Daylight Software Version 4.92 Release Notes

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




   This document describes changes and features specific to
   version 4.92 of Daylight Chemical Information Systems
   software.  If there is a machine-specific file for your
   machine in this directory (e.g. "readme-v492-sgi"),
   please read it too.

   Version 4.92 includes new Daycart features, new conversion
   tools, toolkit fixes and enhancements.

   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, Mac, Windows

   Version 4.92 is supported on: SPARC Solaris 7 and
   higher (32- and 64-bit), SGI MIPS/IRIX 6.5 and higher
   (32- and 64-bit), x86 Linux RHEL2.1, RHEL3, and RHEL4.
   AMD64 Linux RHEL3, Mac OSX 10.3, x86 Windows
   2000 Professional and higher.  See the Operating System
   specific readme for more details.

   Release 4.92 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.

Conversion Tools

   Molecule conversions using mol2smi and smi2mol and
   DayCart dayconvert have been improved with regard to
   stereochemistry detection and completeness of data

   Reaction conversions are now possible using rd2smi and
   smi2rd and using additional features in dayconvert
   within DayCart.

   Query conversions from MDL to Daylight format are
   now available using sd2smarts, rd2smarts and additional
   features in dayconvert within DayCart.  Multiple
   queries can be converted from SDfile and RDfile formats.

   Molecule conversions now use a periodic table that 
   users can modify to control conversions.  The conversions 
   from MDL format now retain all depiction information 
   if the appropriate output format is selected.  
   Conversions using mol2smi, rd2smi, sd2smarts and
   rd2smarts all can create files suitable for direct 
   loading into Oracle tables, making the creation of 
   databases with user-defined schema much easier.  
   Options to control business rules have been added to 
   MDL->Daylight conversions.  Users may specify any data 
   type as the idenitier for database  conversions.  Using 
   new options, users can split the conversion process across 
   multiple CPUs.

   Conversions from MDL to Daylight format can process
   V2000 formated CTABs in molfile, SDfile, rxnfile, 
   and RDfile formats.  R-group and S-group information
   is not converted.

Oracle Cartridge

   Daycart is supported on 9.0x (9i), 9.2x (9iR2),
   10.1 (10g), and 10.2 (10gR2) under release 4.92.

   The function matches() has been overloaded with a 
   third "count" argument (analoguous to contains()) to
   return the best matches for a SMARTS query.  The best
   hits are those with the lowest number of bits set in
   the target.

   A time-based interrupt and abort mechanism for ddblob-
   based queries has been added.  There are three new
   session-level parameters which can be used to control
   the behavior of long-running ddblob queries.

     timeout_abort - this settable parameter is the total
       number of seconds to spend on a ddblob query.  When
       this time expires, the query will abort and return
       answers found to that point.

     timeout_progress - this read-only parameter is the
       number of rows examined during a query.  It is only
       set after a search is aborted via the timeout_abort.
       From this value one can project the expected number
       of answers for a full search.

     timeout_interrupt - this is the number of seconds 
       to spend on a ddblob query before returning partial
       results.  Daycart returns results to Oracle in 
       chunks.  If this timeout is used, Daycart will
       return smaller chunks of results more frequently.
       This can make an interactive application appear more
       responsive as the client can display partial results
       rapidly.  Also, because Oracle doesn't provide a
       separate out-of-band interrupt mechanism for cartridges,
       the round-trip communication is the only time when
       searches can be cancelled.

   A new function matchcover() returns the fractional percentage
   of atoms in a SMILES which are hit by a given SMARTS query.
   Useful as an alternate measurement of the nearness of a
   SMARTS query to a target.

   The conversion functionality within Daycart has been
   expanded with query conversion, and the ability to
   specify an alternate PTable file.

   Additional experimental functionality has been added.
   This may be promoted to fully-supported functionality
   in a later release.  For now it's considered beta or

   Best-similarity functionality has been added to the
   Daycart similarity functions.  For the functions:

    - euclid()
    - fingertest()
    - similarity()
    - tanimoto()
    - tversky()

   if either argument is a comma-separated list of SMILES
   or fingerprints, the functions now compute the best pairwise
   similarity of all combinations of arguments.  The 
   computation works in both the functional and index forms
   of queries.

