============================ CONTENTS ============================

    1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.62
    2. DETAILS OF CHANGES MADE IN RELEASE 4.62
    3. BUGS FIXED FOR VERSION 4.62
    4. KNOWN BUGS IN VERSION 4.62
    5. DAYLIGHT SOFTWARE-RELEASE HISTORY



========= 1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.62 =========

DAYLIGHT CIS SOFTWARE, VERSION 4.62
Rev: March 5, 1999

This document describes changes and features specific to version 4.62
of Daylight Chemical Information Systems software.  If there is a
machine-specific file for your machine in this directory (e.g.
"readme-v462-sgi"), please read it too.

Version 4.62 is a bug-fix release.  There are few externally visible new
features.

    - Upgrade path
    - Dynamic shared object linking
    - Java Tools
    - THORDBFIX461

====================== 2. DETAILS OF CHANGES =====================

Upgrade path

    For any sites which have not yet installed version 4.61, we
    recommend skipping the installation of 4.61 and going
    directly to 4.62.  Since the database formats in 4.61 and
    4.62 are identical, the conversion utility "thordbfix461"
    can be used for the upgrade.  Those of you who choose this
    upgrade path should still consult the README-461 files for
    information about the changes which were introduced
    between 4.51 and 4.61.

    Note also that there is no 4.62 release of the remote toolkit for
    Macintosh or PC.  The version 4.61 remote toolkit is 100%
    compatible with both 4.61 and 4.62 daytoolservers.

Dynamic shared object linking

    Dynamic shared objects were introduced in version 4.61.
    All Daylight binary executables have been converted to use
    dynamic shared objects for runtime execution.  The Daylight
    toolkits are now provided as shared objects (libXXX.so), and
    these objects must be available at runtime.

    As part of our effort to remove platform dependancies from the
    core toolkits, we have substantially reorganized the internals
    of the toolkits in 4.62.  Hence, 4.61 and 4.62 executables
    and shared libraries are not compatible with one another.

    Furthermore, many of our internal utility functions have been
    packaged in a new object library:  libdt_apputils.so (and its
    static counterpart libdt_apputils.a).  This library contains
    internal, platform-specific utility functions.  These utilities
    are not needed by the core toolkits, but are required by the
    XView libraries.  Hence, one must add libdt_apputils to the
    final link statement for any XView applications.  Take a look
    at the makefile in $DY_ROOT/contrib/src/c/widgets for an example.

Java Grins

    A Java based version of Grins had been introduced in Release 4.61. 
    This version has been updated to now include the following major changes:

  
JavaGrins would previously get killed on moving to a different web page.
      It now stays up until the user explicitly exits it bychoosing
      File->Exit from the main menu.
  
JavaGrins now appears as a resizable external window.
  
 Templates have altered behavior to be more useful.
  
Numerous bugs have been removed.
  
The Java Runtime is now supplied with the Daylight release and is the 
      one that is used by dayutilserver.
  
Installation of the Java Runtime is now fully automated.
  
Numerous changes in dayutilserver, allow for collection of logs,
      monitoring and altering feedback email for bugs/help.

    Information on installing, using and developing with this applet is
    located at $DY_ROOT/dayhtml/java/grins/admin.html. Information on its
    use is located at $DY_ROOT/dayhtml/java/grins/TOC.html.

THORDBFIX461

    Since 4.61 and 4.62 use the exact same database format, no
    database update is required when going from version 4.61 to 4.62.
    Users who are currently running 4.51 can use the "thordbfix461"
    utility to convert directly from 4.51 databases to 4.62 format.

    "thordbfix461" is available to rebuild pre-4.61
    databases for compatability with the 4.6x releases.  The main
    incompatability between pre-4.6x databases and 4.6x is the format
    change for fingerprint data.

    This is a program which uses thorfilters to dump, modify and 
    rebuild pre-4.61 Thor databases.  It also depends upon the binary
    program 'tdtfpid', which is included in the release.

========================== 3. BUGS FIXED ==========================

>   SGI libraries for '-N32' now built with 'mips3' flag by
    default.  This option is compatible with more hardware configurations
    than the default 'mips4' with no significant performance penalty.

>   Fingerprint generation in the toolkit slowed down as it ran.
    dt_fp_generatefp() was asking for more and more memory as it ran, to the
    point that the malloc() system call dominated processing.

>   Thordbinfo could not access read-only databases.

>   Merlinserver crashed on ASMILESANY searches in breakout rows
    within a Merlin pool.  This only happened when using merlinsmartstalk
    program object for searching.

