Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
Foundation, Inc.

   This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.


Simple Instructions for those Fortunate enough to have a well-configured system
===============================================================================

System Requirements

   -- technically any *nix with Motif and OpenGL libraries installed
   -- some sort of C and C++ compiler
   -- make
   

PRE-INSTALL: 

-- IMPORTANT: Unless MSMS is already installed, you need it as well to compute 
moleculer surface (install first, before GEM. GEM automatically calls MSMS). 
Without this step, GEM can only be tested on several pre-calculated structures
available as examples in data/ directory. 

You can get MSMS from Michael Sanner's website 
			http://www.scripps.edu/~sanner/
or
			http://mgltools.scripps.edu/downloads#msms


-----------------------------------------
Mac OS X Installation Process
-----------------------------

For Mac OS X 10.5.x - 10.7.x:

   1.) Install X-11 and Xcode tools from the disks that came with your computer
       you can find these by using the "search" command on the disk, 
       searching for "X". The Xcode installer comes with every MacOS X install disk 
       or you just register for it online at apple's developer website.  
       After you install Xcode, do a Mac software update 
       (click the apple in the upper left corner of the standard menu of
       the Mac and go to Software update). 
       Sometimes, Apple has a patch to Xcode that should be installed.

For Mac OS X 10.8.x:

   1.) Install Xcode and XQuartz 

     a.) Xcode is obtained from the "App Store". Once downloaded and installed, 
         open Xcode and go to preferences, choose the Downloads tab, 
         and then install "Command Line Tools".

     b.) Download and Install XQuartz (http://xquartz.macosforge.org/landing/) 

All versions of Mac OS X:

   2.) Obtain OpenMotif for your architecture from any number of sources
        Two options below, a.) and b.).

     a.) This, less automated, option is for those experts 
	 that really know the MacOS X. 
	 (dryden.biol.yorku.ca/macosx/ has some other useful packages as well)
         Make sure that after you install OpenMotif, you have the following
         directories on your system:
             /usr/X11R6/include/Xm
             /usr/X11R6/include/Mrm
             /usr/X11R6/include/uil
             /usr/X11R6/include/GL
         If these are there, then your Motif has been correctly installed
         otherwise you will have the arduous task of building symlinks
         for each of these directories and all library files (/usr/X11R6/lib/)

     b.) This option is for everyone else: Install Macports.
 
	 Go to http://www.macports.org to download the proper
	 DMG file for the Mac OSX version you are using. Also see:
	 http://guide.macporgs.org for a comprehensive set of instructions
	 on installing and using Macports. Once you have
	 Macports installed run the following commands:
	 
	 sudo port install openmotif
	 sudo port install glw
         sudo port install gcc44
         sudo port install gcc_select
         sudo port select --set gcc mp-gcc44
         
	 Macports should then install all the dependencies necessary to
	 use these libraries. The default area for Macports to store
	 any of the installed packages is /opt/local/ (bin/include/lib).
	 Therefore it might be necessary to use the following configure
	 line in step 4 below:

	 ./configure LDFLAGS=-L/opt/local/lib CFLAGS=-I/opt/local/include CPPFLAG=-I/opt/local/include

 
   3.) Download the distribution of GEM for which you are currently reading 
       the INSTALL notes and unpack it (probably already done...)

   4.) Change directory into the gem directory and execute ./configure
       (if you are using Macports or installed your libraries in a
       nonstandard location, you may have to use the following line:

       ./configure LDFLAGS=-L/opt/local/lib CFLAGS=-I/opt/local/include CPPFLAG=-I/opt/local/include

       You can change the /opt/local/lib and /opt/local/include to whatever
       path points to your OpenMotif and GL libraries if these were 
       pre-installed.

   5.) run 'make'

   6.) assuming make was successful, run sudo 'make install' (as "root")

   7.) you should now find the executable and man pages installed to 
          /usr/local/bin and /usr/local/man as one would expect.
	
	However, if you do not see it there, check the src/ directory 
	of GEM. If the executable is there, move it to /usr/local/bin  

   8.) Assuming you are new to X and terminal programs:
          Macintosh does not correctly set your paths, in that it does not
             include /usr/local/bin and man in your standard paths.

          I suggest that if you cannot run gem directly after 'make install'
             you should do the following
                 echo "export $PATH=$PATH:/usr/local/bin" >> ~/.profile
                 echo "export $MANPATH=$MANPATH:/usr/local/man" >> ~/.profile
                 (assuming you are using bash as a shell)

  9.) Ideally, everything has run smoothly and you are all set, have fun!

