)/-D\1=\2/g
t quote
b any
:quote
s/[      `~#$^&*(){}\\|;'\''"<>?]/\\&/g
s/\[/\\&/g
s/\]/\\&/g
s/\$/$$/g
H
:any
${
        g
        s/^\n//
        s/\n/ /g
        p
}
'
DEFS=`sed -n "$ac_script" confdefs.h`


ac_libobjs=
ac_ltlibobjs=
for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
  # 1. Remove the extension, and $U if already installed.
  ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
  ac_i=`echo "$ac_i" | sed "$ac_script"`
  # 2. Prepend LIBOBJDIR.  When used with automake>=1.10 LIBOBJDIR
  #    will be set to the directory where LIBOBJS objects are built.
  ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
  ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
done
LIBOBJS=$ac_libobjs

LTLIBOBJS=$ac_ltlibobjs


if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
  { { echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
Usually this means the macro was only invoked conditionally." >&5
echo "$as_me: error: conditional \"AMDEP\" was never defined.
Usually this means the macro was only invoked conditionally." >&2;}
   { (exit 1); exit 1; }; }
fi
if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
  { { echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
Usually this means the macro was only invoked conditionally." >&5
echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
Usually this means the macro was only invoked conditionally." >&2;}
   { (exit 1); exit 1; }; }
fi

: ${CONFIG_STATUS=./config.status}
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files $CONFIG_STATUS"
{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
echo "$as_me: creating $CONFIG_STATUS" >&6;}
cat >$CONFIG_STATUS <<_ACEOF
#! $SHELL
# Generated by $as_me.
# Run this file to recreate the current configuration.
# Compiler output produced by configure, useful for debugging
# configure, is in config.log if it exists.

debug=false
ac_cs_recheck=false
ac_cs_silent=false
SHELL=\${CONFIG_SHELL-$SHELL}
_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF
## --------------------- ##
## M4sh Initialization.  ##
## --------------------- ##

# Be Bourne compatible
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
  emulate sh
  NULLCMD=:
  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '${1+"$@"}'='"$@"'
  setopt NO_GLOB_SUBST
else
  case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
fi
BIN_SH=xpg4; export BIN_SH # for Tru64
DUALCASE=1; export DUALCASE # for MKS sh


# PATH needs CR
# Avoid depending upon Character Ranges.
as_cr_letters='abcdefghijklmnopqrstuvwxyz'
as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
as_cr_Letters=$as_cr_letters$as_cr_LETTERS
as_cr_digits='0123456789'
as_cr_alnum=$as_cr_Letters$as_cr_digits

# The user is always right.
if test "${PATH_SEPARATOR+set}" != set; then
  echo "#! /bin/sh" >conf$$.sh
  echo  "exit 0"   >>conf$$.sh
  chmod +x conf$$.sh
  if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
    PATH_SEPARATOR=';'
  else
    PATH_SEPARATOR=:
  fi
  rm -f conf$$.sh
fi

# Support unset when possible.
if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
  as_unset=unset
else
  as_unset=false
fi


# IFS
# We need space, tab and new line, in precisely that order.  Quoting is
# there to prevent editors from complaining about space-tab.
# (If _AS_PATH_WALK were called with IFS unset, it would disable word
# splitting by setting IFS to empty value.)
as_nl='
'
IFS=" ""        $as_nl"

# Find who we are.  Look in the path if we contain no directory separator.
case $0 in
  *[\\/]* ) as_myself=$0 ;;
  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  test -z "$as_dir" && as_dir=.
  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
done
IFS=$as_save_IFS

     ;;
esac
# We did not find ourselves, most probably we were run as `sh COMMAND'
# in which case we are not to be found in the path.
if test "x$as_myself" = x; then
  as_myself=$0
fi
if test ! -f "$as_myself"; then
  echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
  { (exit 1); exit 1; }
fi

# Work around bugs in pre-3.0 UWIN ksh.
for as_var in ENV MAIL MAILPATH
do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
done
PS1='$ '
PS2='> '
PS4='+ '

# NLS nuisances.
for as_var in \
  LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
  LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
  LC_TELEPHONE LC_TIME
do
  if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
    eval $as_var=C; export $as_var
  else
    ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
  fi
done

# Required to use basename.
if expr a : '\(a\)' >/dev/null 2>&1 &&
   test "X`expr 00001 : '.*\(...\)'`" = X001; then
  as_expr=expr
else
  as_expr=false
fi

if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
  as_basename=basename
else
  as_basename=false
fi


# Name of the executable.
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
         X"$0" : 'X\(//\)$' \| \
         X"$0" : 'X\(/\)' \| . 2>/dev/null ||
echo X/"$0" |
    sed '/^.*\/\([^/][^/]*\)\/*$/{
            s//\1/
            q
          }
          /^X\/\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\/\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`