   For example, the function:

     tanimoto(smi, 'CCC,CCN')

   will return the highest of the two pairwise values:

     max(tanimoto(smi, 'CCC'), tanimoto(smi, 'CCN'))


     tanimoto('CCC,CCN', 'CCc1ccccc1,NCc1ccccc1')

   will return the highest of the four pairwise possible

     max( tanimoto('CCC', 'CCc1ccccc1'),
          tanimoto('CCC', 'NCc1ccccc1'),
          tanimoto('CCN', 'CCc1ccccc1'),
          tanimoto('CCN', 'NCc1ccccc1')  )


   The Daylight system now can make use of FLEXnet floating
   licenses. FLEXnet license servers are supported on Solaris 
   and Linux. Cients (i.e. floating Daylight products ) are 
   supported on Windows, Solaris and Linux.  All Daylight toolkits,
   programs, and servers can be licensed using floating
   licenses.  Contact Daylight at for more
   information on availability and pricing of floating licenses.

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

The 4.92 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.

Daycart 4.92 requires a full reinstallation from 
4.7x, 4.8x, and 4.91.  This entails dropping all Daycart
indexes, dropping the old Daycart packages, installing the
4.92 Daycart packages, and recreating all Daycart indexes.
The documentation in dayhtml/doc/sql/index.html describes
this process in detail.

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

>   Treetops crashed and/or gave poor error message when 
    given incorrect input (#415).

>   MCL crashed when an unknown datatype was referenced (#808).

> had incorrect, leftover definitions
    relating to the monomer toolkit (#879).

>   dt_addh() and dt_suppressh() have incorrect return
    values (#886).

>   dt_addh() resulted in strange SMILES output for certain
    molecules (#887).

>   The function dt_fp_similarity() wrote to stderr (#888).

>   mol2smi could not perceive double bond stereo for colinear
    bonds.  It ignored them without warning.  Now it uses a better algorithm
    to detect the DB stereo and warns when it can't figure it out (#889).

>   in mol2smi, the option -smi_is_ism true now applies to
    regular smiles output in addition to TDT and SQLLDR output (#890).

>   Strange depictions of a benzene TDT in smi2gif (#892).

>   Added dimensional code to smi2mol output for programs which
    expect it, even though it's optional in the format (#893).

>   smi2gif on SGI crashed with 11-character names (#895).

>   clogp crashed for particular SMILES on SGI (#897).

>   N-tuple data in Thor gets mangled if the input has empty
    values (#898).

>   dayprop dropped input datatypes from TDT output (#899).

>   the dt_merlin.h file had references to float instead of
    dt_Real.  Caused problems on Windows (#900).

>   the webdayprop output for minhtml=true was changed from
    a table to a list of NAME=VALUE lines.  This is much more easily
    parsed (#901).

>   dt_smirkin() crashed on certain smirks; an overflow in
    the warning message output caused the problem (#910).

>   Thordump -help true option has incorrect value for default
    for TDT_OUTPUT_FORMAT (#918).

>   Thorlist -help gave incorrect option name for

>   Nearneighbors crashed on certain datafiles (#926).

>   Dayhttp smi2gif didn't handle ALAB data properly (#933).

>   For the ALAB output of smi2gif, the highest color value
    is now either black or white (opposite of the background) (#936).

>   Merlinserver crashed when dt_mer_combinehitlists() is
    called with hitlists from two different pools (#935).

>   ddblob index creation in Daycart corrupted for tables
    containing mostly duplicate structures (#939).

>   smi2jme required the smiles toolkit license.  It should
    be licensed with the daycgi program license (#940).

>   merlinls and thorls commands gave misleading return codes (#941).
>   Substruct objects in the toolkit returned their type
    as TYP_PATH (#942).

>   kmodes clustering has incorrect obitset for the output
    modal fingerprints (FPP<> datatypes).  These are rejected by other
    programs which use fingerprints (#943).

>   Fingerprint toolkit can't fingerprint an atom or bond
    object; must be part of a substruct or path containing one member (#944).