Rev: March 6, 2001

CONTENTS

1. INTRODUCTION AND HIGHLIGHTS
2. LICENSING
3. DETAILS OF CHANGE
4. BUGS FIXED
5. KNOWN BUGS
6. RELEASE HISTORY

1. INTRODUCTION AND HIGHLIGHTS

This document describes changes and features specific to version 4.72 of Daylight Chemical Information Systems software. If there is a machine-specific file for your machine in this directory (e.g. "readme-v472-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 4.72 includes Oracle cartridge support for Linux and SGI, a new dayutilserver which doesn't require a JRE, and bug fixes to ClogP, Smiles toolkit, thorserver, merlinserver, and Java grins.

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

An installation script, named dayinstall472, is provided for upgrading version 4.71 to 4.72. Execute 'dayinstall472' to interactively configure and upgrade your software. Execute 'dayinstall472 -help' for installation options.

2. LICENSING

Usage and Evaluation Licenses

The usage license for the Daylight software is accessible at http://www.daylight.com/cgi-bin/download.cgi. This license is also included with the software. For any further clarification, contact our business office at 949-367-9990.

3. DETAILS OF CHANGE

Upgrade Path

Thor database file formats in 4.72 are identical to those in version 4.71.

Oracle Cartridge

The cartridge is updated in 4.72. Added is support for Red Hat 6.2 and SGI IRIX 6.4+. 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, Red Hat 6.2, and IRIX 6.4+. We have done minimal testing under Solaris 8 and the cartridge runs fine.

The main new features added are additional screening steps during substructure search. These decrease search times for some queries by 1/10th, and do not hurt performance overall. These additional screening steps are not otherwise evident to the user.

Several bugs have been fixed in the Solaris version, including floating point precision problems and a memory error on some hardware (bus error relating to memory allocation).

Several minor changes to the SQL install scripts were made to streamline the installation.

Indexes created using the 4.71 cartridge are 100% compatible with the 4.72 cartridge. One can simply replace the 4.71 ddlib.so file with the 4.72 ddlib.so file and continue using the Oracle indexes. Note however that the verification scripts in the dcischem/TEST subdirectory have changed to reflect the slightly different floating-point results. The verification scripts do check the cartridge version running; this should minimize confusion about discrepancies.

Note that the file ddlib.so has been relocated from the 'dcischem' to the 'lib' directory to make it easier to support multiple versions.

JavaGrins Applet

A few operational bugs have been fixed. In addition some speed enhancements were made.

Dayutilserver

A runtime bug has been fixed.

Clogp

Revisions of clogp & clogptalk have been included. These correct bugs that occur on some platforms when computing clogp's for molecules with large numbers of cycles, and stem in part from Biobyte's implementation of clogp, which they have kindly provided us. This problem had also led to platform dependence where the Sun version (in 4.71) behaved slightly differently in some cases than the SGI and Linux versions.

smi2gif

The DayCGI tool smi2gif has been revised such that supplied 2D coordinates are not re-oriented by default. This solves the problem where 2D coords were not consistently represented due to re-orientation. Also, supplied coords are now scaled to average bond length of 1.0, which corrects improperly scaled labels and aromatic circles. The #o option is introduced to invoke (possible) re-orienting. The option #x added to force explicit CHx (not "suppress"). And, "hint12" now works with tdt-supplied coords.

4. BUGS FIXED

• SMILES canonicalization of structures with multiple relative charilites on ring systems with a plane of symmetry has been corrected. The stereochemistry of the prototypical cyclohexane-1,2-diol is now preserved.
• A specific scenario of merging a TDT has been corrected. The scenario is
  1. a hole in the database (caused by a deletion or a merge),
  2. a TDT merge to the record preceeding the hole, and
  3. insufficient space to merge.
  The record relocation algorithm now correctly determines the location for the newly merged TDT. This bug was introduced in 4.71.
• Determination of the MerlinServer memory size is corrected. The program properly reclaims released pool memory.
• A ClogP4 boundary overrun while processing consecutive SMILES strings has been patched by increasing the size of a static array.
• Clogp:
  • Bug Symptoms:
    • When computing clogp's for molecules with large numbers of cycles on the Solaris OS, the program either
      • coredumped or
      • gave answers that differed from those obtained on Linux or Irix
    • The computed clogps on Linux, Irix seem to agree within numerical precision with the Biobyte version.
    The bug was caused by a memory overrun in the Fortan source in the clogp computation algorithm. This was partially addressed by increasing the size of the offending array, so as to deal with large numbers of cycles. However the process unearthed several other array overruns that Biobyte is currently addressing in the code. A future release (once Biobyte completes their process) will deal with these array overruns. As Biobyte uses a different compiler from ours, these bugs do not manifest similarly even on the same platform.
  • The error codes returned from the command
    
    clogp +PCMODELS_ERRORTEXT
    
    previously did not reflect the exact wording for the verbose error codes used by the program. Also error code 59 was missing. These have been fixed.
• The Solaris cartridge, on some hardware, crashed with intermittent bus errors in fingertest() and tanimoto() searches. This was a problem with memory alignment in the Oracle-allocated memory used by the cartridge. The Oracle memory allocator uses 4-byte boundaries. Unfortunately, we used the -ldalign option in the final production compile.
• So all cartridges give consistant floating-point results for similarity calculations, the internal precision of all cartridge floating-point operations was changed to 8-byte doubles. The conversion between Oracle NUMBER types and 4-byte floats was inconsistant between platforms.
• The fprogob(CLOB...) function incorrectly truncated the results to 4000 bytes.
• JavaGrins:
  • The Tools->Fixed/Variable Lengths menu item did not work in Release 4.71. This is now fixed.
  • The Tools->Fixed/Variable Angles menu item did not work in Release 4.71. This is now fixed.
  • It was possible under certain circumstances for a single web page to invoke several JavaGrins applet windows, causing several licenses to be caught up. This problem is now fixed.
• dayutilserver:
  • The previous release of dayutilserver (Release 4.71) performed incorrectly when configured with simultaneous use licensing. An interim patch for libsmilesTalker.so was released to temporarily deal with this problem. This problem has been corrected in the latest release which includes a new shared library libsmilesTalker.so

5. KNOWN BUGS

> TBA

6. 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 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.