The current release is Daylight Software v4.82. It is minor release that requires v4.81 and upgrades parts of the software and documentation. Supported platforms are Sun, Red Hat, SGI, and Macintosh. Areas of new development include DayCart, the HTTP Toolkit, the Property Package, ClogP, the SMILES Toolkit, the DEPICT Toolkit, and licensing.

Daylight Software

Daylight Software v4.81 is a major release and includes all software and documentation. Daylight Software v4.82 is a minor release and includes only new and altered components. Information on how to license, download, and install Daylight software is available at http://www.daylight.com/support.

Table 1: Product Platform Matrix
	with 8.1.7, 9i, 9iR2		Toolkits		ThorServer		MerlinServer		Applications
	32-bit	64-bit	32-bit	64-bit	32-bit	34-bit1	32-bit	64-bit	32-bit
Solaris 7, 8, 9	X	X	X	X	X	X	X	X	X
Linux 7.1, 7.2, 7.3	X		X		X		X		X
Irix 6.4, 6.5			X	X	X	X	X	X	X2
OSX 10.2			X		X		X		X3

¹ That's not a typo - it really is a 34-bit ThorServer. See the MUG '00 talk A "Bit" Larger Database for details.
² On Irix, the new 32-bit library (-n32) is supported and the old 32-bit library (-o32) is not supported
³ On OSX, X Window and FORTRAN application are not supported

Migration. Installation of v4.81 is required prior to migration to v4.82, which comes with a procedure that provides an interactive, simple and reversible way to migrate between versions. Language specifications have not changed between v4.7x and v4.8x. Thor databases made with v4.7x are 100% compatible with v4.8x, so there is no Thor database upgrade procedure. A v4.7x to v4.81 upgrade procedure is required for DayCart package specifications and "backing" index object formats. It is not necessary to modify data in base tables of DayCart as part of the upgrade.

New Developments

DayCart. Many powerful new developments have been made to DayCart. Details of change were accurately forecasted in Jack Delany's EuroMUG '02 talk DayCart - What's New and the following summarizes the new items in the current release. For complete documentation, see the Daylight Chemistry Cartridge manual. Examples on how to use the new functionality described here and all DayCart routines are located in the $DY_ROOT/dcischem/TEST directory.

• New Capability - alter index ... rename | rebuild
  • rename an index and it's "backing tables"
  • rebuild a internal data structure of a ddblob index
    • compacts by removing holes from deleted data
    • faster than index drop and recreation
    • "no-op" for ddexact, ddgraph, and ddrole indexes

• New Option - fpinitcolumn=<name of FINGERPRINT column>
  • for convenience only
  • applies to the ddblob indextype
  • significantly decreases creation time of SMILES column
  • no ongoing SMILES/FINGERPRINT relationship is established

• New Functions
  • finfo() - get version and host information
  • smi2xsmi() - convert SMILES to eXchange SMILES
  • partnorm() - order N-tuple parts
  • usmiles() - compare unique SMILES
  • asmiles() - compare absolute SMILES
  • component() - determine if molecule is in a mixture or reaction
  • isin() - perform substructure search, inversely related to contains()
  • setinfo() - set session-level properties
  • vcs_desalt() - separate salts according to user-defined rules
  • vcs_normalize() - standardize structure according to user-defined rules

• New Features
  • support for CLOB everywhere a VARCHAR2 can be used
  • improved handling of predicates for boolean (T/F) and continuous functions (eq, gt, lt, lte, gte, range).
  • best "number" limit on queries for contains(), isin(), fingertest(), tanimoto(), tversky(), euclid(), fingertest()

• Not Yet
  • use of index for FALSE role search, e.g. ... where reactant(smiles, 'CCO') = 0.
  • support for CLOB optimizer - statistics not provided

• Upgrade Procedure
  • list_indexes - program provided to migrate indexes from v4.7x to 4.81.

• Performance Suggestions
  • consider usmiles() and asmiles() with the ddgraph index as compared to use of exact() and the ddexact index
  • use the best "number" limit on ddblob searches when you can
  • use FINGERPRINTS in the base table with SMILES and use the "fpinitcolumn" option for index builds

HTTP Toolkit. The HTTP Toolkit is a web-based programmer library and conforms to HTTP/1.0 specifications. The HTTP Toolkit allows you to receive requests to and send responses from Daylight tools over the web, quickly and easily. The HTTP Toolkit was release in v4.81 with the Application Programmers Interface, server and CGI program structure, and the essential and complete list of properties used to construct HTTP services. For complete documentation, see the HTTP Toolkit Programmer's Guide.

• Application Programmer Interface
  • dt_alloc_http_server
  • dt_http_get
  • dt_http_put

• DayCGI Replacements
  • smi2gif
  • depict
  • General Database Interface

• DayCart Development
  • General Database Interface

Property Package.. The Property Package is a new tool that allows the calculation of a large number of molecular properties which are commonly used in compound screening. The calculations can be performed on TDT files and also perfomed within Oracle using Daycart. For complete documentation, see the Property Package Manual. The following illustrates calculation of hydrogen-bond donor count using a TDT and using DayCart.

