Daylight Software Version 4.83 Release Notes

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




This document describes changes and features specific to
version 4.83 of Daylight Chemical Information Systems
software.  See also the machine-specific readme files,
which have more information on machine-specific issues
and limitations.

Version 4.83 is a cumulative patch, so it includes all of
the changes which were introduced in the 4.82 patch.  The
4.82 changes include bug fixes, new Daycart features, new 
HTTP toolkit-based SMI2GIF and DEPICT utilities, and the 
new property package.

New features specific to Version 4.83 include bug fixes, 
new DayPerl, new Daycart Optimizer code, additional 
Depiction control over layout, and a first public Windows
toolkit/Daycart release (beta).

The "upgrade" software distribution contains an install script
and another tar file.  The installation script, named 
install.daylight.v483, is used to perform the upgrade from 
either version 4.81 or 4.82 to 4.83.  The "full" software
distribution does not contain an install script and is fully
functional.  The full release contains 4.81 with the 4.83 patch
applied to it.

To upgrade, execute 'install.daylight.v483' to interactively
apply the patch to your software.  With this release, the default
behavior of the installer has changed to create a new installation
without affecting the current one.  Now, the installer copies the
the current Daylight installation subdirectory (i.e., v481 or
v482 to v483), then installs the patch onto it.  In this way, the
patch release is completely separate from the current installation.
The old behavior symbolically linked minor releases and can be
invoked with the "-l" option.  For options, give the  command
'install.daylight.v483 -help'.

========================== 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 =====================

==CHANGES for 4.83==

New DayPerl

   A completely new build procedure for DayPerl eliminates
   many of the version related problems with the previous 
   build.  The new build files are 
   in $DY_ROOT/contrib/src/perl/DAYPERL_BUILD/

New Daycart Optimizer Code

   A new, experimental optimizer package is included with 
   Daycart in this version.  It is specific to Oracle 9i
   and 9iR2 and gives the user the ability to query and
   scale the statistics provided to Oracle.  See the file
   $DY_ROOT/dcischem/README.optimizer9 for details.

Depiction Options

   Depiction objects now pay attention to three new named
   properties: "old_style", "hide_chi_h", and "hlen_pct".
   These are documented in $DY_ROOT/man/man3ob/depiction.3ob.
   Also, programs obey the options: DEPICT_OLD_STYLE,
   DEPICT_HIDE_CHI_H, and DEPICT_HLEN_PCT, which control
   these three style options globally in each program.
Windows Toolkits and Daycart

   The Toolkits and Daycart are available under Windows
   in native form.  This is a public beta release.  See
   the Windows-specific README for details on the state of
   the release and any limitations.

==CHANGES for 4.82==

New SMI2GIF & DEPICT Web Interfaces
   The release includes new HTTP toolkit-based version of the
   SMi2GIF and DEPICT utilities.  They are located in the
   $DY_ROOT/dayhttp directory.  Instructions on use of the
   utility can be found at $DY_ROOT/dayhtml/doc/dayhttp/index.html.
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.
   For more information, see the manual pages on dt_setcoord,
   dt_calcxy, xvthor, and xvmerlin.

Oracle Cartridge

   There are several new functions in Daycart.  The function
   ddpackage.fsetinfo() is a new generic utility for setting
   session-level properties of Daycart.  Two functions for
   structure normalization (vcs_desalt() and vcs_normalize()) 
   can be used to support registration functions.  These two
   functions operate based on tables of user-defined rules so
   they are customizable based on each sites business rules.

Property Package

   A new tool 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.

CLOGP/CMR Programs

   The ClogP and CMR programs have a new option "PCMODELS_ERRORWORST"
   which can be set to suppress output above a user-defined 
   error threshold.  High-error computations can easily be

========================== 4. BUGS FIXED ==========================

== BUGS fixed in 4.83 ==

>  Tetrahedral chiral centers with double bonds (eg. [P])
    were not depicted correctly; the double bond was drawn as
    single. (#368)

>  EZ depictions were often layed out poorly.  The tee
    indicators are always correct, now the actual layout actually
    matches the tee indicators. (#471, #731, #813, #814)

>  MCL no longer printed the hitlist position or length. (#623)

>  Print hitlist from xvmerlin (using tablet) would not
    depict structures unless the columns were named SMILES, Isomer,
    or IsomSMILES.  Now obeys the option -PRINT_DEPICT which lists
    the structural column names. (#792)

>  HTTP toolkit logged unnecessary info in CGI mode. (#793)

>  Internal buffer overflow for environment variables
    caused crash. (#794)

>  HTTP toolkit responses were incorrectly labeled 
    as HTTP/1.1 for HTTP/1.1 requests; all responses are 
    HTTP/1.0. (#795)

