Daylight Software Version 4.81 Release Notes
============================ CONTENTS ============================
1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.81
3. DETAILS OF CHANGES MADE IN RELEASE 4.81
5. BUGS FIXED FOR VERSION 4.81
6. KNOWN LIMITATIONS IN VERSION 4.81
========= 1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.81 =========
DAYLIGHT CIS SOFTWARE, VERSION 4.81
This document describes changes and features specific to
version 4.81 of Daylight Chemical Information Systems
software. If there is a machine-specific file for your
machine in this directory (e.g. "readme-v481-sgi"),
please read it too.
Version 4.81 includes new Daycart features, new HTTP toolkit, new ClogP
version, toolkit fixes and enhancements.
Installation and configuration instructions can be found
in the file dayhtml/doc/admin/install.html.
========================== 2. LICENSING ==========================
Usage and Evaluation Licenses
The usage license for the Daylight software is accessible at
http://www.daylight.com/jj-cgi/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 CHANGES =====================
Supported Platforms: Solaris, IRIX, Linux
Version 4.81 supports: Solaris 2.7 and higher (32 bit and 64 bit),
IRIX 6.4 and higher (n32 bit and 64 bit), and Linux Red Hat 7.x.
See the Operating System specific readme for more details.
Version 4.81 includes a number of new licensing features. A license file
may now contain multiple license blocks. Multiple license files can be
used. The new environment variable DY_LICENSEDIR allows the user to
specify a directory which contains multiple license files.
Starting with Version 4.8, the Daylight software has a version-specific
tag in the license. Customers who are paying regular annual support fees
are entitled to upgrades to the software and will receive a new license
There is a new option to testlicense (-v) which gives verbose details about
the license file(s) being read and features licensed.
The toolkits and merlinserver are now supported under 64-bit Solaris. The
files are included in the Solaris distribution under bin64 and lib64.
To build contrib using 64-bit objects, see the instructions in
The SGI/IRIX Xview programs and libraries are now all compiled with
the -N32 flag and use the newer SGI object-file format. 4.81 includes
a distribution of the Xview 3.2 client libraries compiled N32. The older
-32 object file format is no longer used or supported by version 4.81.
The toolkits and programs are available as a beta release on
Macintosh, OSX, version 10.2+. As this is a beta release, there is no
guarantee that it will be supported long-term. Consider the Macintosh
port as experimental.
A number of dependancies on the CEX libraries have been eliminated from
the Daylight binaries. In addition, the CEX datatypes file has been copied
to $DY_ROOT/data. Daylight programs have CEX v1.32 built-in, so neither
CX_ROOT, nor a built CEX distribution are required to run Daylight programs.
CEX v1.42 is available and both versions of CEX are included as a source tar
archive under the exotic/cex subdirectory.
The SMILES toolkit has a new funtion, dt_xsmiles(), which outputs a kekule
SMILES for any valid molecule or reaction. See the manpage for
dt_xsmiles() for more info.
Imine and Oxime EZ stereochemistry is now supported in the toolkit.
Structures like C/C=N/O, C/C=[N+](/C)(\[O-]), C/C=N/C and
C/C=[N+](/C)(\CC) all preserve the EZ-stereo and properly canonicalize
molecules containing this stereo.
The valence warnings in the toolkit have been revamped. Many of the
superfluous warnings have been eliminated.
The toolkit now 'knows' its own version numbers. At the programming
level, the constants DX_TOOLKIT_VERSION and DX_TOOLKIT_DATE give the
version number and 'born-on' date for the toolkit. The function
dt_info(NULL, "toolkit_version") and dt_info(NULL, "creation_date")
gives the analogous runtime version and date. The date is in
A new version of ClogP is included. This corresponds to the Biobyte
version 4.3 algorithm and uses the Biobyte database version 22. In
the past, there have been some small platform-specific discrepancies
which have shown up between the Biobyte version and Daylights version.
These discrepancies have been remedied, so the results are consistant
(+/- 0.001 for 45k test structures of the Biobyte reference set) between
Biobytes version and all four Daylight versions.
The new HTTP toolkit allows the easy implementation and deployment of
HTTP servers and CGI applications. See the HTTP Toolkit Programmers
Guide (dayhtml/doc/prog/prog.http.html) for details.
There are a huge number of new features and options in Daycart. See the
Daycart manual (dayhtml/doc/sql/index.html) for details.
========================== 4. UPGRADING ===========================
The thor database format is identical between 4.7x and 4.81. No Thor database
upgrade is require. One can simply start using 4.81 thorserver, merlinserver
and applications against ones 4.7 database files.
Daycart requires a full upgrade from 4.7x to 4.81. This entails dropping all
Daycart indexes, dropping the Daycart 4.7 packages, installing the 4.81
Daycart packages, and recreating all Daycart indexes. The documentation in
dayhtml/doc/sql/index.html describes this process in detail.
========================== 5. BUGS FIXED ==========================
> Kekule smiles (#553).
> Rubicon help text outdated (#569).
> Toolkit Version feature, implemented as dt_info() and as
constants in dt_smiles.h (#665).
> Merlinsmartstalk welcome messages (#721).
> xvpcmodels garbage text in output (#722).
> Licensing should handle umlats, other non-ASCII printable
characters better (#723).
> mcl -i filename didn't work on Linux. The workaround was
cat filename | mcl instead (#734).
> Listclusters -d "tags" sometimes core dumped. (#742).
> Fingerprint size of less than 32 to dt_fp_generatefp() caused
> Not having a writeable /tmp/extproc.log caused a crash of
> Thorfilters error messages were inconsistant; some went to
stdout, some to stderr. Unified. (#764).
> Thordump couldn't handle DP files greater than 2gb size (#767).
> Merlinserver; remove non-matches search failed if it resulted in
a list with zero hits (#769).
> Xvmerlin sometimes didn't update the hitlist size to zero when
a search resulted in zero hits. You ended up with 'n/a' in all the
> If thorserver can't open the datatypes database associated with
a database it defaulted to use the main database as the datatypes, which
is not correct. Datatypes weren't found and streams of datatypes over
the database failed (#771).
========================== 6. KNOWN LIMITATIONS ===================
> Cost-based optimizer statistics for Daycart do not work for CLOB
searches. Also, there seem to be discrepancies in execution plans which
are chosen depending on the Oracle version (8i vs 9i). If you choose to
use the optimizer statistics provided with this release, please make
sure to check the behavior and statistics on your application carefully.
This is an issue which is being addressed with Oracle.