COMPILING AND INSTALLING DAYPERL2

Contents:
  * Compiling Swig
  * Compiling
  * Testing
  * Installing


Unfortunately, this is a bit more complicated than the traditional "perl
Makefile.PL" installation.  Maybe some day...

Compiling Swig
--------------

The hard part of compiling DayPerl2 is getting swig(1) (but your computer
may have it already).  The source for swig version 1.3.19 is included in
the DayPerl2 distribution.  If you want to try a more recent version of
swig, go to:

	http://www.swig.org

(More recent versions of swig may work, but we haven't tried them.)

If you don't have swig, compile the version supplied:

	cd swig
	gunzip <swig-1.3.19.tar.gz | tar xvf -
	cd SWIG-1.3.19
	./configure
	make
	make install  (optional --  see below)

If you don't have root permission on your computer, you won't be able to
install swig in the normal place.  In that case, you can usually run it
without installing by setting the SWIG_HOME environment variable to the
SWIG-1.3.19 directory.

(The makefiles supplied for Linux and Solaris are set up for a local,
non-installed SWIG by default.  If you install SWIG, edit the appropriate
makefile for your machine.)
	

Compiling DayPerl2
------------------

See "Compiling Swig", above, if you don't have swig(1).

To compile:

   ln -s makefile.<arch> makefile    # where <arch> is linux or solaris
   make

To start fresh, type "make clean".

To start completely out-of-the-box fresh, type "make distclean".  This will
erase DayPerl2 and all of the graphics libraries.


Testing
-------

Before you install, you can run a few of the examples.  You must stay in
the main dayperl2-1.x.x directory (i.e. do NOT cd to the examples
directory).  

A simple one is:

	$ echo "c1ccccc1O" | ./examples/cansmi.pl
	Oc1ccccc1

If you have Thor running:

	$ ./examples/thortest.pl 

	Got thor server: 1, isnew = 1
	   dt_stringvalue() = 'moonunit2:thor'
	   dt_typename()    = 'server'
	Directories:
	  /usr/local/daylight/thordb
	Databases:
	  /usr/local/daylight/thordb/medchem00demo.THOR
	  /usr/local/daylight/thordb/medchem00demo_datatypes.THOR
	  /usr/local/daylight/thordb/medchem00demo_indirect.THOR
          ... etc.
	Opening medchem00demo database...$db = 0, $isnew = 1

	Got merlin server: 48, isnew = 1
	   dt_stringvalue() = 'moonunit2:merlin'
	   dt_typename()    = 'merlinserver'
	Directories:
	  /usr/local/daylight/thordb
	Databases:
	  /usr/local/daylight/thordb/medchem00demo.THOR
	  ... etc.
	Opening medchem00demo database...$db = 0, $isnew = 1

If you have the Depict Toolkit, the following will produce a file "test_out.png"

	$ ./examples/depicttest.pl

DayPerl2 has not been thoroughly tested.  The stuff that's been used a lot
(primarily the SMILES, SMARTS and Depict toolkits) seems to work pretty
well.  Other toolkits, particularly Thor and Merlin, have had their basics
tested but there are many functions that have not been tested.  And the
more obscure functionality, such as the Monomer Toolkit, has not been
tested at all. DayPerl2 needs a comprehensive set of tests.

The Swig compiler seems to work pretty well, so if you encounter errors
they're most likely to be oddball functions that have unusual parameters
that Swig can't handle.  The symptom is usually that Perl complains you've
given the wrong number or type of parameters to the function, or you get a
core dump.  In almost all cases, a core dump will be from a function that
takes a length-and-string parameter, one whose "signature" is not in the
typemaps.i file.


Installing
----------

As the "root" user, type "make install".  This will copy the .pm and .so
files to your Perl library directory.

If you can't be the root user, you can use DayPerl2 without installing it,
but DayPerl2.so must be in your LD_LIBRARY_PATH, and DayPerl2.pm must be in
your @INC path.  If you're using Apache, you may need to use

   SetEnv LD_LIBRARY_PATH <path...>

directive in your httpd.conf file; see the Apache documentation for
details.

If you're on an SGI, it's even trickier because IRIX has more than one
LD_LIBRARY_PATH variable, for 32-bit, 64-bit and o-32 and n-32 object
files.  If you know what I'm talking about, good luck, and if you don't,
don't even try it.