I am using BIOVIA Direct and want to retrieve molfiles of my chemical structures stored as binary CTABs
Can I calculate and store them in my database?

You could add a ‘molfiles’ or similar column, using the CLOB data type. You could then use the BIOVIA Direct molfile operator to populate that column with the molfiles of that structure column. 

The example below uses the sample2d table from the BIOVIA Direct ‘demonstration’ database:

SQL> alter table sample2d add my_molfiles clob;
SQL> update sample2d set my_molfiles=molfile(ctab);
SQL> commit;

where:
‘my_molfiles’ is the molfiles column you added to the table.
 ‘ctab’ is the BLOB column containing the binary chemical structures.

Note: Current BIOVIA products support reading and writing of both V2000 and V3000 formats, and will default to writing V2000 versions of molfiles when possible. Structures containing enhanced stereochemistry, structure highlighting, or certain other features require the V3000 format.

SQL> select cdbregno, molname, molformula 
          from sample2d 
          where my_molfiles like '%V3000%';

  CDBREGNO  MOLNAME                    MOLFORMULA
  -----------------  ------------------------------   ---------------------
                367                                          C5 H10 O5
                366                                          C27 H32 N2 O5
                287  Zirconocene dichloride    2 C5 H5 . Cl2 Zr
                329  Titanocene dichloride      2 C5 H5 . Cl2 Ti

SQL> set long 10000
SQL> select my_molfiles from sample2d where cdbregno = 367;

MOLFILES
---------------------------------------

  SciTegic09042116412D

  0  0  0  0  0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 10 9 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -4.7032 0.1897 0 0
M  V30 2 C -4.2259 0.8384 0 0 CFG=2
. . .
. . . .

For more information about the BIOVIA Direct demonstration database, see “Chapter 6, Setting Up the Direct Demonstration Database” in the BIOVIA Direct Installation Guide for your version of BIOVIA Direct.

For more information about BIOVIA Direct operators, refer to the following documents:
BIOVIA Direct Reference Guide
BIOVIA Direct Developers Guide

For more information about V2000 and V3000 formats, refer to the BIOVIA CTFILE Formats document. 
All of the above documents are available from the Dassault Systèmes Software Download site, in the BIOVIA Direct ‘Documentation’ zip file.