Thordbfix461

Introduction

Commercial databases distributed by Daylight and current during Daylight release 4.51 will be upgraded by Daylight and provided to licensees of Daylight 4.61. If you are unsure of the availability of databases please contact info@daylight.com.

User databases and versions no longer supported as per the above must be upgraded by the user (local Daylight administrator). This document provides a fairly detailed overview of this procedure.

Why

Daylight Software Version 4.61 contains bug fixes and enhancements that make it necessary to update pre-4.61 databases before they will work correctly with Version 4.61 software. These changes have to do with the fingerprint dataitems.

1. The ASCII representation of binary fingerprints has changed to allow n-tuples of binary data.
2. A bug in fingerprint generation for polycyclic structures where aromatic and non-aromatic rings occured (eg. Fluorene: c1cccc(C2)c1c3ccccc23) causes incorrect search results.
3. The representation for FPP<> data changes.

How

4.61 includes a script, $DY_ROOT/bin/thordbfix461, which upgrades older databases to 4.61 compatibility.

This program proceeds follows:

1. You specify:
   1. The database to be fixed.
   2. Write passwords for the database and the datatypes database.
2. The datatypes database is updated to represent the change in specification of the FPP<> datatype.
3. The regular database is rebuilt. The old primary datafile is thorlisted, refingerprinted, and reloaded.

This usually works silently, and requires minimial additional disk space during the processing. The database may grow slightly during the reload processs, but this growth is typically less than 5% of the original size.

WARNINGS

YOU SHOULD BACK UP ALL DATABASES BEFORE BEGINNING.

Although this update process is well tested, there is always the possibility of a power failure or other catastrophy that could result in loss of data.

If the disk becomes full during database reloading, you will need to discard the partially rebuilt database and begin again. If the old database was saved, move it back to the original directory. If it was not saved, you will need the backup copy to restore the original.

Running thordbfix461

To use this program, you must be the Thor database administrator. That is, you must be logged in as the user who owns Thor database files and has permission to write to those files.

In addition, you environment variables should be set up to be identical to those defined for the Thorserver and Merlinserver programs when they normally run. In particular, DY_ROOT must be defined, and any environment variables used when creating your databases (e.g. DY_THORDB) must be defined.

USAGE:

thordbfix461 [-d database] [-p write_pw] [t write_pw] [-q] [-r] [-s service]
         -d database ... database to be fixed
         -p write_pw ... write password on database
         -t write_pw ... write password on datatypes database
         -q          ... quiet: minimize questions
         -r          ... real-quiet: completely non-interactive
         -s service  ... Thor IPC service
   or: thordbfix461 -h ... print short help message and quit
   or: thordbfix461 -H ... print long help message and quit

Example

% thordbfix461

  +----------------------------------------------------------------------+
  | THORDBFIX461: CONVERSION OF 4.51 DATABASES TO 4.61 COMPATIBILITY     |
  +----------------------------------------------------------------------+
 
THORDBFIX461 ============================================================= WHY
 
Daylight Software Version 4.61 contains several bug fixes and enhancements
that make it necessary to update 4.51 databases before they will work with
Version 4.61 software:
 
  1. The external ASCII representation of binary data has changed.  This
     primarily impacts fingerprints, but also impacts any user-generated
     binary data.
 
  2. A significant bug in the SMILES toolkit causes the fingerprints to
     be incorrect for one class of molecules.  This problem causes the
     substructure searching to work incorrectly for this class.  Replacement
     of the fingerprint is the only solution for this problem.
 
Note: the database must already be updated to 4.5 before running this
script.  If a pre-4.51 database requires updating, the database must be
updated with thordbfix451 before running this script.
 
 
Press [Return] to continue... 
 
THORDBFIX461 ============================================================= HOW
 
This program proceeds as outlined below:
 
1. You specify:
     a.  The database to be fixed.
     b.  Write passwords for the database.
 
2. The regular database is dumped and reloaded with new correct fingerprint
   data.
 
3. A report is generated with statistics and messages about the process.
 
 
Press [Return] to continue... 
 
