Daylight Software Version 4.91 Release Notes
============================ CONTENTS ============================
1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.91
3. DETAILS OF CHANGES MADE IN RELEASE 4.91
5. BUGS FIXED FOR VERSION 4.91
6. KNOWN LIMITATIONS IN VERSION 4.91
========= 1. INTRODUCTION AND HIGHLIGHTS OF RELEASE 4.91 =========
DAYLIGHT CIS SOFTWARE, VERSION 4.91
This document describes changes and features specific to
version 4.91 of Daylight Chemical Information Systems
software. If there is a machine-specific file for your
machine in this directory (e.g. "readme-v491-sgi"),
please read it too.
Version 4.91 includes new Daycart features, new conversion
tools, and clustering programs, toolkit fixes and
Installation and configuration instructions can be found
in the file dayhtml/doc/admin/install.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 949-367-9990.
====================== 3. DETAILS OF CHANGES =====================
Supported Platforms: Solaris, IRIX, Linux, Mac, Windows
Version 4.91 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.
The following platform support changes occur with this
- Adding support for Solaris 10,
- Adding support for RHEL4,
- Adding support for 64-bit Opteron (AMD64),
- Dropping support for IRIX 6.4,
- Dropping support for Red Hat Linux v 7 -> 9.
Product Support Discontinued
The monomer toolkit and database functionality have
been removed. It is no longer supported. The following
monomer-specific functions have been removed from the
toolkit: dt_define(), dt_monomertable(3),
In addition, Thor and Merlin no longer support databases
with monomer specifications.
The remote toolkit has been removed. It is no longer
JavaGrins is no longer supported. Within the Daycgi
and Dayhttp applications a new mechanism has been
implemented in place of JavaGrins for calling out to a
structure editor. This is now a user-configurable
option. JME, Marvin, Chemdraw plugin, and the Daylight
GIF-based Grins editor have all been integrated into
the daycgi and dayhttp applications. Example configuration
files may be found in: $DY_ROOT/dayhtml/edit/. The
relevant configuration options are defined in
- dt_molgraph(3) - returns a hydrogen-, charge-, and
valence-suppressed graph for a molecule object. Useful
for generating canonical graph smiles.
- dt_fp_similarity(3) - computes generic similarity values
between two fingerprints, given a user-provided similarity
- dt_smilin_addh(3) - A new version of dt_smilin() which
does not automatically suppress hydrogens in the input
SMILES and also adds, as explicit atoms, stereosignificant
hydrogens (those attached to chiral centers). This is
useful for full control of depiction attributes in
conjunction with the new dt_setbondstyle(3),
dt_setvisible(3), and dt_visible(3) functions.
- dt_addh(3) - Modifies a molecule or reaction by converting
implicit hydrogens into explicit hydrogen atoms. The
molecule or reaction must be in mod-on state.
- dt_suppressh(3) - Modifies a molecule or reaction to
suppress any unnecessary explicit hydrogens, by making
them implicit hydrogen attachments. The molecule or
reaction must be in mod-on state.
- dt_ischiral(3) - Utility function which returns whether or
not an atom in a molecule or reaction is chiral.
- dt_setbondstyle(3) - Function which allows the user to
set the bond style on a visible bond in a depiction.
- dt_visible(3), dt_setvisible(3) - Controls the
depiction atom property whether or not the given atom
is rendered to the display device during a depiction.
Typically used for controlling hydrogens.
- dt_errors(3), dt_smilinerrors(3) - The SMILES parsing
error queue and regular error queue have been merged.
All errors, warnings and notes from the toolkit go into
a single errorqueue. dt_smilinerrors() now is equivalent
Also, the format of SMILES-parsing errors has been improved
in the error queue. The errors are much more informative
for tracking down incorrect SMILES.
- dt_mer_similarselect(3) - Merlinserver now has the ability
to perform a similarity search based on an input fingerprint
A new, supported set of tools for structure conversions
are provided. The conversions are integrated into Daycart.
New command-line utilities, mol2smi and smi2mol are
provided for converting data between formats.
Additional conversion features will be added in the
Daycart is supported on 9.0x (9i), 9.2x (9iR2), and
10.x (10g) under release 4.91.
Daycart now supports any database characterset (single-
or multi-byte) which is a superset of ASCII. This
includes the various Unicode versions, common European
and Asian charactersets. See Oracle documentation
(Oracle 9i Database Globalization Support Guide,
Part Number A96529-01, Appendix A) for the complete
Daycart now can be used to index and search range-
The new function ddpackage.fdayconvert() and operator
dayconvert() provides conversion capabilities;
the user has access to all the built-in conversions
The new function ddpackage.fsimilarity() and SQL
operator similarity() allows the user to perform
index-based similarity searches given a user-defined
similarity expression. The function supports a number
of named expressions (e.g. DICE, COSINE) and the ability
to define the expression in terms of bits on/off in
common and bits on exclusively in either input item.
The new functions ddpackage.fgen_molecules(),
ddpackage.fgen_reactions() and operators gen_molecules(),
and gen_reactions() perform reaction transforms within
Daycart. Given a reaction SMIRKS and set of reagents
the user can enumerate molecules or reactions.
A new optimizer package, which allows the user to scale
the statistics provided to the cost-based optimizer, is
The new function ddpackage.fsmi2pmw() and operator
smi2pmw() computes the high-precision molecular mass
based on the 2001 IUPAC masses.
The new function ddpackage.fgeterrors() allows the
user to retrieve informational notes, warnings, and
errors from the toolkit.
The new tautomer enumeration capability (see below) is
also available within Daycart via program objects.
