Create a database named drugs for the eight molecules listed
in the $DY_ROOT/data/drugs.smi file and include their assoc
iated data found in the wdi023demo database.
PROCEDURE:
Verify that the thor server is running
% thorping sun1 (replace sun1 with your server name)
thorping: Connection to sun1:thor succeeded
Verify that the server has access the wdi023demo database
Extract the tdts from the wdi023demo database for the molecules in the $DY_ROOT/data/drugs.smi file by using thorlookup.
% thorlookup wdi023demo < drugs.smi > drugs.tdt
Enter server access password for sun1:thor:heather >>
Enter password for database wdi023demo@sun1:thor:* >>
NOTE: [DEMO] World Drug Index 2002.3 [DEMO]
NOTE:
NOTE: COPYRIGHT 2002 DERWENT INFORMATION LTD.
View the file and make sure it looks correct.
Use thorlist on the wdi023datatypes database to create a drugs_datatypes.tdt file.
% thorlist wdi023demo_datatypes drugs_datatypes.tdt
Enter server access password for sun1:thor:heather >>
Enter password for database wdi023demo_datatypes@sun1:thor:* >>
....
Done: 47 TDTs written, 11464 bytes total
Create an empty database named drugs_datatypes
First, use tdtcount
on file drugs_datatypes.tdt to determine the values for sizepri and sizexref:
% tdtcount drugs_datatypes.tdt
11014 47 356 0 47 drugs_datatypes.tdt
^^ ^^
|| ||
sizexrefsizepri
So we can set the values of sizepri and sizexref both at 47.
% thormake '$DY_THORDB/drugs_datatypes' 47 47
Enter server access password for sun1:thor:heather >>
Enter READ password for database:
Confirm READ password for database:
Enter WRITE password for database:
Confirm WRITE password for database:
Enter EXECUTIVE password for database:
Confirm EXECUTIVE password for database:
Created database.
thormake: Done.
Create an empty database named drugs
First, use tdtcount
on file drugs.tdt to
determine the values for sizepri and sizexref:
% tdtcount drugs.tdt
40509 254 557 8 8 drugs.tdt
^ ^
| |
sizexrefsizepri
So we can set the values of sizepri and
sizexref at 8 and 254, respectively.
(Note: These values would be higher if we plan on
adding tdts to this database.)
FONT>
% thormake -DATATYPES_DATABASE drugs_datatypes '$DY_THORDB/drugs' 8 254
Enter server access password for sun1:thor:heather >>
Enter READ password for database:
Confirm READ password for database:
Enter WRITE password for database:
Confirm WRITE password for database:
Enter EXECUTIVE password for database:
Confirm EXECUTIVE password for database:
Created database.
thormake: Done.
Load the drugs_datatypes.tdt file into the drugs_datatypes database
% thorload drugs_datatypes drugs_datatypes.tdt
Enter server access password for sun1:thor:heather >>
Enter password for database drugs_datatypes@sun1:thor:* >>
....
Done: 47 TDTs, 0 errors
If you have not done so already, set -DATATYPES_DATABASE for the database drugs.
database, we already
specified the -DATATYPES_DATABASE to be drugs_datatypes.
However, you will be missing the datatypes specification if you failed
to specify it using the command-line option by only typing:
% thormake '$DY_THORDB/drugs' 10 300
To check to see if the datatypes db is set correctly:
% thordbinfo drugs
Enter server access password for sun1:thor:heather >>
Enter password for database drugs@sun1:thor:* >>
name: /usr/local/daylight/thordb/drugs.THOR
modified: Thu Jul 24 14:35:10 2003
datatypes db: $DY_THORDB/drugs_datatypes
indirect db:
Number TDTs: 0
Number Xrefs: 0
TDT bytes: 0
Xref bytes: 0
TDT hash table: 11
Xref hash table: 307
Autocrunch limit: 50%
"HOLD" database: FALSE
Read-only: FALSE
Record locking: DISABLED
As shown above, we want
datatypes db: to be set to $DY_THORDB/drugs_datatypes
If DATATYPES_DATABASE is set correctly, go to the next step:
Load the drugs.tdt file into the drugs database
If there nothing listed after datatypes db:,
the correct database needs to be set using thorchange.
You can assign the -DATATYPES_DATABASE using thorchange:
% thorchange '$DY_THORDB/drugs' -DATATYPES_DATABASE '$DY_THORDB/drugs_datatypes'
Enter server access password for sun1:thor:heather >>
Enter EXECUTIVE password for database:
thorchange: Database opened.
Changing passwords: [Return] means no change
"" means remove existing password
Enter READ password for database:
Confirm READ password for database:
Enter WRITE password for database:
Confirm WRITE password for database:
Enter EXECUTIVE password for database:
Confirm EXECUTIVE password for database:
Datatypes database set.
thorchange: Done.
Load the drugs.tdt file into the drugs database
% thorload drugs drugs.tdt
Enter server access password for sun1:thor:heather >>
Enter password for database sun1@cooper:thor:* >>
Done: 8 TDTs, 0 errors