# CDPATH.
$as_unset CDPATH


  as_lineno_1=$LINENO
  as_lineno_2=$LINENO
  test "x$as_lineno_1" != "x$as_lineno_2" &&
  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {

  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
  # uniformly replaced by the line number.  The first 'sed' inserts a
  # line-number line after each line using $LINENO; the second 'sed'
  # does the real work.  The second script uses 'N' to pair each
  # line-number line with the line containing $LINENO, and appends
  # trailing '-' during substitution so that $LINENO is not a special
  # case at line end.
  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
  # scripts with optimization help from Paolo Bonzini.  Blame Lee
  # E. McMahon (1931-1989) for sed's syntax.  :-)
  sed -n '
    p
    /[$]LINENO/=
  ' <$as_myself |
    sed '
      s/[$]LINENO.*/&-/
      t lineno
      b
      :lineno
      N
      :loop
      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
      t loop
      s/-\n.*//
    ' >$as_me.lineno &&
  chmod +x "$as_me.lineno" ||
    { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
   { (exit 1); exit 1; }; }

  # Don't try to exec as it changes $[0], causing all sort of problems
  # (the dirname of $[0] is not the place where we might find the
  # original and so on.  Autoconf is especially sensitive to this).
  . "./$as_me.lineno"
  # Exit status is that of the last command.
  exit
}


if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
  as_dirname=dirname
else
  as_dirname=false
fi

ECHO_C= ECHO_N= ECHO_T=
case `echo -n x` in
-n*)
  case `echo 'x\c'` in
  *c*) ECHO_T=' ';;     # ECHO_T is single tab character.
  *)   ECHO_C='\c';;
  esac;;
*)
  ECHO_N='-n';;
esac

if expr a : '\(a\)' >/dev/null 2>&1 &&
   test "X`expr 00001 : '.*\(...\)'`" = X001; then
  as_expr=expr
else
  as_expr=false
fi

rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
  rm -f conf$$.dir/conf$$.file
else
  rm -f conf$$.dir
  mkdir conf$$.dir
fi
echo >conf$$.file
if ln -s conf$$.file conf$$ 2>/dev/null; then
  as_ln_s='ln -s'
  # ... but there are two gotchas:
  # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
  # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
  # In both cases, we have to default to `cp -p'.
  ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
    as_ln_s='cp -p'
elif ln conf$$.file conf$$ 2>/dev/null; then
  as_ln_s=ln
else
  as_ln_s='cp -p'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null

if mkdir -p . 2>/dev/null; then
  as_mkdir_p=:
else
  test -d ./-p && rmdir ./-p
  as_mkdir_p=false
fi

# Find out whether ``test -x'' works.  Don't use a zero-byte file, as
# systems may use methods other than mode bits to determine executability.
cat >conf$$.file <<_ASEOF
#! /bin/sh
exit 0
_ASEOF
chmod +x conf$$.file
if test -x conf$$.file >/dev/null 2>&1; then
  as_executable_p="test -x"
else
  as_executable_p=:
fi
rm -f conf$$.file

# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"

# Sed expression to map a string onto a valid variable name.
as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"


exec 6>&1

# Save the log message, to keep $[0] and so on meaningful, and to
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by PDB2PQR $as_me 1.3.0, which was
generated by GNU Autoconf 2.60.  Invocation command line was

  CONFIG_FILES    = $CONFIG_FILES
  CONFIG_HEADERS  = $CONFIG_HEADERS
  CONFIG_LINKS    = $CONFIG_LINKS
  CONFIG_COMMANDS = $CONFIG_COMMANDS
  $ $0 $@

on `(hostname || uname -n) 2>/dev/null | sed 1q`
"

_ACEOF

cat >>$CONFIG_STATUS <<_ACEOF
# Files that config.status was made for.
config_files="$ac_config_files"
config_commands="$ac_config_commands"

_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF
ac_cs_usage="\
\`$as_me' instantiates files from templates according to the
current configuration.

Usage: $0 [OPTIONS] [FILE]...

  -h, --help       print this help, then exit
  -V, --version    print version number, then exit
  -q, --quiet      do not print progress messages
  -d, --debug      don't remove temporary files
      --recheck    update $as_me by reconfiguring in the same conditions
  --file=FILE[:TEMPLATE]
                   instantiate the configuration file FILE

Configuration files:
$config_files

Configuration commands:
$config_commands

Report bugs to <bug-autoconf@gnu.org>."

