T06-2021 Notification regarding BIOVIA Direct 2021

BIOVIA Direct

Operating System

Red Hat Enterprise Linux 8.1+

Red Hat Enterprise Linux 7.5+

Oracle Linux 8.1+

Oracle Linux 7.5+

Microsoft Windows Server 2019

Microsoft Windows Server 2016

Description

We are providing this Technical Note to inform you about the release of BIOVIA Direct 2021 Golden that includes the following enhancements and fixed defects.

Enhancements

This release of BIOVIA Direct includes the following enhancements.

DIR-4107 — Since Direct 9, a molecule or reaction containing a symmetrically tetra-substituted double bond, one that cannot be cis or trans, might not match itself with a FLEXMATCH search. The same symmetrically tetra-substituted structure with an "either" double bond might not match the structure with the normal double bond. This issue corrected in Direct 2021.
Newly inserted molecules or reactions will search correctly—structures in existing databases must be updated to correct the problem.

DIR-1218 — Direct FLEXMATCH queries which are meso (have stereocenters but no overall chirality) may now match more targets. Meso stereocenters have always been treated as wildcard stereochemistry. However stereo groups in the query were ignored. Stereo groups are now allowed to participate in the matching, disambiguating parity differences, which can allow more structures to be returned as hits.

DIR-3711 — Improved documentation for the CHIME operator. The Direct operator CHIME is a synonym for the operator MOLCHIME and is only meant to provide backward compatibility to older Direct versions. Because it is just a synonym it cannot be used within a PL/SQL procedure or function. This is now more clearly documented in the Direct Reference Guide.

DIR-3725 — BIOVIA Direct domain indexes are now tested and supported with Oracle Materialized Views created with the ' REFRESH ON COMMIT' and 'FAST' options.

DIR-3836 — Added a new indexed similarity search type, in addition to the standard similarity search that uses substructure keys. The new search type allows the user to create an index using either Accord or Scitegic fingerprints. The structure of the index is identical to that used for the standard substructure key similarity search, the difference being the length of the bit vector and the meaning of each bit.

DIR-3886 — MDLAUX.SMILESTOMOLFILE now converts an argument that is NULL or an empty string into a molecule with zero atoms and bonds (a "no-structure"). It is still an error to provide a NULL or empty string molecule argument to other operators such as MOLFMLA, SSS, or FLEXMATCH.

DIR-3969 — Direct now allows a molecule or reaction to be registered even if it has Sgroup data fields with empty (blank) field names. The data values are for such fields are ignored during substructure or exact match searching.

DIR-4019 — Direct can now compute and return InChI AuxInfo for molecules and reactions. Additionally, the function that converts a reaction InChI string to a reaction now accepts an optional argument containing the reaction AuxInfo to assist in the conversion.

DIR-4025 — Improved the documentation for the MDLAUX.PREPAREINDEXEXPORT function. The function creates a table that must explicitly be included in exported Oracle dump file as it is not a member of the secondary Oracle tables of the domain index. This is now described more clearly in the Direct Administration Guide.

DIR-4043 — Improved the BIOVIA Direct Reference Guide to describe how molecules and reactions used as query in the molsim, similar, rxnsim, and rxnmolsim operators must not include query features.

DIR-4044 — Added a new function and operator to return the HELM version 2 (HELM2) string for a biological sequence molecule. The primary difference between HELM and HELM2 in Direct is that annotations are stored at the end of the string in HELM and adjacent to the relevant monomer in HELM2.

DIR-4066 — Enhanced the Direct Administration Guide to document that a change in the perception of coordinate bonds and hydrogen bonds in the count of ring bonds requires the recreation of molecular keys when updating existing domain indexes to Direct version 2021.

Fixed Defects

This release of BIOVIA Direct includes the following fixed defects.

DIR-4006 — Fixed an issue where an SSS query that includes a 6-member ring, one C-C aromatic bond (fused benzene ring), one or more A query atoms, and five single bonds would miss hits with an aromatic bond.

DIR-4041 — Fixed an issue in Pipeline Pilot Chemistry where polymer type brackets were partially lost when the structure was converted to V3000 molfile format.

DIR-4076 — Added an additional restriction when the HYD flexmatch switch is present, to prevent erroneous matching of two unequal structures. This restriction was preventing some tautomers from matching one another when the both the TAU and HYD flags were present. This problem is fixed. The additional HYD restriction is only added with an exact match when the flexmatch switches include BON, CHA, and RAD.

DIR-4037 — Fixed a memory issue where the MDLAUX.SCANINDEX function with a 'CTAB' option was consuming ~600 bytes of memory for each row scanned.

DIR-4053 — Renamed and revised the appendix “Direct 8 to Direct 9 Chemistry Update” in the Direct Administration Guide to reflect recent releases. The appendix is renamed to “Direct 8 to Direct 2021 Chemistry Update”.

DIR-4064 — Direct 2020 added support for returning the InChI key of a molecule with zero atoms (a "no-structure"). The computed key was incorrect, it should not have included the InChI prefix. This problem has been fixed in Direct 2021—the string returned by INCHIKEY and MDLAUX.INCHIKEY for a molecule with zero atoms is now correct.

Resolution

BIOVIA Direct 2021 Golden was released in December 2020 and is available for download at https://software.3ds.com under BIOVIA products and can be found under

Product line: Lab, Scientific and Content Solutions

Release: 2021

Level: BIOVIA 2021 Golden

How to contact BIOVIA Support

If you have any questions, please contact BIOVIA Support.