Daylight Software Version 4.71 Release Notes

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



Rev: August 1, 2000

This document describes changes and features specific to
version 4.71 of Daylight Chemical Information Systems
software.  If there is a machine-specific file for your
machine in this directory (e.g. "readme-v471-sgi"),
please read it too.

Version 4.71 includes the Oracle cartridge on Solaris,
updates to Clogp, Javagrins, Thor, daycgi, contrib, and
numerous bug-fixes.

Installation and configuration instructions can be found
in the file dayhtml/doc/admin/install.html.  Instructions
for upgrading databases from previous versions can be
found in the file dayhtml/doc/admin/install/thordbfix471.html.

========================== 2. LICENSING ==========================

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. 

====================== 3. DETAILS OF CHANGES =====================

Supported Platforms: Solaris, IRIX, Linux

   Version 4.71 is the first version of the Daylight products to
   fully support the Linux operating system.  This version of
   the system supports: Solaris 2.5 and higher (32 bit),
   IRIX 6.4 and higher, and Linux Red Hat 6.1 and higher.  See
   the Operating System specific readme for more details.

Upgrade path / thordbcheck471

   Thor database file formats in 4.71 are identical to those
   in version 4.6X.  There are several classes of SMILES for
   which the canonical representations change.  The program
   conversion utility "thordbcheck471" is provided
   to identify and clean up these cases.

   See the man page for thordbcheck471 for usage instructions.

   Note also that there is no 4.71 release of the remote toolkit 
   for Macintosh or PC.  The version 4.61 remote toolkit is 100%
   compatible with 4.61, 4.62 and 4.71 daytoolservers.