THORDBFIX461 ======================================================== WARNINGS
 
>>>  YOU SHOULD BACK UP ALL DATABASES BEFORE BEGINNING.  <<<
 
Although this update process is well tested, there is always the
possibility of a power failure or other catastrophy that could result
in loss of data.
 
If the disk becomes full during database reloading or if the update
process fails, you will need to discard the partially rebuilt 
database and begin again.  You will need the backup copy to restore 
the original.
 
 
Press [Return] to continue... 

 
THORDBFIX461 ==================================================== INSTRUCTIONS
 
As this program progresses, you will be asked a series of questions;
during the question/answer part, the following rules apply:
 
  1. Most questions contain default answers in {braces}.  Enter just
     RETURN to select the default answer.
 
  2. You may abort this installation at any question by pressing the EOF
     character (usually either the CONTROL-D or the DELETE key).
 
 
Press [Return] to continue... 
 
THORDBFIX461 ========================================================== USERID
 
To use this program, you must be the Thor database administrator.  That
is, you must be logged in as the user who owns Thor database files and
has permission to write to those files.
 
In addition, you environment variables should be set up to be identical
to those defined for the Thorserver and Merlinserver programs when they
normally run.  In particular, DY_ROOT must be defined, and any
environment variables used when creating your databases (e.g.
DY_THORDB) must be defined.
 
 
Press [Return] to continue... 
 
THORDBFIX461 ==================================================== ??BACKED UP??
 
This program is well tested, and should update your databases without any
problems.  However, there is always the possibility that problems, such
as power failures, "crashes" and so on, could interrupt this update process
and result in corrupted databases.  Because of this, you should be sure that
all of your databases have been backed up to a safe place, such as tape.
 
 
Have you backed up your database safely? {Yes} 
 
 
Name of database (full path)> /usr2/thordb/medchem98demo

Database write password>  writepw

Datatypes database write password>  writepw
 
Getting fingerprint ID and generation parameters from the database.  This
will take a minute or two.  Please be patient...
 
THORDBFIX461 ================================================== FINAL APPROVAL
 
If the information below is not correct, or you haven't backed up your
databases, or for any reason you aren't ready to do the update for Daylight
Software Version 4.61, then answer "no" to the question below.
 
Here are the values you have entered:
 
                    DB name: /usr2/thordb/medchem98demo
          DB write password: writepw
datatypes DB write password: writepw
 
The following fingerprints will be fixed:
 
               Normal FP ID: <none>
                  arguments: -b 64 -c 2048 -d 0.3 -s 0/7
 
>>> You are logged in as the Thor database administrator (thor).
>>> You HAVE backed up your database.
 
CAREFULLY INSPECT THE FINGERPRINT ARGUMENTS LISTED ABOVE.
THIS IS THE LAST QUESTION YOU WILL BE ASKED BEFORE WORK BEGINS.
 
OK to proceed? (You must type in "yes" to proceed) yes
Confirmed -- proceeding.
Rebuilding /usr2/thordb/medchem98demo ...
......................................................
......................................................
.................................. 500 TDTs, 569662 bytes
.........500 TDTs, 500 fingerprints added
. 500 TDTs, 0 errors
......................................................
......................................................
................................ 1000 TDTs, 1155312 bytes
..........1000 TDTs, 1000 fingerprints added
. 1000 TDTs, 0 errors
......................................................
......................................................
............................... 1500 TDTs, 1711676 bytes
..........1500 TDTs, 1500 fingerprints added
. 1500 TDTs, 0 errors
......................................................
......................................................
............................... 2000 TDTs, 2280143 bytes 
Done: 2000 TDTs written, 2280143 bytes total
.......2000 TDTs, 1999 fingerprints added 
2000 TDTs, 1999 fingerprints added, 0 errors
Done.
. 2000 TDTs, 0 errors
 
Done: 2000 TDTs, 0 errors
 
THORDBFIX461 ==================================================== FINAL REPORT
 
Your database "/usr2/thordb/medchem98demo" has been updated.