  10.) For a quick test, go to data/ directory and do 'gem Mb.Hhelix.bondi 80.0 1.0 .15 -visualize'  
	This should work even if MSMS is not installed as you have some 
	pre-compiled surfaces in the data/ directory. A window should open 
	showing the red and blue structure. 

  11) On some systems, you have "rubygem" code that has its own man page gem.1.
	As a result, gem's man page does not show when you do 'man gem'. 
	Move away or rename rubygem's gem.1 in /usr/share/man/man1, and 
	run 'make install' again as root. 

-----------------------------------------------------------------------------
         
*NIX Installation Process (Works for Fedora 9, CENT OS 6.x, and, most likely, 
for the earlier versions of both of these OS. Does not work for UBUNTU. 
Untested for others )
-------------------------

   1.) Make sure you have libs installed for X11 (X11-devel) 
          yum list installed libX11-devel
       and OpenMotif (OpenMotif-devel and X11-deprecated-libs)
          yum list installed openmotif
          yum list installed openmotif-devel
          yum list installed libXp
   1a.) X11-deprecated-libs is required for OpenMotif running on newer
         distributions of X.org's implementation of X11.  It is done
         in quite an unruly manner, and you may run into:
            "error while loading shared libraries: libXp.so.6"
         If you see this error, then libXp.so.6 is not in your LD_LIBRARY_PATH.
         It is typically installed in /usr/X11R6/lib (in deprecated libs)
         You can symlink it to /usr/lib (/usr/lib64) or add it to your LD_LIBRARY_PATH

   2.) Make sure you have OpenGL installed.
         yum list installed mesa-libGLU
         yum list installed mesa-libGLw

   2a.) For Fedora 9, if you are building GEM, 
         yum install mesa-libGLw-devel

   2b.) For CENT OS 6.x, if you are building GEM,
         yum install openmotif-devel
         yum install mesa-libGLU-devel
         yum install mesa-libGLw-devel

   3.) Download and install MSMS from Michael Sanner's website 
	http://www.scripps.edu/~sanner/
	(unless you only want to play with the examples that come with 
	the distribution. For those ones, the relevant vertex information 
	is available in the .face and .vert files; these will be read 
	in automatically if GEM does not find MSMS installed. )

   4.) download and unpack this distribution.

   5.) change directory to the base distribution directory.

   6.) execute ./configure

   7.) Run 'make'

   8.) Run 'make install'

   9.) If you do not have sudo configured, and had to become superuser to install GEM,
       run ./find_or_prompt_msms.sh to configure your environment so that GEM can find
       your MSMS installation.

  10.) You should be good to go.  Have fun!
        

Advanced Installation (oh no trouble!)
==================

If GEM did not build, then more than likely it has to do with Motif.
Go to /usr/X11R6/include/ and look for 'Xm', 'Mrm', 'uil' and 'GL'
directories.  If they aren't there, your OpenMotif is goofed up.
I think they are moving toward hiding OpenMotif in some secret place,
but for now let's call this a "misconfigured Motif".  If such a thing
happens and you can find your motif base directory, link the files
over to their appropriate locations or get another version of motif
that is correctly configured.  (Of course you could also go further down
these directions and add the correct motif path into the libpath and
include paths searched by the make process).

Now, assuming the problem is more insidious than Motif being bratty...

   The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation.  It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions.  Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, and a
file `config.log' containing compiler output (useful mainly for
debugging `configure').

   It can also use an optional file (typically called `config.cache'
and enabled with `--cache-file=config.cache' or simply `-C') that saves
the results of its tests to speed up reconfiguring.  (Caching is
disabled by default to prevent problems with accidental use of stale
cache files.)

   If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release.  If you are using the cache, and at
some point `config.cache' contains results you don't want to keep, you
may remove or edit it.

   The file `configure.ac' (or `configure.in') is used to create
`configure' by a program called `autoconf'.  You only need
`configure.ac' if you want to change it or regenerate `configure' using
a newer version of `autoconf'.

The simplest way to compile this package is:

  1. `cd' to the directory containing the package's source code and type
     `./configure' to configure the package for your system.  If you're
     using `csh' on an old version of System V, you might need to type
     `sh ./configure' instead to prevent `csh' from trying to execute
     `configure' itself.

     Running `configure' takes awhile.  While running, it prints some
     messages telling which features it is checking for.

