Contrib Changes

• Introduction
• Distributed Code
• Downloadable Code
• Wrappers

Introduction

• Daylight contributed source code, "Contrib", has been reorganized.
• Some of the software will remain in the distribution.
• Some of the software, including the Toolkit Wrappers, has been moved to the Daylight website.

Distributed Code

• Contributed source code is located in the Daylight distribution under $DY_ROOT/contrib/src.
• It can be compiled and installed into $DY_ROOT/contrib/bin , $DY_ROOT/contrib/include and $DY_ROOT/contrib/lib via the following command (typically executed by the Daylight Administrator, Thor):
  % cd $DY_ROOT/contrib/src
  % make install
• Installation also copies an appropriate makefile_include from $DY_ROOT/contrib/src/machine_dependent/ to $DY_ROOT/contrib/src/.
• The directory structure has ben slightly simplified.
  • The language-specific directories (perl, fortran and python) have been removed from under $DY_ROOT/contrib/src/ in the distribution hierarchy.
  • DayPerl/Perl, PyDaylight and Fortran wrappers and programs have been moved to the Daylight website.
  • The c directory has been removed but can be effectively retained by executing the following command:
    % cd $DY_ROOT/contrib/src
    % ln -s . c
    % ls -l $DY_ROOT/contrib/src/c/smiles/cansmi.c
    -rw-r--r-- 1 thor thor 2196 Mar 22 2005 /usr/local/daylight/v491/contrib/src/c/smiles/cansmi.c
  • The remaining directories continue to be arranged by topic or toolkit:
    % ls -1 $DY_ROOT/contrib/src
    depict
    fingerprint
    http
    libdu
    mcl
    merlin
    oracle
    progob
    reaction
    rubicon
    smarts
    smiles
    thor
    transform
• The make_index script ...
  • Has been updated but remains easy to configure and run :
    % cd ${DY_ROOT}/contrib/src
    % ./make_index -html -link /daycontrib > index.html
    % su
    # vi /usr/local/apache2/conf/httpd.conf
      <add the following text>
      Alias /daycontrib/ "/usr/local/daylight/v491/contrib/src/"
      <Directory "/usr/local/daylight/v491/contrib/src/">
          Options Indexes MultiViews
          AllowOverride None
          Order allow,deny
          Allow from all
      </Directory>
    # /usr/local/apache2/bin/apachectl restart
  • The script has been moved from $DY_ROOT/contrib to the $DY_ROOT/contrib/src directory.
  • The script now includes itself in it's output.
• The summary description text has been removed from the _readme files and integrated into the code headers them selves.
• Otherwise non-essential _readme files have been eliminated.

Downloadable Code

• All downloads except very large items (specifically, the NCI database) are available via http .
• FTP downloads have been otherwise eliminated.
• The downloadable make files utilize a makefile_include file from the Distributed code.
• Individual software download pages have been updated and standardized.
• The index page has been reworked and moved from www.daylight.com/support/contrib/index.html to www.daylight.com/download/contrib/index.html.

Wrappers

• The toolkit wrappers have been consolidated into a single location on the Daylight website.
• None of the wrappers (including Fortran) remain in the Daylight distribution.
• Several of them have been recently updated for v491 compatibility.

Copyright 2005, Daylight CIS, Inc.