Java Grins

    Java Grins now include the following major changes:
  • Handles both the SMARTS and SMILES languages. The SMARTS module is completely graphical and requires no knowledge of the SMARTS syntax.
  • JavaGrins now includes both simultaneous user licensing and IP-based licensing. With simultaneous user licensing, it is possible to use JavaGrins in DHCP based networks.
  • We are releasing a separate 4.71 version of a native Microsoft Windows client application for JavaGrins. The client application uses the dayutils server and allows copy and paste to a SMILES/SMARTS text window.
  • Integrating JavaGrins into a web-page is now easier. Involves adding 3 lines to a web page.
  • Improved speed of operation
  • The dayutils server is now socket based and responds faster
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. Large Thor Databases (34-bit thorserver) The Thor database size limit is now 16GB on IRIX 6.4 and higher and Solaris 2.6 and higher. The thorserver simulates 34-bit file access, yet the database format remains 32-bit. Therefore, the 34-bit thorserver is compatible with existing databases. The transition to larger databases is seemless. To exceed the old limit of 2GB, just start using the new product. For more information, see Michael A. Kappler's presentation titled A "Bit" Larger Database given at MUG `00. SMILES changes There are several changes to the SMILES syntax. Canonical SMILES will now be output with the "-" bond in cases where there is a single bond between two aromatic atoms. The prototypical case is fluorene; its canonical SMILES in 4.71 is: C1c2ccccc2-c3ccccc13. This fixes a problem with ambiguous kekule assignments which cause oscillating canonical SMILES. Four-valent neutral nitrogen can no longer be aromatic. Prior to version 4.71, [Fe]n1ccccc1 was allowed as input. This was in part due to the idea of a dative bond, which was (poorly) supported in earlier toolkit versions. Unfortunately, these ambiguous valences cause other problem (such as the failure in 4.6x of [Fe]n1cccc1 to parse). In 4.71, the semantics and valences for Nitrogen have been made consistant. [Fe]N1=CC=CC=C1 is the proper input SMILES for Iron-pyridine in 4.71. Nitrogen anion is now possibly aromatic. The prototypical pyrole anion (c1cc[n-]c1) is correctly handled. This fixes several reported bugs. Unusual valence aromatics. Several classes of molecules would be written out as aromatic by the toolkit in 4.6x but could not be read back in. These all had to do with a mismatch in the dt_smilin() and dt_cansmiles() rules for aromaticity. These have been unified. Uncorrelated EZ stereochemistry. In some cases, canonical SMILES didn't get these right. They are fixed. Oscillating SMILES. Most have been fixed. See 'Known Bugs' for one known exception. Relative stereochemistry (Fischer). This has been added. Basically, the toolkit will now preserve multiple relative chiralities on ring systems. Extended aromaticity perception. The toolkit will now perform a combinatorial analysis of ring systems, when necessary, to identify extended aromatic systems. This is not perfect (see known bugs), but is better than 4.6x at finding extended aromatic systems. Oracle Cartridge The Daylight/Oracle Chemistry Cartridge for Solaris is included in this release. See the documentation: $DY_ROOT/dayhtml/doc/sql/daycart.html for installation information. Clogp4 ClogP 4.0 from BioByte has been fully integrated into Daylight 4.71 PCModels and PCFilters. ClogP 4.0 is a significant upgrade with the new capability estimating values for unknown fragments. As a result, ClogP is able to generate high quality calculations for many many more compounds, and useful calculations for all compounds in many typical organic datasets. Daycgi Changes smi2gif has been enhanced so that depictions can reflect stored 2D coordinates. If passed a TDT string (supported since 4.61) containing 2D data, and the switch "#t", all hex-encoded as usual, smi2gif will use the 2D coords instead of generating a layout with dt_calcxy. Stereo-isomeric SMILES are handled, and hydrogen coordinates will be used if they are present in correct SMILES order (none, some, or all is ok). Rubicon Changes The rules for invention of conformations has been expanded for a wider range of support for large and small molecules. Missing parameters are becoming less of an issue. Enhanced hybridization recognition has improved the geometry of isonitriles, triazoles, carbon anions, dioxides, and diazo compounds. Also, planarity of aromatic rings with more than six atoms and embedded cyclobutadienes is enforced. Rubicon now rates second in a 3D conformation generation benchmark. Using the test set described in: Sadowski, Gasteiger, and Klebe; J. Chem. Inf. Comput. Sci., 1994, 34, 1000-1008, Rubicon converts 87% of the structures, outperforming CONCORD v3.0.1 (84%), putting it behind CORINA in the benchmark and beyond most other programs (<79%). Rubicon performance on internal benchmarks has improved. The conversion rate of the Interbioscreen99sc database is nearly 100%. The unprocessed cases are caused by organic elements, i.e., B and Si. Also, due to SMARTS pattern optimization, Rubicon is 18% faster on in-house tests. Depiction Changes Some work has been done to make depictions more aestetically pleasing. Specifically, long chains are layed out better, large rings are layed out better, and single-atom molecules are displayed better. A new depiction-object boolean property ("suppress") is provided. This property controls an intermediate display mode beteen schematic and non-schematic. In suppressed mode, long-chain carbons are not shown. Unlike schematic mode, aromatic rings and terminal atoms are shown. Xvthor and Xvmerlin now support the new option "DEPICT_SUPPRESS_LABELS" which controls this display mode in the applications. The default is to use the "suppress" mode. ========================== 4. BUGS FIXED ========================== > Numerous SMILES fixes. > DX_SORT_ANCW was incorrect for xvmerlin. > DX_SORT_ASCENDING and DX_SORT_DESCENDING were not defined in the dt_merlin.h include file. > TDT_GRAPHIC_PREFS option for the TDT widget didn't work properly in xvmerlin. > Xvmerlin always required thorinfo pseudo-user, even if a full server specification was given as input to scan for databases. > Merlinserver crashed for a sort of a column with no data. > Thormake and thorchange didn't set the indirect database properly. > Sthorman sometimes set the monomer database improperly. > $D3D-rooted datatrees caused a crash for thorload. SMILES ntuple normalized datatypes require a SMILES root. > In thor, the NOPUNCT normalization didn't remove the '+' character. > The long listing format of thorls was incorrect, it didn't properly show the 'opened' or 'closed' status. > Thorlookup -raw_data true is incompatible with the -include_datatypes and -exclude_datatypes options. > In the fingerprint toolkit, dt_fp_nbits() wasn't set correctly for a fingerprint which was input by dt_setstringvalue(fpob). > In the fingerprint toolkit, dt_fp_setrange() didn't work correctly for non-byte-aligned data. > Fingerprinting a pathset or cycle didn't work. > The fingerprint program now outputs the XFP<> tag by default for difference fingerprints. > In the depict toolkit, dt_setbondstyles() caused a crash for some structures. > Depictions for water, ammonia, hydrogen sulfide, etc. look better. > Depictions lay out long chains better, in zig-zag orientation. > Depictions of large rings are layed out better. > Tabs in a name in Prado input caused a crash. Also, Prado didn't scale fonts properly for text output. > In MCL, the 'structures not matching' didn't work. > Smi2gif sometimes hung and ran 100% cpu forever. > SMARTS is documented to imply low-precedence and between primitives, however this didn't work for bonds. C-=C in SMARTS now has identical semantics to C-&=C. > When a transform failed mod-off, dt_smirkin() returned an invalid handle instead of NULL_OB. ========================== 5. KNOWN BUGS ========================== > Ring perception, using our SSSR algorithm, causes problems with aromaticity perception. Basically, the SSSR is not the right set of rings upon which to perceive aromaticity. Molecules which have multiple SSSR's can have oscillating canonical SMILES. This will be fixed in a future toolkit version with an overhaul of ring finding and aromaticity. ======================= 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 ?? 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 05 1999 Bug fixes, Java tools. 4.71 Aug 01 2000 Bug fixes, Java, Oracle cartridge, ClogP, 34-bit thorserver, daycgi fixes, SMILES fixes.