  2. Type `make' to compile the package.

  3. Optionally, type `make check' to run any self-tests that come with
     the package.

  4. Type `make install' to install the programs and any data files and
     documentation.

  5.    >> see here look this is what makes it not generic
     If you install to /usr/local/bin or other protected areas as the 
     'root' user, you will likely want to configure the MSMS_EXECUTABLE_PATH
     for your user by running ./find_prompt_msms.sh manually as that user
     or by simply setting the path in your .profile.

  6. You can remove the program binaries and object files from the
     source code directory by typing `make clean'.  To also remove the
     files that `configure' created (so you can compile the package for
     a different kind of computer), type `make distclean'.  There is
     also a `make maintainer-clean' target, but that is intended mainly
     for the package's developers.  If you use it, you may have to get
     all sorts of other programs in order to regenerate files that came
     with the distribution.

Compilers and Options
=====================

   Some systems require unusual options for compilation or linking that
the `configure' script does not know about.  Run `./configure --help'
for details on some of the pertinent environment variables.

   You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment.  Here
is an example:

     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix

   *Note Defining Variables::, for more details.

Compiling For Multiple Architectures
====================================

   You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory.  To do this, you must use a version of `make' that
supports the `VPATH' variable, such as GNU `make'.  `cd' to the
directory where you want the object files and executables to go and run
the `configure' script.  `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'.

   If you have to use a `make' that does not support the `VPATH'
variable, you have to compile the package for one architecture at a
time in the source code directory.  After you have installed the
package for one architecture, use `make distclean' before reconfiguring
for another architecture.

Installation Names
==================

   By default, `make install' will install the package's files in
`/usr/local/bin', `/usr/local/man', etc.  You can specify an
installation prefix other than `/usr/local' by giving `configure' the
option `--prefix=PATH'.

   You can specify separate installation prefixes for
architecture-specific files and architecture-independent files.  If you
give `configure' the option `--exec-prefix=PATH', the package will use
PATH as the prefix for installing programs and libraries.
Documentation and other data files will still use the regular prefix.

   In addition, if you use an unusual directory layout you can give
options like `--bindir=PATH' to specify different values for particular
kinds of files.  Run `configure --help' for a list of the directories
you can set and what kinds of files go in them.

   If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.

Optional Features
=================

   Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System).  The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.

   For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.

Specifying the System Type
==========================

   There may be some features `configure' cannot figure out
automatically, but needs to determine by the type of machine the package
will run on.  Usually, assuming the package is built to be run on the
_same_ architectures, `configure' can figure that out, but if it prints
a message saying it cannot guess the machine type, give it the
`--build=TYPE' option.  TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:

     CPU-COMPANY-SYSTEM

where SYSTEM can have one of these forms:

     OS KERNEL-OS

   See the file `config.sub' for the possible values of each field.  If
`config.sub' isn't included in this package, then this package doesn't
need to know the machine type.

   If you are _building_ compiler tools for cross-compiling, you should
use the `--target=TYPE' option to select the type of system they will
produce code for.

   If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the
"host" platform (i.e., that on which the generated programs will
eventually be run) with `--host=TYPE'.

Sharing Defaults
================

   If you want to set default values for `configure' scripts to share,
you can create a site shell script called `config.site' that gives
default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists.  Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.

Defining Variables
==================

   Variables not defined in a site shell script can be set in the
environment passed to `configure'.  However, some packages may run
configure again during the build, and the customized values of these
variables may be lost.  In order to avoid this problem, you should set
them in the `configure' command line, using `VAR=value'.  For example:

     ./configure CC=/usr/local2/bin/gcc

will cause the specified gcc to be used as the C compiler (unless it is
overridden in the site shell script).

`configure' Invocation
======================

   `configure' recognizes the following options to control how it
operates.

`--help'
`-h'
     Print a summary of the options to `configure', and exit.

`--version'
`-V'
     Print the version of Autoconf used to generate the `configure'
     script, and exit.

`--cache-file=FILE'
     Enable the cache: use and save the results of the tests in FILE,
     traditionally `config.cache'.  FILE defaults to `/dev/null' to
     disable caching.

`--config-cache'
`-C'
     Alias for `--cache-file=config.cache'.

`--quiet'
`--silent'
`-q'
     Do not print messages saying which checks are being made.  To
     suppress all normal output, redirect it to `/dev/null' (any error
     messages will still be shown).

`--srcdir=DIR'
     Look for the package's source code in directory DIR.  Usually
     `configure' can determine that directory automatically.

`configure' also accepts some other, not widely useful, options.  Run
`configure --help' for more details.


IF ALL ELSE FAILS
=====================

If you are still having trouble configuring or running GEM, please feel free to contact us at John.Gordon@microsoft.com or alexey@cs.vt.edu.