>   Performing dt_transform() on some classes of molecules with
    EZ stereochemistry caused a crash.

>   Some classes of transforms where atoms were added or deleted
    didn't work correctly.

>   The error buffer used by dt_smirkin() sometimes overflowed.

>   XVGrins incorrectly generated the SMARTS for the explicit
    hydrogen atom.

>   Thorlookup crashed during the lookup of non-SMILES identifiers.

>   Thorlookup now supports the option -RAW_DATA TRUE for lookup of
    raw root identifiers.

>   Thorload crashed during the loading of quoted identifiers in
              some cases.


======================= 5. RELEASE HISTORY =======================

Daylight releases are numbered using the following scheme:

   The "system number" (e.g. 3.xx, 4.xx) indicates completely different
   systems.  Each system is a complete new design and coding.

   Major releases (e.g. 4.1x, 4.2x, 4.3x) contain new features and
   enhancements.  Often, programs and databases from one major release
   aren't compatible with those from another.

   Minor releases, or "updates" (e.g. 4.32, 4.33) are for bug fixes and
   minor additional features.  They are also occasionally for adding
   new platforms (computers and/or operating-system version).

The first two releases of system 4 were called "4.1" and "4.2"; under the
above-described scheme they would have been called "4.11" and "4.21".
There were two additional releases of the "demo" tape, which would have
been "4.22" and "4.23".  Release 4.24 (October '92) was the first to use
this new version-numbering scheme.


4.1    20 Dec 1991   First 4.x release: SunOS only

4.21   20 Mar 1992   Second release: bug fixes, added SGI platform

4.22   ??            Demo Tape update (applics and toolkits not affected).
                     Updated the demo database: added clustering data to
                     illustrate Daylight's clustering product.

4.23   22 Sep 1992   Demo Tape update (applics and toolkits not affected)
                     Same as 4.22, but added workaround for a bug in the
                     SGI X window system.

4.24   02 Oct 1992   Update: many bug fixes, some added features.

4.25   13 Nov 1992   SGI Toolkit Tape only; corrects incompatibility between
                     versions of SGI IRIX Operating system.  All other 4.24
                     SGI and Sun tapes are unaffected.

4.31   01 May 1993   Added Print Package, Merlin Toolkit.  Many bug fixes
                     and enhancements.  Added support for VAX/VMS (Toolkits,
                     servers, and some non-X-Windows programs).  Added Thor
                     and Merlin management utilities.

4.32   01 Jul 1993   Added Rubicon program and Rubicon Toolkit.  Added
                     support for HPUX on HP9000/7xx series, and for
                     Solaris on Sun machines.  Improved "man" pages and
                     help-widget text files.  A number of minor bug fixes.

4.33   28 Jan 1994   Improved merlinserver, thorserver, and Merlin and
                     Thor Toolkits.  Improved printing.  A number of minor
                     bug fixes.  Restructured & added to "contrib" programs.

4.34   25 Feb 1994   Revamped clustering programs.  Partial molecular
                     fingerprint generation.  Fixed bugs introduced in 4.33.

4.40   Nov 23 1994   Preliminary "beta-test" versions of 4.41.  
4.40b  Feb 12 1995   Preliminary "beta-test" versions of 4.41.  

4.41   Mar 17 1995   Databases of mixtures, "monomer" toolkit (CHUCKLES,
                     CHORTLES, & CHARTS), Program-Object Toolkit, parallel-
                     ized (multi-CPU) version of clustering, MCL.

4.42   Feb 02 1996   HTML Documentation, CGI application programs, record
		     locking, thordestroy(1), Thor/Merlin messages,
		     Thor/Merlin eviction, faster TDT merging, Merlin
		     parallel SMARTS searches, better Merlin performance
		     under heavy load, Merlin program objects.

4.42p1 Apr 02 1996   Merlinserver, Merlinsmartstalk, and 
                     Daytoolserver bugs fixed in this patch.

4.51   May 01 1997   Reaction Toolkit, reaction databases in Thor/Merlin,
		     formal object properties, read-only (CDROM) databases,
		     cross-referencing non-identifiers in THOR, Merlin
		     "similarity as sub/superstructure", and more.

4.60   Feb 20 1998   MUG'98 version. Preliminary "alpha-test" version of 4.6.
4.61b  May 05 1998   Preliminary "beta-test" version of 4.6.

4.61   Jul 15 1998   ClogP, bug fixes, Reaction Tookit enhancements, 
                     Java tools.

4.62   Mar  5 1999   Bug fixes, Java tools.