_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF
ac_cs_version="\\
PDB2PQR config.status 1.3.0
configured by $0, generated by GNU Autoconf 2.60,
  with options \\"`echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"

Copyright (C) 2006 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."

ac_pwd='$ac_pwd'
srcdir='$srcdir'
INSTALL='$INSTALL'
_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF
# If no file are specified by the user, then we need to provide default
# value.  By we need to know if files were specified by the user.
ac_need_defaults=:
while test $# != 0
do
  case $1 in
  --*=*)
    ac_option=`expr "X$1" : 'X\([^=]*\)='`
    ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
    ac_shift=:
    ;;
  *)
    ac_option=$1
    ac_optarg=$2
    ac_shift=shift
    ;;
  esac

  case $ac_option in
  # Handling of the options.
  -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
    ac_cs_recheck=: ;;
  --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
    echo "$ac_cs_version"; exit ;;
  --debug | --debu | --deb | --de | --d | -d )
    debug=: ;;
  --file | --fil | --fi | --f )
    $ac_shift
    CONFIG_FILES="$CONFIG_FILES $ac_optarg"
    ac_need_defaults=false;;
  --he | --h |  --help | --hel | -h )
    echo "$ac_cs_usage"; exit ;;
  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
  | -silent | --silent | --silen | --sile | --sil | --si | --s)
    ac_cs_silent=: ;;

  # This is an error.
  -*) { echo "$as_me: error: unrecognized option: $1
Try \`$0 --help' for more information." >&2
   { (exit 1); exit 1; }; } ;;

  *) ac_config_targets="$ac_config_targets $1"
     ac_need_defaults=false ;;

  esac
  shift
done

ac_configure_extra_args=

if $ac_cs_silent; then
  exec 6>/dev/null
  ac_configure_extra_args="$ac_configure_extra_args --silent"
fi

_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF
if \$ac_cs_recheck; then
  echo "running CONFIG_SHELL=$SHELL $SHELL $0 "$ac_configure_args \$ac_configure_extra_args " --no-create --no-recursion" >&6
  CONFIG_SHELL=$SHELL
  export CONFIG_SHELL
  exec $SHELL "$0"$ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
fi

_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF
exec 5>>config.log
{
  echo
  sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
## Running $as_me. ##
_ASBOX
  echo "$ac_log"
} >&5

_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF
#
# INIT-COMMANDS
#
AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"

_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF

# Handling of arguments.
for ac_config_target in $ac_config_targets
do
  case $ac_config_target in
    "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
    "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
    "pdb2pka/Makefile") CONFIG_FILES="$CONFIG_FILES pdb2pka/Makefile" ;;
    "pdb2pka/substruct/Makefile") CONFIG_FILES="$CONFIG_FILES pdb2pka/substruct/Makefile" ;;
    "tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;;
    "tests/test/Makefile") CONFIG_FILES="$CONFIG_FILES tests/test/Makefile" ;;
    "tests/adv-test/Makefile") CONFIG_FILES="$CONFIG_FILES tests/adv-test/Makefile" ;;

  *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
   { (exit 1); exit 1; }; };;
  esac
done


# If the user did not use the arguments to specify the items to instantiate,
# then the envvar interface is used.  Set only those that are not.
# We use the long form for the default assignment because of an extremely
# bizarre bug on SunOS 4.1.3.
if $ac_need_defaults; then
  test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
  test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
fi

# Have a temporary directory for convenience.  Make it in the build tree
# simply because there is no reason against having it here, and in addition,
# creating and moving files from /tmp can sometimes cause problems.
# Hook for its removal unless debugging.
# Note that there is a small window in which the directory will not be cleaned:
# after its creation but before its name has been assigned to `$tmp'.
$debug ||
{
  tmp=
  trap 'exit_status=$?
  { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
' 0
  trap '{ (exit 1); exit 1; }' 1 2 13 15
}
# Create a (secure) tmp directory for tmp files.

{
  tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
  test -n "$tmp" && test -d "$tmp"
}  ||
{
  tmp=./conf$$-$RANDOM
  (umask 077 && mkdir "$tmp")
} ||
{
   echo "$me: cannot create a temporary directory in ." >&2
   { (exit 1); exit 1; }
}

#
# Set up the sed scripts for CONFIG_FILES section.
#

# No need to generate the scripts if there are no CONFIG_FILES.
# This happens for instance when ./config.status config.h
if test -n "$CONFIG_FILES"; then

