Daylight Software Version 4.95 Release Notes
============================ CONTENTS ============================
1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.95
3. DETAILS OF CHANGES MADE IN RELEASE 4.95
5. BUGS FIXED FOR VERSION 4.95
========= 1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.95 =========
DAYLIGHT CIS SOFTWARE, VERSION 4.95
This document describes changes and features specific to
version 4.95 of Daylight Chemical Information Systems
software. If there is a machine-specific file for your
machine in this directory (e.g. "readme-v495-sun"),
please read it too.
Version 4.95 includes bug fixes, performance and reliability
improvements for Daycart for Oracle, the addition of Daycart
for Postgresql and new versions of ClogP and CMR.
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, Linux, Windows
Version 4.95 is supported on: SPARC Solaris 10 and
higher (32- and 64-bit), X84_64 Solaris 10, x86 Linux RHEL5
and higher, and x86 Windows 2000 Professional and higher.
Release 4.95 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.
Daycart is supported on 10.1 (10g), 10.2 (10gR2),
11.1 (11g) and 11.2 (11gR2) under release 4.95.
Because of two Extproc bugs in Oracle 11.1
(Oracle Bugids: 7447098, 8507458) we strongly
recommend running the latest patch release of
11gR2 (188.8.131.52 or higher).
Daycart provides additional capabilities on ddblob
index creation for scaffold-based structure data
handling. One can now precompute and store the
scaffold data and use it in the ddblob index creation.
The dramatically improves index creation times.
Several minor bugs have been fixed.
Daycart functionality is now provided under Postgresql
8.4.x and 9.0.x. Daycart under Postgresql provides a
full functional interface and rapid row-at-a-time
searching. Custom structural indexes are not implemented
at this time.
ClogP and CMR
A new version of the ClogP algorithm is included.
This version of the algorithm is v5.4, with database
========================== 4. UPGRADING ===========================
The 4.95 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 4.95 Daycart packages, and recreating all
Daycart indexes. The documentation in
dayhtml/doc/sql/index.html describes this process in detail.
========================== 5. BUGS FIXED ==========================
> Changed dt_charge() to return symbolic DX_CHARGE_NONE
when an incorrect or invalid object is passed to it (#946).
> In mol2smi, change the DB_RING_CISTRANS option to
apply only to rings of 7 or larger atoms; smaller rings
don't need the orientation specified (#1016).
> Tablet generated erroneous postscript when the input
file wasn't properly terminated. Now handles that case more
> Toolkit licenses were incorrectly required in order
to use webservices (#1026).
> Webservices conversion which resulted in a null
structure caused a crash (#1027).
> smi2mol did not correctly handle structures where the
name contains a pipe (|) character (#1028).
> mol2smi would not handle records with 'M REG' data (#1029).
> Java wrappers missing DX_EDGE_IS_BOWTIE constant (#1030).
> SMARTS incorrectly handled unpaired ring closures
in recursive expressions (#1031).
> SMARTS incorrectly handled parse errors
in recursive expressions (#1032).
> Handling of S SKP lines in molfiles (#1042).
> smi2mol incorrectly handled ntuples of coordinate
data if the comment field contained info which looked like
additional coordinates (#1043).
> Updated MCL documentation to reflect the ability to
perform similarity searches using an ASCII fingerprint query
rather than SMILES (#1045).
> The option SKIP_RECORDS didn't work in rd2smi (#1046).
> Fix of SMARTS searching in Daycart for the [A]
> mol2smi incorrectly dropped deuterium isotope
from certain molecules on conversion (#1112).
> Memory overflow caused intermittent crash of role
search in Daycart (#1153).