Daylight Software Version 4.73 Release Notes

Rev: November 15, 2001




This document describes changes and features specific to version 4.73 of Daylight Chemical Information Systems software. If there is a machine-specific file for your machine in this directory (e.g. "readme-v473-sgi"), please read it too.

This version supports Red Hat Linux, SGI IRIX and SUN Solaris systems. See the operating system-specific readme for more details.

Version 4.73 includes a new smi2gif, new printing options, new thorlist options, a dayutilserver which doesn't require a JRE, and bug fixes to the Oracle cartridge, SMARTS, and Program object toolkits.

Version 4.73 is a patch release requiring an existing 4.71 or 4.72 installation.

An installation script, named dayinstall473, is provided for upgrading version 4.71 or 4.72 to 4.73. Execute 'dayinstall473' to interactively configure and upgrade your software. Execute 'dayinstall473 -help' for installation options.


Usage and Evaluation Licenses

The usage license for the Daylight software is accessible at This license is also included with the software. For any further clarification, contact our business office at 949-367-9990.


Upgrade Path

Thor database file formats in 4.73 are identical to those in versions 4.71 and 4.72.

Oracle Cartridge

The cartridge is updated in 4.73. The cartridge has been tested on Oracle 8.1.5, 8.1.6, and 8.1.7, both Standard and Enterprise edition, on Solaris 7 & 8, Red Hat 6.2, and IRIX 6.4+.

Several bugs have been fixed. The most critical being an index corruption which occured during multiple simultaneous updates. This appears to be related to a known Oracle Bug (From Oracle support: Bug #1668041.1, Note #161528.1). Version 4.73 implements a successful workaround of the Oracle problem.

Two bugs in the fprogob() functions were corrected. Blank lines were stripped from messages. One character messages were garbled.

The function ftversky() had alpha and beta switched. The index form of tversky() was correct.

Indexes created using the 4.71 or 4.72 cartridge are 100% compatible with the 4.73 cartridge. The patch installer will replace the older file with the new one.


Dayutilserver is now a native executable. The 4.73 dayutilserver no longer depends upon an installed Java runtime environment. Dayutilserver now uses the regular Daylight option manager. See the Java Grins administration documentation for more details.

smi2gif/depict CGI

The DayCGI tool smi2gif now supports two new modes: reactions and SMIRKS. The reaction mode (-r option) will show atom map class numbers as subscripts on each atom label for reaction SMILES. The SMIRKS mode (-s option) will layout and display reaction SMIRKS and some generic SMARTS. SMIRKS mode preprocesses the input string and depicts any SMARTS atomic expressions as simple atom labels in the output depiction. The dcgi example program depict has been updated to allow SMIRKS to be input and displayed using the new smi2gif features. See the test-smi2gif.html example page for more information.


The PRINT_LINEWIDTH and PRINT_BOLDWIDTH options were corrected for prado and added to treetops and tablet. Also the DEPICT_SUPPRESS_LABELS option was added. The default for printing is to suppress labels; hence printed structures now look more like what is displayed in xvthor/xvmerlin.


Thorlist supports two new options: -BEFORE and -SINCE. These allow the user to control the listed datatrees by the timestamps in the database. The options take a timestamp string in YYYY[MM[DD[HH[MM[.SS]]]]] format.


  • PRINT_LINEWIDTH and PRINT_BOLDWIDTH options didn't work after first page in prado. Also added these options to treetops and tablet.
  • An aromaticity perception problem in transform processing caused dt_transform() to generate incorrect aromatic structures for transforms which contained three aromatic rings in some circumstances.
  • In the cartridge the alpha and beta parameters to the function ftversky() were switched. The index form of the tversky() function was correct.
  • In the cartridge the function fprogob() stripped blank lines in a message and garbled one-character messages.
  • In the program object toolkit (and merlinsmartstalk) a memory leak was corrected. This leak caused merlinsmartstalk and user-written program object programs to use memory.
  • In merlinserver, the superstructure search sometimes failed for specific SMILES queries.
  • In mcl, the output was missing a newline when a field was empty.
  • In sthorman (Linux only), a segmentation fault occurred after display of database content summary [menu sequence: 5) Databases..., 3) Get database information..., 2) Content summary]




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 Summer 1992

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, parallelized (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 05 1999

Bug fixes, Java tools.

4.71 Aug 01 2000

Bug fixes, Java, Oracle cartridge, ClogP, 34-bit thorserver, daycgi fixes, SMILES fixes.

4.72 Mar 06 2001

Bug fixes, Oracle cartridge on SGI and Linux.

4.73 Nov 15 2001

Bug fixes, printing, smi2gif, dayutilserver.