% echo '$SMI<NCCc1ccc(O)c(O)c1>|' | dayprop -property hdonor_count
$SMI<NCCc1ccc(O)c(O)c1>PPROP<4;4;0;>|

SQL> select hdonor_count('NCCc1ccc(O)c(O)c1') from dual;

HDONOR_COUNT('NCCc1ccc(O)c(O)c1')
--------------------------------------------------------------------------------
4

ClogP. The best computed logP program is better than ever. We've worked closely with Biobyte and currently provide algorithm v4.3 and database v22. ClogP computations using the Biobyte reference set (45,000 structures) are within 0.001 units of Biobytes results across all our platforms. As a sample, here's a look at dopamine.

SMILES Toolkit. Several new entrypoints have been added to the SMILES Toolkit and several problems have been solved.

• dt_appendstring() - append to the string value of a named property
• dt_appendstringvalue() - append a string to string value of an object
• dt_fp_commonbitcount() - compute the count of bits 'on' in common between two fingerprints
• dt_info() - retrieve runtime information, such as version number and creation date
• dt_xsmiles() - retrieve the exchange SMILES string of an object
• a 64,000 atom and bond limit has been removed
• oscillating SMILES with Fischer chirality has been resolved
• imine/oxime stereochemistry properly handled with respect to canonicalization, for example:

  CC/C=N/C.CC/C=[N+](\C)/[O-]

ThorFilters. The THORDUMP application has been upgraded to use the 34-bit ThorServer access routines on 64-bit architectures.

Applications. XVMERLIN database list limit of 100 was removed in v4.82. RUBICON always produced the same coordintes for chiral structures in v4.81 and was corrected in v4.82.

Contrib. Building of Daylight open source software has been made as easy as "cd $DY_ROOT/contrib/src ; make install". Running "Contrib" programs need your PATH and LD_LIBRARY_PATH environment variables to include $DY_ROOT/contrib/bin and $DY_ROOT/contrib/lib, respectively. A glitch in the MOL2SMI software has been corrected.

Licensing. There are several new licensing features in v4.81. For complete details, see the licensing(5) manual page.

• A license file may contain multiple blocks and the new environment variable DY_LICENSEDIR can be set to specify a directory contain multiple license files.
• Starting with Version 4.81, Daylight software has a version-specific tag in the license file. Customers who are paying regular annual support fees are entitled to upgrades to the software and will receive a new license file.
• There is a new option to testlicense (-v) which gives verbose details about the license file(s) and authorized features. For more information, see the testlicense(1) manual page.

DEPICT Toolkit. Layout of structure with fully or partially specified coordinates is possible. Programmers can set all coordinates of a structure or set a substructure then use the DEPICT Toolkit to layout the remaining portion. Users can view structures with the 2D-coordinates datatype in THOR and MERLIN applications. Below is an example of a depiction with and without 2D coordinates:

Comparison of Depictions With and Without 2D Coordinates
Name	With 2D Coordinates	Without 2D Coordinates
Betametbe

For more information, see the MUG '02 Talk Incorporation of 2D Coordinates in Daylight Applications and the manual pages on dt_setcoord(3), dt_calcxy(3), xvthor(1), and xvmerlin(1).

Forthcoming Improvements

DEPICT Toolkit. Traditionally, depiction of chiral center have been overspecified and unconventional, making it ackward or cumbersome to recognize stereochemistry. Use of "wedge" and "hash" bond styles have been reduced to two or one per chiral center. Bonds in rings, to sp2 centers, along major axes, and between chiral centers are preferencially drawn as lines. Implicit hydrogen are shown only when needed to illustrate sterchemistry, and they're bond length has been shorted to two-thirds of a heavy-heavy atom bond.. Depiction of cis and trans stereochemistry involving ring closure bonds were wrong 50% of the time and has been corrected. The following illustrates forthcoming inprovements in the DEPICT Toolkit:

Comparison of Depictions
Name	v4.82	v4.83	Change in Depiction
Carbidopa			Reduced bond styles from four to two
Pencillam			Reduced bond styles from four to one Hydrogen is hidden
Amygdalin			Many hydrogens are hidden
Ajmaline			Ring bond style is preferencially placed in plane
Fosinopri			Bonds to an sp2 center, a ring, or along major axis are preferencially placed in plane
Suloctidi			Bonds between chiral centers is preferencially placed in plane
Cycotiami			exocyclic cis/trans stereochemistry is correctly displayed

ThorServer. The default value for the caching of hash tables has been changed from "always" to "on request". Caching used to ocurr with any database operation, so this avoids loading overwhelming large hash tables during creation of the database (THORMAKE) and alteration of database settings (THORCHANGE). The performance consequence of this change is small (creation of our WDI '03.2 database took less than 1% more time). If you want to cache hash tables as before, you'll need to use -CACHE_WHEN ALWAYS -CACHE_LEVEL READWRITE options.