Michael A. Kappler
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.
Table 1: Product Platform Matrix
Solaris 7, 8, 9
Linux 7.1, 7.2, 7.3
Irix 6.4, 6.5
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.
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.
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.
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.
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|
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).
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.