Two new clustering/classification methods are provided
in the Clustering Package. Spherex is a simple
sphere-exclusion algorithm for selection of subsets of
data files. Kmodes is a variation of the common K-Means
clustering algorithm which has been adapted to work well
with categorical data (e.g. fingerprints).
Nearneighbors, part of the Jarvis-Patrick clustering
tools, now handles ties in similarity values by generating
variable-length neighbors lists. Jarpat and Jpscan both
take variable-length neighbors lists as input and allow
the user to decide how ties are handled during the clustering
All of the clustering tools can optionally take a user-
defined similarity measure as part of their input options.
This measure will override the default Tanimoto similarity
There is a new program for generating custom fingerprints
called filter_fingertalk. It generates key-like fingerprints
where each bit position is set based on whether or not the
given SMARTS patterns (provided as a separate input file)
match the molecule.
The new program, Tautomer, and program object, Tautomertalk
perform enumeration of tautomers of input molecules. One
can perform an exhaustive enumeration of tautomers or get
the canonical tautomer. The canonical tautomer is useful
for indexing or cross-referencing tautomers within a
collection; it is not necessarily the low-energy tautomer.
There is a new Web application application for generation
properties. It has a simple checkbox interface for
interactive use and also has a minimal mode suitable for
a web service. Both modes can take multiple input SMILES
and will return a table of results.
The $DY_ROOT/contrib directory has been reorganized. Now,
code within the $DY_ROOT/contrib directory within each
release will be supported code. Some of the
older applications have been removed from the release.
Unsupported contributed code, including code which was
removed from $DY_ROOT/contrib, will be available on the
website at: http://www.daylight.com/support/contrib/.
The Perl and Java wrappers are now available on the
website as supported code.
Thor/Merlin Large Files
Thor and Merlin now support large files (16GB data
files) on all platforms. The database format in
4.9 has not changed.
- Aesthetics improvements introduced in v4.83 are the
default settings for SMILES. In other words, the
default value of the old_style option is now FALSE.
- EZ direction bonds are no longer drawn on top of
RS chiral (up, down) bonds.
- Truncation of coordinates (formerly to two decimal
places) no longer occurs in dt_calcxy(3) for atom
coordinates specified with dt_setcoord(3).
- The hydrogen atomic symbol now appears in schematic
smi2gif supports several new options which control
layout and display of structures and reactions.
- TDT input has been extended to include datatypes
for bond styles (BST) and atom visibility (VIS).
In conjunction with the 2D coordinates datatype (2D)
the new dt_smilin_addh(3) entry point and output
from the conversion toolkit, it is easy to
completely control a depiction.
- The new schematic option controls the dt_schematic()
property and allows the generation of minimal
- The new scale option allows the user to specify
a scaling factor (pixels/Angstrom), which is used
to set the size of the gif image generated. When
provided, the scaling factor overrides the height
and width values.
- SMI2GIF now correctly parses SMARTS and SMIRKS
strings which contain zero-level parentheses. The
display does not indicate grouping of components
- The default value of the old_style aesthetic option
agrees with the depict toolkit, which is FALSE.
========================== 4. UPGRADING ===========================
The thor database format is identical between 4.7x, 4.8x
and 4.91. No Thor database upgrade is require. One can
simply start using 4.91 thorserver, merlinserver and
applications against ones 4.7 and 4.8 database files.
Daycart requires a full upgrade from 4.7x and 4.8x
to 4.91. This entails dropping all Daycart indexes,
dropping the Daycart 4.8 packages, installing the 4.91
Daycart packages, and recreating all Daycart indexes.
The documentation in dayhtml/doc/sql/index.html describes
this process in detail.
========================== 5. BUGS FIXED ==========================
> The Wizard ignore case string search was
> Merlinserver - request to support FP string
as input to similarity search. (#671).
> thorserver crashed if the user started thorserver
with -DATABASE_PASSWORDS_FILE "" (#772).
> Attempting to perform dt_delete() on an empty
sequence caused a crash. (#834).
> Positioning of sequences at the end wasn't
consistent with docs. (#835).
> canstream/reaction iso/uniq problem. dt_canstream()
incorrectly returned agent atoms as part of a
canstream with iso=FALSE. (#836).
> Depict toolkit core dumped on dt_alloc_conformation()
when passed a bogus handle. (#837).
> A conformation object, when deallocated, was not
completely cleaned up. An attempt to access the
previously deallocated and invalid object caused
a crash. (#838).
> In HTTP toolkit, multi-line POST data was
incorrectly truncated at the first line break. (#841).
> Core dump on certain invalid SMIRKS. The function
dt_smirkin() crashed on certain input strings with
illegal empty atom specifications, eg. [:1]. (#846).
> Directional bonds exo to an aromatic ring
lost their directionality. The simplest prototype
example is: C=c1cccc/c1=C\C. On canonicalization
the SMILES didn't have the directional bond in
the ring; on reinput the toolkit warned about
incomplete specification. (#847).
> Prado wouldn't print a title if it started with
77 or 78. Some obsolete internal debugging code
was clashing. (#851).
> clogp - error level 44 was not included in the
dump_errors output. (#852).
> In the http toolkit, long URLs (> 1Kbyte) caused
a timeout. (#853).
> In the http toolkit, a request length of 1Kbyte
plus 1 character caused a timeout. (#854).
> In smi2gif, zero-level parentheses were not being
handled in SMARTS/SMIRKS mode. (#855).
> The xsmiles mode for a depiction had no effect
on reactions. (#857).
> dt_canstream(..., iso=FALSE) returned atoms in
the incorrect order if previously called with
iso=TRUE. It incorrectly cached the older
symmetry info. (#866).
> In daycart, a contains() index search on an
empty, but indexed table caused an error. (#867).
========================== 6. KNOWN LIMITATIONS ===================