_ACEOF


ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
  cat >conf$$subs.sed <<_ACEOF
SHELL!$SHELL$ac_delim
PATH_SEPARATOR!$PATH_SEPARATOR$ac_delim
PACKAGE_NAME!$PACKAGE_NAME$ac_delim
PACKAGE_TARNAME!$PACKAGE_TARNAME$ac_delim
PACKAGE_VERSION!$PACKAGE_VERSION$ac_delim
PACKAGE_STRING!$PACKAGE_STRING$ac_delim
PACKAGE_BUGREPORT!$PACKAGE_BUGREPORT$ac_delim
exec_prefix!$exec_prefix$ac_delim
prefix!$prefix$ac_delim
program_transform_name!$program_transform_name$ac_delim
bindir!$bindir$ac_delim
sbindir!$sbindir$ac_delim
libexecdir!$libexecdir$ac_delim
datarootdir!$datarootdir$ac_delim
datadir!$datadir$ac_delim
sysconfdir!$sysconfdir$ac_delim
sharedstatedir!$sharedstatedir$ac_delim
localstatedir!$localstatedir$ac_delim
includedir!$includedir$ac_delim
oldincludedir!$oldincludedir$ac_delim
docdir!$docdir$ac_delim
infodir!$infodir$ac_delim
htmldir!$htmldir$ac_delim
dvidir!$dvidir$ac_delim
pdfdir!$pdfdir$ac_delim
psdir!$psdir$ac_delim
libdir!$libdir$ac_delim
localedir!$localedir$ac_delim
mandir!$mandir$ac_delim
DEFS!$DEFS$ac_delim
ECHO_C!$ECHO_C$ac_delim
ECHO_N!$ECHO_N$ac_delim
ECHO_T!$ECHO_T$ac_delim
LIBS!$LIBS$ac_delim
build_alias!$build_alias$ac_delim
host_alias!$host_alias$ac_delim
target_alias!$target_alias$ac_delim
build!$build$ac_delim
build_cpu!$build_cpu$ac_delim
build_vendor!$build_vendor$ac_delim
build_os!$build_os$ac_delim
host!$host$ac_delim
host_cpu!$host_cpu$ac_delim
host_vendor!$host_vendor$ac_delim
host_os!$host_os$ac_delim
target!$target$ac_delim
target_cpu!$target_cpu$ac_delim
target_vendor!$target_vendor$ac_delim
target_os!$target_os$ac_delim
INSTALL_PROGRAM!$INSTALL_PROGRAM$ac_delim
INSTALL_SCRIPT!$INSTALL_SCRIPT$ac_delim
INSTALL_DATA!$INSTALL_DATA$ac_delim
CYGPATH_W!$CYGPATH_W$ac_delim
PACKAGE!$PACKAGE$ac_delim
VERSION!$VERSION$ac_delim
ACLOCAL!$ACLOCAL$ac_delim
AUTOCONF!$AUTOCONF$ac_delim
AUTOMAKE!$AUTOMAKE$ac_delim
AUTOHEADER!$AUTOHEADER$ac_delim
MAKEINFO!$MAKEINFO$ac_delim
install_sh!$install_sh$ac_delim
STRIP!$STRIP$ac_delim
INSTALL_STRIP_PROGRAM!$INSTALL_STRIP_PROGRAM$ac_delim
mkdir_p!$mkdir_p$ac_delim
AWK!$AWK$ac_delim
SET_MAKE!$SET_MAKE$ac_delim
am__leading_dot!$am__leading_dot$ac_delim
AMTAR!$AMTAR$ac_delim
am__tar!$am__tar$ac_delim
am__untar!$am__untar$ac_delim
PDB2PQR_VERSION!$PDB2PQR_VERSION$ac_delim
CXX!$CXX$ac_delim
CXXFLAGS!$CXXFLAGS$ac_delim
LDFLAGS!$LDFLAGS$ac_delim
CPPFLAGS!$CPPFLAGS$ac_delim
ac_ct_CXX!$ac_ct_CXX$ac_delim
EXEEXT!$EXEEXT$ac_delim
OBJEXT!$OBJEXT$ac_delim
DEPDIR!$DEPDIR$ac_delim
am__include!$am__include$ac_delim
am__quote!$am__quote$ac_delim
AMDEP_TRUE!$AMDEP_TRUE$ac_delim
AMDEP_FALSE!$AMDEP_FALSE$ac_delim
AMDEPBACKSLASH!$AMDEPBACKSLASH$ac_delim
CXXDEPMODE!$CXXDEPMODE$ac_delim
am__fastdepCXX_TRUE!$am__fastdepCXX_TRUE$ac_delim
am__fastdepCXX_FALSE!$am__fastdepCXX_FALSE$ac_delim
py_path!$py_path$ac_delim
PY_SHARED!$PY_SHARED$ac_delim
PY_LDFLAGS!$PY_LDFLAGS$ac_delim
PY_HEADER!$PY_HEADER$ac_delim
PY_FLAGS!$PY_FLAGS$ac_delim
PY_CFLAGS!$PY_CFLAGS$ac_delim
PDB2PQR_SUBDIRS!$PDB2PQR_SUBDIRS$ac_delim
URL!$URL$ac_delim
install_dir_var!$install_dir_var$ac_delim
website_install_var!$website_install_var$ac_delim
_ACEOF

