Daylight Software Version 4.82 Release Notes
============================ CONTENTS ============================
1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.82
3. DETAILS OF CHANGES MADE IN RELEASE 4.82
4. BUGS FIXED FOR VERSION 4.82
5. KNOWN LIMITATIONS IN VERSION 4.82
========= 1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.82 =========
DAYLIGHT CIS SOFTWARE, VERSION 4.82
This document describes changes and features specific to
version 4.82 of Daylight Chemical Information Systems
software. Note that 4.82 does not include machine-specific
readme files. The information contained in the previous
machine-specific 4.81 readmes still applies.
Version 4.82 includes bug fixes, new Daycart features, new HTTP
toolkit-based SMI2GIF and DEPICT utilities, and the new property
The software distribution contains an install script and another tar file.
The installation script, named install.daylight.v482, is used to perform
the upgrade from version 4.81 to 4.82. Execute 'install.daylight.v482'
to interactively configure and upgrade your software. For options, give
the command 'install.daylight.v482 -help'.
========================== 2. LICENSING ==========================
Usage and Evaluation Licenses
The usage license for the Daylight software is accessible at
http://www.daylight.com/cgi-bin/download.cgi. This license
is also included with the software. For any further
clarification, contact our business office at 949-367-9990.
====================== 3. DETAILS OF CHANGES =====================
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.
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.
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.
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.
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 ==========================
> 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
> 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
> 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
> 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.
This is an issue which is being addressed with Oracle.