Daylight Software Version 4.62 Release Notes

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



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

    - 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 (, 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: (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.