  if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then
    break
  elif $ac_last_try; then
    { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
   { (exit 1); exit 1; }; }
  else
    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
  fi
done

ac_eof=`sed -n '/^CEOF[0-9]*$/s/CEOF/0/p' conf$$subs.sed`
if test -n "$ac_eof"; then
  ac_eof=`echo "$ac_eof" | sort -nru | sed 1q`
  ac_eof=`expr $ac_eof + 1`
fi

cat >>$CONFIG_STATUS <<_ACEOF
cat >"\$tmp/subs-1.sed" <<\CEOF$ac_eof
/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
_ACEOF
sed '
s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g
s/^/s,@/; s/!/@,|#_!!_#|/
:n
t n
s/'"$ac_delim"'$/,g/; t
s/$/\\/; p
N; s/^.*\n//; s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g; b n
' >>$CONFIG_STATUS <conf$$subs.sed
rm -f conf$$subs.sed
cat >>$CONFIG_STATUS <<_ACEOF
CEOF$ac_eof
_ACEOF


ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
  cat >conf$$subs.sed <<_ACEOF
action_install_var!$action_install_var$ac_delim
with_propka!$with_propka$ac_delim
with_pdb2pka!$with_pdb2pka$ac_delim
LIBOBJS!$LIBOBJS$ac_delim
LTLIBOBJS!$LTLIBOBJS$ac_delim
_ACEOF

  if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 5; then
    break
  elif $ac_last_try; then
    { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
   { (exit 1); exit 1; }; }
  else
    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
  fi
done

ac_eof=`sed -n '/^CEOF[0-9]*$/s/CEOF/0/p' conf$$subs.sed`
if test -n "$ac_eof"; then
  ac_eof=`echo "$ac_eof" | sort -nru | sed 1q`
  ac_eof=`expr $ac_eof + 1`
fi

cat >>$CONFIG_STATUS <<_ACEOF
cat >"\$tmp/subs-2.sed" <<\CEOF$ac_eof
/@[a-zA-Z_][a-zA-Z_0-9]*@/!b end
_ACEOF
sed '
s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g
s/^/s,@/; s/!/@,|#_!!_#|/
:n
t n
s/'"$ac_delim"'$/,g/; t
s/$/\\/; p
N; s/^.*\n//; s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g; b n
' >>$CONFIG_STATUS <conf$$subs.sed
rm -f conf$$subs.sed
cat >>$CONFIG_STATUS <<_ACEOF
:end
s/|#_!!_#|//g
CEOF$ac_eof
_ACEOF


# VPATH may cause trouble with some makes, so we remove $(srcdir),
# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
# trailing colons and then remove the whole line if VPATH becomes empty
# (actually we leave an empty line to preserve line numbers).
if test "x$srcdir" = x.; then
  ac_vpsub='/^[  ]*VPATH[        ]*=/{
s/:*\$(srcdir):*/:/
s/:*\${srcdir}:*/:/
s/:*@srcdir@:*/:/
s/^\([^=]*=[     ]*\):*/\1/
s/:*$//
s/^[^=]*=[       ]*$//
}'
fi

cat >>$CONFIG_STATUS <<\_ACEOF
fi # test -n "$CONFIG_FILES"


for ac_tag in  :F $CONFIG_FILES      :C $CONFIG_COMMANDS
do
  case $ac_tag in
  :[FHLC]) ac_mode=$ac_tag; continue;;
  esac
  case $ac_mode$ac_tag in
  :[FHL]*:*);;
  :L* | :C*:*) { { echo "$as_me:$LINENO: error: Invalid tag $ac_tag." >&5
echo "$as_me: error: Invalid tag $ac_tag." >&2;}
   { (exit 1); exit 1; }; };;
  :[FH]-) ac_tag=-:-;;
  :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
  esac
  ac_save_IFS=$IFS
  IFS=:
  set x $ac_tag
  IFS=$ac_save_IFS
  shift
  ac_file=$1
  shift

  case $ac_mode in
  :L) ac_source=$1;;
  :[FH])
    ac_file_inputs=
    for ac_f
    do
      case $ac_f in
      -) ac_f="$tmp/stdin";;
      *) # Look for the file first in the build tree, then in the source tree
         # (if the path is not absolute).  The absolute path cannot be DOS-style,
         # because $ac_f cannot contain `:'.
         test -f "$ac_f" ||
           case $ac_f in
           [\\/$]*) false;;
           *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
           esac ||
           { { echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
echo "$as_me: error: cannot find input file: $ac_f" >&2;}
   { (exit 1); exit 1; }; };;
      esac
      ac_file_inputs="$ac_file_inputs $ac_f"
    done

