T53-2017: The 'directupgrade tool skips reactions that contain R, Pol or H2 atoms.

Direct

The BIOVIA Direct versions 9.0 and later provide a 'directupgrade' tool which converts molecules and reactions from the Direct version 8.0 SP1 or earlier format into the respective format of Direct 9.0 or later. It turned out that the 'directupgrade' tool up to and including Direct version 2017 R2 skips reactions that include R or Pol pseudo atoms or molecular hydrogen (H2). The skipped reactions are written along with a record identifier to the directupgrade logfile or the errorlog table when specified. The conversion of molecules is not impacted by this defect.
Resolution:
This issue has been logged as a defect (issue numbers DIR-3652 and DIR-3686) and has been fixed in the soon to be released Direct 2018 version. BIOVIA therefore recommends to upgrade to Direct version 2018 before running the 'directupgrade' tool. If running Direct 2018 as the production Direct version is not feasible, BIOVIA recommends to use a parallel installation of the BIOVIA Direct version 2018 for the initial upgrade and then rewrite and re-index the converted structures using the target Direct version (for example Direct 2017 R2). The following workflow describes the details of the recommended procedure to convert a reaction table. Note that molecule tables are not impacted by the defect and must be converted using the original directupgrade tool of the target Direct version.

1. Install Direct 2018 in parallel to the target Direct version. Note: as of version 2017, Direct uses a separate Oracle Extproc Listener for each particular Direct version installed; a parallel installation of Direct 2018 therefore does not interfere with existing installations of BIOVIA Direct.
2. Run the Direct 2018 'directupgrade' tool to convert the Direct 8 or older database into the Direct 2018 format. This is basically the same procedure that you need to run when converting the database with the Direct 2017 R2 or older 'directupgrade' tool. For details on the directupgrade procedure please consult the chapters 'Upgrading Direct 6-8' and 'Direct 8 to Direct 9 Chemistry Update' in the BIOVIA Direct 2018 Administration Guide. BIOVIA recommends that you complete the corrections to the reactions that might be suggested by the directupgrade tool before proceeding to the next steps.
3. Drop the Direct 2018 domain index that was created during the directupgrade procedure. For details please consult the BIOVIA Direct 2018 Administration Guide.
4. Enable the Oracle schema for the target Direct version, for example Direct 2017 R2. For details please consult the BIOVIA Direct 2018 Administration Guide.
5. Repack the reactions in Direct 2018 format into the format of the target Direct version. The attached SQL script file creates two procedures that you can run to repack the reactions in your table and capture potential failures into a logtable. Open the SQL script file in a text editor and edit it as follows:

•      replace all (2) occurrences of AAAAA with the name of the table that holds the reactions to repack.
•      replace all (2) occurences of BBBBB with the name of the field that holds the reactions to repack
•      replace all (7) occurrences of CCCCC with the name of the primary key field (or unique identifier field) of the table that holds the reactions to repack.
•      locate the two occurrences of 'DDDDD' in the file, and replace them with the Oracle data type of the of the primary key field (or unique identifier field), for example 'VARCHAR2(12)'.

Error Mesage:
MDL-1921: Reaction failed registration check:

Error: (reactant-1) No query features allowed for registration

Error: (reactant-1) Unknown atom symbols: Pol

Error: (reaction) Unknown atom symbols: Pol

Unable to register new structure, updating record with NULL structure

MDL-5062: Error processing structure at
ROWID=AAAfaRAANAAAACDAAA