Daylight Software Version 4.94 Release Notes

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




   This document describes changes and features specific to
   version 4.94 of Daylight Chemical Information Systems
   software.  If there is a machine-specific file for your
   machine in this directory (e.g. "readme-v494-sgi"),
   please read it too.

   Version 4.94 includes additional new web services, performance
   and reliability improvements for Daycart, R-group conversion,
   RTable generation, and PNG image support.

   Installation and configuration instructions can be found
   in the file dayhtml/doc/install/index.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 949-831-9990. 

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

Supported Platforms: Solaris, IRIX, Linux, Windows

   Version 4.94 is supported on: SPARC Solaris 7 and
   higher (32- and 64-bit), X84_64 Solaris 10, SGI MIPS/IRIX
   6.5 and higher (32- and 64-bit), x86 Linux RHEL2.1,
   RHEL3, RHEL4, and RHEL5. AMD64 Linux RHEL3, RHEL4, and x86
   Windows 2000 Professional and higher.

   Release 4.94 does not include static libraries for 
   toolkit programmers.  Because of the linking requirements
   for incorporation of FLEXnet licensing features, only
   shared object libraries are included.

   See the Operating System specific readme for more details.

Web Services

   In release 4.94, the following new services are available for
   installation under Apache tomcat-5.5:

     generateRTable  - represents a set of structures and a scaffold
                       as rows containing SMARTS for R-groups

     executeProgram  - enables users to deploy programs as web 

     getClogP        - Biobyte ClogP from structures

     getTautomers    - computes all or canonical tautomers from 

     desaltSmiles    - removes salts or solvents from mixture 
     normalizeSmiles - applies business rules to normalize structures

     getTransforms   - generates reactions or products from 
                       structures and transforms

     listLicense     - shows all Daylight web services that are
                       licensed on a server

   A simple example SOAP client with verification tests
   is provided.

R-Group Conversion

   The ability to convert R-group files from MDL to Daylight 
   SMARTS has been added to the conversion package, DayCart,
   and the conversion web service.  R-groups are query features
   which, themselves, may have query features.  R-Groups may also
   have multiple attachment points.  R-group logic is not supported.

RTable generation

   Following on the prior release of tools, programs and services
   that derive scaffolds and perform scaffold-directed clustering,
   this release provides a web service to generate R-tables from
   a set of molecules and a scaffold.  The scaffold may have up to
   4 fragments.  The R-table generated consists of one row per
   input molecule where the row contains SMARTS representations of
   all scaffolds and R-group fragments and the molecule identifier.
   The R-table generator optimizes the alignment of groups with
   similar physical properties where possible. 

PNG Image support

   The smi2gif http program and the getDepiction web
   service can generate PNG images.  The PNG's use
   anti-aliasing.  One also can control the linewidth of
   the PNG images.  These result in *much* nicer images,
   although PNG images are generally 5x larger than GIF
   images for the same structure.


   sdcluster now can accept TDT input, controlled by
   the -INPUT_FORMAT option.  It outputs an additional
   statistic for each cluster: average coverage for each

Oracle Cartridge

   Daycart is supported on 9.0x (9i), 9.2x (9iR2),
   10.1 (10g), and 10.2 (10gR2) under release 4.94.

   Daycart includes new scaffold-based structure 
   characterization as part of it's screening algorithms.
   This results in improvements in performance of contains()
   and matches() searches of 2-10x for many queries.

   Daycart users have better control of session-level log
   data which can aid debugging.

========================== 4. UPGRADING ===========================

The 4.94 release is a full distribution.  It does not 
depend on having a 4.91 release already installed and
can be installed in parallel with any previous releases.

The thor database format is identical between 4.7x, 4.8x
and 4.9x.  No Thor database upgrade is require.  One can
simply start using 4.9x thorserver, merlinserver and
applications against 4.7 and 4.8 database files.

An upgrade of Daycart from any previous version
requires a full reinstallation.  This entails dropping
all Daycart indexes, dropping the old Daycart packages,
installing the 4.94 Daycart packages, and recreating all
Daycart indexes.  The documentation in
dayhtml/doc/sql/index.html describes this process in detail.

========================== 5. BUGS FIXED ==========================

>  Additional default values for conversion for: Si (2, -1),
    P (3, -1), Br (3, 0), Hg (0, 1).  Also added Li, Be, Na, Mg, Al, K
    Ti, Ca as (0, 0)  (#975, #976).

>  Merlinserver couldn't read in a hitlist of reaction SMILES
    correctly; the quoting was not handled (#997).

>  Scaffold & sdcluster webservice gave garbled error messages
    for invalid SMILES input (#998).

>  Certain large structures caused sdcluster to hang and/or
    crash (#1000, 1001).

>  Sdcluster and dt_commonsubstruct() failed with structures
    where a single atom is in more than seven rings (#1003, #1007).

>  If sdcluster input includes names (eg. smi name), the names
    are preserved in the output as PCN<> datatypes (#1004).
>  Output SMA<> dataitems for sdcluster are now quoted for
    loading into thor (#1005).

>  Scaffold web service gave error instead of a normal message
    when no scaffold is possible for an input set (#1013).

>  Java wrappers now include support for streams in
    get/setChiralValue methods (#1014).

>  In Daycart, the mol2smi conversion for a molfile with a
    missing ptable entry caused an ORA-03113 error (#1015).

>  In java wrapper, H atoms didn't have bondstyles when
    attached to a chiral center (#1017).

>  In Daycart, a multithreaded contains() and matches()
    search with the "nearest" parameter can crash and/or give bogus
    results (#1018).

>  In Daycart, multithreaded searches did not reclaim
    child threads on certain OS versions (Solaris 9 & 10, Linux).
    Also, threads were not reclaimed when searches were interrupted
    by the client (#1019).

>  In sdcluster, if a cluster has only one atom common between
    the members, the algorithm would return an empty SMARTS (#1021).

>  Certain very small images with aromatic rings would cause
    smi2gif to go into an infinite loop (#1023).