    # Let's still pretend it is `configure' which instantiates (i.e., don't
    # use $as_me), people would be surprised to read:
    #    /* config.h.  Generated by config.status.  */
    configure_input="Generated from "`IFS=:
          echo $* | sed 's|^[^:]*/||;s|:[^:]*/|, |g'`" by configure."
    if test x"$ac_file" != x-; then
      configure_input="$ac_file.  $configure_input"
      { echo "$as_me:$LINENO: creating $ac_file" >&5
echo "$as_me: creating $ac_file" >&6;}
    fi

    case $ac_tag in
    *:-:* | *:-) cat >"$tmp/stdin";;
    esac
    ;;
  esac

  ac_dir=`$as_dirname -- "$ac_file" ||
$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
         X"$ac_file" : 'X\(//\)[^/]' \| \
         X"$ac_file" : 'X\(//\)$' \| \
         X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$ac_file" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
            s//\1/
            q
          }
          /^X\(\/\/\)[^/].*/{
            s//\1/
            q
          }
          /^X\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`
  { as_dir="$ac_dir"
  case $as_dir in #(
  -*) as_dir=./$as_dir;;
  esac
  test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
    as_dirs=
    while :; do
      case $as_dir in #(
      *\'*) as_qdir=`echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #(
      *) as_qdir=$as_dir;;
      esac
      as_dirs="'$as_qdir' $as_dirs"
      as_dir=`$as_dirname -- "$as_dir" ||
$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
         X"$as_dir" : 'X\(//\)[^/]' \| \
         X"$as_dir" : 'X\(//\)$' \| \
         X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$as_dir" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
            s//\1/
            q
          }
          /^X\(\/\/\)[^/].*/{
            s//\1/
            q
          }
          /^X\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`
      test -d "$as_dir" && break
    done
    test -z "$as_dirs" || eval "mkdir $as_dirs"
  } || test -d "$as_dir" || { { echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
echo "$as_me: error: cannot create directory $as_dir" >&2;}
   { (exit 1); exit 1; }; }; }
  ac_builddir=.

case "$ac_dir" in
.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
*)
  ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
  # A ".." for each directory in $ac_dir_suffix.
  ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
  case $ac_top_builddir_sub in
  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
  esac ;;
esac
ac_abs_top_builddir=$ac_pwd
ac_abs_builddir=$ac_pwd$ac_dir_suffix
# for backward compatibility:
ac_top_builddir=$ac_top_build_prefix

case $srcdir in
  .)  # We are building in place.
    ac_srcdir=.
    ac_top_srcdir=$ac_top_builddir_sub
    ac_abs_top_srcdir=$ac_pwd ;;
  [\\/]* | ?:[\\/]* )  # Absolute name.
    ac_srcdir=$srcdir$ac_dir_suffix;
    ac_top_srcdir=$srcdir
    ac_abs_top_srcdir=$srcdir ;;
  *) # Relative name.
    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
    ac_top_srcdir=$ac_top_build_prefix$srcdir
    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
esac
ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix


  case $ac_mode in
  :F)
  #
  # CONFIG_FILE
  #

  case $INSTALL in
  [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
  *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
  esac
_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF
# If the template does not know about datarootdir, expand it.
# FIXME: This hack should be removed a few years after 2.60.
ac_datarootdir_hack=; ac_datarootdir_seen=

case `sed -n '/datarootdir/ {
  p
  q
}
/@datadir@/p
/@docdir@/p
/@infodir@/p
/@localedir@/p
/@mandir@/p
' $ac_file_inputs` in
*datarootdir*) ac_datarootdir_seen=yes;;
*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
  { echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF
  ac_datarootdir_hack='
  s&@datadir@&$datadir&g
  s&@docdir@&$docdir&g
  s&@infodir@&$infodir&g
  s&@localedir@&$localedir&g
  s&@mandir@&$mandir&g
    s&\\\${datarootdir}&$datarootdir&g' ;;
esac
_ACEOF

