Daylight Software Version 4.92 Release Notes
============================ CONTENTS ============================
1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.92
3. DETAILS OF CHANGES MADE IN RELEASE 4.92
5. BUGS FIXED FOR VERSION 4.92
========= 1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.92 =========
DAYLIGHT CIS SOFTWARE, VERSION 4.92
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
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 949-831-9990.
====================== 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.
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
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
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.
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
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:
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
For example, the function:
will return the highest of the two pairwise values:
max(tanimoto(smi, 'CCC'), tanimoto(smi, 'CCN'))
will return the highest of the four pairwise possible
max( tanimoto('CCC', '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 firstname.lastname@example.org 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).
> dt_f_datatype.inc had incorrect, leftover definitions
relating to the monomer toolkit (#879).
> dt_addh() and dt_suppressh() have incorrect return
> dt_addh() resulted in strange SMILES output for certain
> 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
> 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
> 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).