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Plans / Futures / Projects

Jack Delany

Release Schedule:

The current release is 4.83. It is a patch release of 4.81, and includes bug fixes and new features. There is an additional Daycart download which adds support for 10g, and international charactersets (daycart483e1.tar.gz). We have no plans for further 4.8x patch releases, but would provide them if needed to support older customer platforms.

4.9 Platform Support:

• Dropping Irix 6.4, RedHat 7.1 - 9, Oracle 8i, 9.0.x.

• Solaris - 7, 8, 9, 10(?); both 32- and 64-bit
    Toolkits, Applications, Servers, Daycart.

• SGI - Irix 6.5; both 32- and 64-bit
    Toolkits, Applications, Servers.

• IA32 - RH ES2.1, ES3. Fedora(?)
    Toolkits, Applications, Servers, Daycart.

• AMD64 - RH ES3, Suse8,9.
    Toolkits, servers (hybrid release with 32-bit), Daycart.

• Windows - 2000 Professional, XP, 2003 Server
    Toolkits & Daycart

• Mac - 10.3 (32-bit)
    Toolkits, applications, servers (no X)

• Oracle - 9iR2, 10g

Platform Trends...

• IRIX Migrations:
  • ~50% to x86
  • ~25% to Sparc
  • ~25% to SGI/Altix (IA64)

• Itanium2: Perhaps 4.92...

• Solaris: Generally sticking with it, IA32 & AMD64 not much interest

• Linux: RHEL, SuSE, some interest in Fedora.

• Discontinuing support for some tools:
  • Remote toolkit
  • Monomer toolkit
  • Monomer database capabilities (Thor/Merlin)
  • Javagrins (DayCGI)

• Conversion toolkit

• New clustering methods
  • Spherex - Sphere exclusion
  • Kmodes - Kmodes
  • Near neighbors - tie handling
  • User-defined similarity expressions

• dt_fp_similarity(3) / expression(5)

• dt_molgraph(3)

• Depictions
  • Templates
  • Improvements to smi2gif

• Tautomer Enumeration

  Tautomer enumeration capabilities are added to the property package; wrapper for Daycart via program objects.

• Thor/Merlin:
  • Thor: Large files under Linux.
  • Merlinserver: generic fingerprint search using dt_mer_similarselect(3)

• Bug fix - Directional (EZ) aromatic bonds in SMILES. Example.

• Distribution of commercial databases in Oracle.
  • ACD
  • WDI
  • WOMBAT
  • Spresi
  • Demo dbs with Daycart, under mug/coffee user.
  • + Others...

• 10g.

  Supported across our platforms. We'll evaluate the "grid" functionality and see where we might take advantage of the new features in later releases.

• Internationalization

  Oracle supports numerous character sets and locales within the database. We now support any character sets within the database which are supersets of ASCII. This includes the common European character sets, the major Unicode versions, etc.

• Partitioned tables, indexes.

  With 9i, Oracle supports domain indexes on range partitioned tables. Partitioning is simply the use of multiple subtables to make up a single logical table. Range partitioning means that the subtables are divided by a series of range values within one of the columns in the table.

  Item	Time, np	Time, part
  Graph Index Create	162.0	159.0
  Search: graph(smi, 'c1ccccc1') = 1	0.21	0.06
  Graph insert 500 rows	1.10	1.05
  Graph delete 500 rows	0.99	0.64
  Blob Index Create	19.7	20.1
  Search: contains(smi, 'Nc1ccccc1O') = 1	1.17	1.19
  Blob insert 500 rows	52.4	19.2
  Blob delete 500 rows	315.2	50.3

  np - 126705 structures; single non-partitioned table
  part - 126705 structures; two partitions, 119K+7705

• Additional similarity searches.

  The new similarity() function and index-based search supports arbitrary similarity computations.

   ... tanimoto(smi, 'c1ccccc1') > 0.9
   ... similarity(smi, 'c1ccccc1', 'TANIMOTO') > 0.9
   ... similarity(smi, 'c1ccccc1', 'c/(a+b+c)') > 0.9
  

• Performing reactions in Daycart.

  Complex functionality: multiple inputs and outputs. Simple functional interface initially, but maybe not ideal. Oracle 9iR2 provides other paradigms (row source, aggregate functionality) that might be more powerful.

• Optimizer; better user-tuneable statistics

  Version 4.83 includes a new optimizer package (included in parallel with the default optimizer) which gives access to our generated statistics and the ability to scale the statistics. It becomes the default in 4.9.

• smi2pmw(), high-precision molecular weight, based on IUPAC2001 values.

• ddpackage spec unwrapped.

• abillity to get errors from dt_smilin()

• Memory use questions resolved

• Replacement database-specific applications (CARD-based)
• Daycart - Basic 3D data handling, searching.
• Daycart - Molecular formula index & searches.
• 64-bit Thor server/databases
• Multithreading - Toolkit
• Multithreaded merlinserver, applications

• Toolkit

  A restructuring of the object heirarchy of the toolkit will allow us to provide an underlying graph object.

• DB stereo:

  A unification of the EZ stereo representation with atom-based stereo is proposed. This will allow better specification of multiple conjugated EZ centers and also allows more robust specification of relative stereochemistry.

• Molecule-level Components:

  There will be another level of components within a molecule and reaction object which will allow easier handling of complex mixtures.

• Arbitrary labels

  A general mechanism for attaching data to the atoms/bonds of a molecule or reaction in the SMILES language is propsed. Although this is not necessarily a user-level feature, it will allow more efficient interchange of structures and data between applications.