# Neutralize VPATH when `$srcdir' = `.'.
# Shell code in configure.ac might set extrasub.
# FIXME: do we really want to maintain this feature?
cat >>$CONFIG_STATUS <<_ACEOF
  sed "$ac_vpsub
$extrasub
_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF
:t
/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
s&@configure_input@&$configure_input&;t t
s&@top_builddir@&$ac_top_builddir_sub&;t t
s&@srcdir@&$ac_srcdir&;t t
s&@abs_srcdir@&$ac_abs_srcdir&;t t
s&@top_srcdir@&$ac_top_srcdir&;t t
s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
s&@builddir@&$ac_builddir&;t t
s&@abs_builddir@&$ac_abs_builddir&;t t
s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
s&@INSTALL@&$ac_INSTALL&;t t
$ac_datarootdir_hack
" $ac_file_inputs | sed -f "$tmp/subs-1.sed" | sed -f "$tmp/subs-2.sed" >$tmp/out

test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
  { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
  { ac_out=`sed -n '/^[  ]*datarootdir[  ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
  { echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
which seems to be undefined.  Please make sure it is defined." >&5
echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
which seems to be undefined.  Please make sure it is defined." >&2;}

  rm -f "$tmp/stdin"
  case $ac_file in
  -) cat "$tmp/out"; rm -f "$tmp/out";;
  *) rm -f "$ac_file"; mv "$tmp/out" $ac_file;;
  esac
 ;;


  :C)  { echo "$as_me:$LINENO: executing $ac_file commands" >&5
echo "$as_me: executing $ac_file commands" >&6;}
 ;;
  esac


  case $ac_file$ac_mode in
    "depfiles":C) test x"$AMDEP_TRUE" != x"" || for mf in $CONFIG_FILES; do
  # Strip MF so we end up with the name of the file.
  mf=`echo "$mf" | sed -e 's/:.*$//'`
  # Check whether this is an Automake generated Makefile or not.
  # We used to match only the files named `Makefile.in', but
  # some people rename them; so instead we look at the file content.
  # Grep'ing the first line is not enough: some people post-process
  # each Makefile.in and add a new line on top of each file to say so.
  # So let's grep whole file.
  if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
    dirpart=`$as_dirname -- "$mf" ||
$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
         X"$mf" : 'X\(//\)[^/]' \| \
         X"$mf" : 'X\(//\)$' \| \
         X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$mf" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
            s//\1/
            q
          }
          /^X\(\/\/\)[^/].*/{
            s//\1/
            q
          }
          /^X\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`
  else
    continue
  fi
  # Extract the definition of DEPDIR, am__include, and am__quote
  # from the Makefile without running `make'.
  DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
  test -z "$DEPDIR" && continue
  am__include=`sed -n 's/^am__include = //p' < "$mf"`
  test -z "am__include" && continue
  am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
  # When using ansi2knr, U may be empty or an underscore; expand it
  U=`sed -n 's/^U = //p' < "$mf"`
  # Find all dependency output files, they are included files with
  # $(DEPDIR) in their names.  We invoke sed twice because it is the
  # simplest approach to changing $(DEPDIR) to its actual value in the
  # expansion.
  for file in `sed -n "
    s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
       sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
    # Make sure the directory exists.
    test -f "$dirpart/$file" && continue
    fdir=`$as_dirname -- "$file" ||
$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
         X"$file" : 'X\(//\)[^/]' \| \
         X"$file" : 'X\(//\)$' \| \
         X"$file" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$file" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
            s//\1/
            q
          }
          /^X\(\/\/\)[^/].*/{
            s//\1/
            q
          }
          /^X\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`
    { as_dir=$dirpart/$fdir
  case $as_dir in #(
  -*) as_dir=./$as_dir;;
  esac
  test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
    as_dirs=
    while :; do
      case $as_dir in #(
      *\'*) as_qdir=`echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #(
      *) as_qdir=$as_dir;;
      esac
      as_dirs="'$as_qdir' $as_dirs"
      as_dir=`$as_dirname -- "$as_dir" ||
$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
         X"$as_dir" : 'X\(//\)[^/]' \| \
         X"$as_dir" : 'X\(//\)$' \| \
         X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$as_dir" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
            s//\1/
            q
          }
          /^X\(\/\/\)[^/].*/{
            s//\1/
            q
          }
          /^X\(\/\/\)$/{
            s//\1/
            q
          }
          /^X\(\/\).*/{
            s//\1/
            q
          }
          s/.*/./; q'`
      test -d "$as_dir" && break
    done
    test -z "$as_dirs" || eval "mkdir $as_dirs"
  } || test -d "$as_dir" || { { echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
echo "$as_me: error: cannot create directory $as_dir" >&2;}
   { (exit 1); exit 1; }; }; }
    # echo "creating $dirpart/$file"
    echo '# dummy' > "$dirpart/$file"
  done
done
 ;;

  esac
done # for ac_tag


{ (exit 0); exit 0; }
_ACEOF
chmod +x $CONFIG_STATUS
ac_clean_files=$ac_clean_files_save