>  Thor graph normalization incorrectly rejects 
    structures with isolated hydrogens. (#796)

>  Previously, when creating thor databases, the 
    hashtable cache value was set to "ALWAYS" by default; it
    was possible to create a database that could not be
    opened (if the cached hashtable was larger than the
    memory available).  The new default is "ON REQUEST". To
    get the old behavior, use "-CACHE_WHEN ALWAYS" with
    thormake. (#797)

>  Recursive SMIRKS with dot-separated recursive
    expressions were incorrectly parsed. (#798)

>  Resizing a ring to a larger size in the toolkit, 
    by deleteing a ring bond and creating a new ring-closure
    bond to form a new ring, didn't clear internal state
    properly; the canonical SMILES was sometimes wrong. (#800)

>  The vcs_normalize() function in Daycart always
    returned the isomeric SMILES; it ignored the 'iso'
    parameter. (#801)

>  The invalid reaction SMILES '[>' caused a
    crash. (#802)

>  When the error queue overflowed a small memory
    leak was caused. (#806)

>  The file widget dropped entries if the directory
    contained more than 1000 entries. (#811)

>  The HTTP toolkit used to depend on the Math
    libary.  This dependancy has been removed. (#820)

>  The IP address provided by testlicense under
    Linux was bogus. (#822)

>  HTTP CGI-based file upload failed. (#825)

>  The TDT widget caused the error:
    "Expecting atomic symbol (dy_parse_smiles)" when depicting
    structures with 2D data. (#826)

>  Testlicense didn't parse additional options
    correctly.  (#827)

>  __ctype_b, __ctype_tolower, __ctype_toupper are
    unresolved symbols on RH9, RHES3.  These were eliminated
    from GLIBC in favor of localization-aware versions. (#828)

>  In thorload, the error queue wasn't cleared until
    messages are printed; irrelevant messages would accumulate
    and eventually get dumped out. (#829)

== BUGS fixed in 4.82 ==

>   Problem with [HH] as a valid SMILES.  Previously, both
    [HH] and [H][H] were valid input and didn't canonicalize to the
    same structure. (#638)

>   Documentation for dt_alloc_program() clarfied regarding
    the required welcome message.  Also now handles bad program objects
    more gracefully if they don't start. (#707)

>   Partially-set coordinates on chiral depictions caused
    core dump.  (#713)

>   Certain rare depictions caused core dumps. (#750)

>   Oscillating smiles with Fischer chirality. (#760)

>   xvmerlin dblist had an arbitrary limit of 100 opened
    pools.  Previously valid pools would disappear from the xvmerlin
    pool menu. (#773)

>   64-bit toolkits crashed on certain ring structures.  This
    was due an internal memory alignment problem. (#775)

>   dt_smarts_opt() didn't work.  It always returned the input
    string. (#776)

>   In rubicon, stereo structures always returned the same
    coordinates.  The rubicon rule file shipped with 4.81 was incorrect.

>   For transforms which added atoms with explicit hydrogens,
    the dt_transform() function lost track of those explicit hydrogens. 
    Chirality on the atom was also lost. (#779)

>   In Daycart, the matches() query missed hits for certain
    classes of queries with multiple aromatic rings. (#780)

>   The toolkits limit of 64K atoms and bonds has been
    removed. (#781)

>   Network license data transfers (using DY_DALI_SERVER or
    DY_DALI_AUTHORITY) over 13Kbytes caused a crash. (#782)

>   SMILES query processing in merlinserver and Daycart for
    queries with [2H] or [3H] caused these searches to fail. (#783)

>   Disconnected atoms, when depicted in terse mode (with 
    suppress or schematic true) were invisible.  All disconnected atoms
    are drawn verbosely, regardless of mode. (#785)

>   The error messages dumped from clogptalk were incorrect if
    requested before any computations were done.  This was an initialization
    problem. (#786)

>   SMARTS processing of directional ring-closures (eg. ...C/1...)
    were sometimes incorrect. (#787)

>   dt_setbondstyles() after dt_calcxy() caused crash for structures
    with implicit hydrogens. (#788)

========================== 5. KNOWN LIMITATIONS ===================

>   Cost-based optimizer statistics for Daycart do not work for CLOB
    searches.  Also, there seem to be discrepancies in execution plans which
    are chosen depending on the Oracle version (8i vs 9i).  If you choose to
    use the optimizer statistics provided with this release, please make 
    sure to check the behavior and statistics on your application carefully.

    The new, experimental optimizer package included with 4.83 attempts
    to address the issues with the quality of optimizer statistics returned
    to Oracle.  See the info in $DY_ROOT/dcischem/README.optimizer9 for
    more details.