# configure is writing to config.log, and then calls config.status.
# config.status does its own redirection, appending to config.log.
# Unfortunately, on DOS this fails, as config.log is still kept open
# by configure, so config.status won't be able to write to it; its
# output is simply discarded.  So we exec the FD to /dev/null,
# effectively closing config.log, so it can be properly (re)opened and
# appended to by config.status.  When coming back to configure, we
# need to make the FD available again.
if test "$no_create" != yes; then
  ac_cs_success=:
  ac_config_status_args=
  test "$silent" = yes &&
    ac_config_status_args="$ac_config_status_args --quiet"
  exec 5>/dev/null
  $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
  exec 5>>config.log
  # Use ||, not &&, to avoid exiting from the if with $? = 1, which
  # would make configure fail if this is the last instruction.
  $ac_cs_success || { (exit 1); exit 1; }
fi

   echo
   echo ---------------------------------------------------------------------------------------
   { echo "$as_me:$LINENO: result: Please run \"make\" followed by \"make install\" to complete the installation. You may also run \"make test\" or \"make adv-test\". " >&5
echo "${ECHO_T}Please run \"make\" followed by \"make install\" to complete the installation. You may also run \"make test\" or \"make adv-test\". " >&6; }
   echo
fi


USER=`whoami`

echo "     ========================"
echo "     Configuration Parameters"
echo "     ========================"
echo
echo "User ID:       ${USER}"
echo "Version:       ${VERSION}"
echo "Install Dir:   ${prefix}"
echo "propka:        ${with_propka}"
echo "pdb2pka:       ${with_pdb2pka}"
echo "PY_CFLAGS:     ${PY_CFLAGS}"
echo
#echo "     ---------------"
#echo "     Based on SRCDIR"
#echo "     ---------------"
#echo
#echo "Note:  You cannot access the server if SRCPATH is not a web viewable directory"
#echo
#echo "SRCPATH (location of your source directory):       ${srcpath}"
#echo "WEBSITE (path to the website directory):           ${website}"
#echo "PDB2PQR_CGI (path to pdb2pqr.cgi):                 ${pdb2pqr_cgi}"
#echo
#echo "     ------------------------------"
#echo "     Based on --preifx / INSTALLDIR"
#echo "     ------------------------------"
#echo
#echo "Note:  You cannot access the server if INSTALLDIR is not a web viewable directory"
#echo

if test $prefix = `pwd` ; then
  echo "WEBSITE (path to the website directory):           ${website}"
  echo "   (WEBSITE can be changed with the --with-url option)"
  echo "PDB2PQR_CGI (path to pdb2pqr.cgi):                 ${pdb2pqr_cgi}"
  echo "OPALURL (url to the pdb2pqr opal service):         ${OPALURL}"
else
  echo "WEBSITE (path to the website directory):           ${website_install}"
  echo "   (WEBSITE can be changed with the --with-url option)"
  echo "PDB2PQR_CGI (path to pdb2pqr.cgi):                 ${pdb2pqr_cgi_install}"
  if test "$OPALURL" = ""; then
    echo "PDB2PQR jobs will be forked on the server"
    echo "MAX_ATOMS (max number of atoms in a protein):     ${MAX_ATOMS}"
  else
    echo "OPALURL (url to the pdb2pqr opal service):         ${OPALURL}"
  fi
  echo
fi
last_website_install=$last_website_install

last_prefix=$last_prefix


echo ${prefix} > prefix_file
first=`awk -F"/" '{ print $2 }' prefix_file`
second=`awk -F"/" '{ print $3 }' prefix_file`
third=`awk -F"/" '{ print $4 }' prefix_file`
rm -f prefix_file

if test `whoami` = "root" ; then
  if test ${first} != "var" || test ${second} != "www" || test ${third} != "html" ; then
    echo
    echo "*** Warning: The install directory is not inside /var/www/html/"
    echo "             A symbolic link will be created when you run \"make install\""
  elif test "${last_website_install}" != "${last_prefix}" ; then
    echo
    echo "*** Warning: The last directory of your prefix = ${last_prefix}"
    echo "             The last directory of your URL    = ${last_website_install}"
    echo "             It's recommended that they are the same.  You may run configure again with a different set of --prefix and --with-url"
    echo "             Or  a symbolic link will be created when you run \"make install\", and you will be able to run the server from the URL you specified, but not the URL based on --prefix"
  fi
else
  echo As a regular user, you must ask your system administrator to create a symbolic link that enables you to view $URL after you run \"make install\"
fi

if test "$zsi_pyxml_install" = "true" ; then
  echo Since you are not root, PYXML and/or ZSI have been installed in your home directory
  echo "You will need to do 'echo export PYTHONPATH=\${PYTHONPATH}:${prefix}lib/python$PY_VERSION/site-packages/: >>~/.bashrc'"
fi
Revision:	54
Committed:	Mon Sep 29 23:37:10 2008 UTC (12 years, 5 months ago) by tjod
File size:	153658 byte(s)
Log Message:	changes for mingw