Daylight Summer School 2002, June 5-7 Santa Fe, NM

Daylight Administration - Lab Exercises & Answers

These notes are intended to be brief notes supplementing and outlining the course material presented in the course Introduction to Daylight. The Daylight manuals should be considered the text for the course and the authoritative documentation, and should be used in conjunction with these notes for best results!

The Daylight Installation and Administration Guide is the relevant manual for this unit.

A. Installation

Licensing
- Gather information about your computer as described at and ask for a license.
  See http://www.daylight.com/dayhtml/doc/admin/install/license.html
- Save your license to the standard location.
  /usr/local/daylight/dy_license.dat
Getting the Software
- Ask for the software on CD or download it from the Daylight website.
  Ask for the software on CD or see http://www.daylight.com/support/download.html
- Extract the software as the Daylight Adminstrator user into the standard directory location.
  if necessary, create thor user account with /usr/local/daylight as its HOME directory.
  login as thor % gzip -dc <PATH-TO-SOFTWARE-CD>/day471-<YOUR-PLATFORM-FULL-OR-LITE>.tar.gz | tar xvf - % gzip -dc <PATH-TO-SOFTWARE-CD>/day473-<YOUR-PLATFORM-FULL-OR-LITE>.tar.gz | tar xvf -
TCP/IP Services
- Define server ports.
  % vi /etc/services dayutils 5553/tcp daytools 5554/tcp thor 5555/tcp merlin 5556/tcp
Environment Variables
- Set DY_ROOT, update your PATH and test.
  % DY_ROOT=/usr/local/daylight/v473 % PATH=$(DY_ROOT)/bin:$(PATH) % which testlicense
- Set DY_LICENSEDATA and test.
  % DY_LICENSEDATA=/usr/local/daylight/dy_license.dat % testlicense
- Update LD_LIBRARY_PATH and test.
  % LD_LIBRARY_PATH=$(DY_ROOT)/lib:$(LD_LIBRARY_PATH) % thorserver
Web Server Configuration
- Define aliases.
  % vi /usr/local/apache/conf/httpd.conf Alias /dayhtml/ $DY_ROOT/dayhtml/ Alias /dayicon/ $DY_ROOT/dayhtml/icons/ ScriptAlias /daycgi/ $DY_ROOT/daycgi/
Automation
- Instead of doing the above steps, use the installation scripts for user root and thor.
  % dayinstall471.root % dayinstall471 % v473patch/dayinstall473

B. Clients & Servers

Storage and Retrieval
- Start THOR, retrieve some data and check the log file
  % thorserver % xvthor (graphical) % thorlist wdi00demo | tdtcat -DO_RECORDS 1 (non-graphical, enter nothing for password) % cat thorserver.log
High-Speed Search
- Start MERLIN, do a search, and check the log file
  % merlinserver wdi00demo % xvmerlin (graphical) % mcl (non-graphical) % cat merlinserver.log
SMILES and SMARTS Editor
- Go to the ClogP CGI on the Daylight website and use JavaGrins.
  See http://www.daylight.com/daycgi/clogp

C. Security

Servers
- Enable Restricted Host Mode and test.
  Use sthorman to add a user, password, and host
  % thorlist wdi00demo%@<YOUR-HOST>::<YOUR-USER>%<YOUR-USER-PASSWORD> | tdtcat -DO_RECORDS 1
- Enable Equivalent Host Mode and test
  Use sthorman to remove the above user
  % thorlist wdi00demo%@<YOUR-HOST>::% | tdtcat -DO_RECORDS 1
- Disable security and test.
  Use sthormanto remove the above host
  % thorlist wdi00demo%@::% | tdtcat -DO_RECORDS 1
Databases
- Enable database security and test.
  Use sthorman to add a database password
  % thorlist wdi00demo%<DATABASE-PASSWORD>@::% | tdtcat -DO_RECORDS 1
- Set database passwords for read permission and test
  Use sthorman to a password for read only access
  % thorlist wdi00demo%readpw=<READ-PASSWORD>@::% | tdtcat -DO_RECORDS 1
- Set database passwords for write permission and test
  Use sthorman to a password for add modify and delete access
  % echo '$SMI|' | thorload -INPUT_FORMAT TDT wdi00demo%writepw=<WRITE-PASSWORD>@::%
- Set database passwords for executive permission and test
  Use sthorman to a password for ultimate access
  % echo '$SMI|' | thordelete -INPUT_FORMAT TDT wdi00demo%rexecutivepw=<EXECUTIVE-PASSWORD>@::%

D. Customization

Options
- Set the system profile to make xvthor appear in the middle of the screen and test
  % vi $DY_ROOT/etc/unix/dy_sysprofile.opt THOR_MAINFRAME_X 300 THOR_MAINFRAME_Y 300 xvthor
- Set the user profile (overriding the system profile) to make xvthor appear in the top middle of the screen and test
  % vi $HOME/dy_profile.opt THOR_MAINFRAME_X 300 THOR_MAINFRAME_Y 0 xvthor
- Use the command line to make xvthor Set the system profile to make xvthor appear in the top left of the screen and test
  % xvthor -THOR_MAINFRAME_X 0 -THOR_MAINFRAME_Y 0

E. Databases

Installation
- Ask for a database CD and extract the database as the Daylight Adminstrator user into the standard directory location.
  % cd $DY_THORDB gzip -dc <PATH-TO-DATABASE-CD>%lt;SAMPLE-DB>.tar.gz | tar xvf -

Creation

Create a database using sthorman.

% sthorman
Version: sthorman 4.73

          ....................................................
          .  STHORMAN -- Serial THOR Manager Program.        .
          .                                                  .
          .  Enter "?" for help at any prompt.               .
          .  The menu selection "." goes to top-level menu.  .
          ....................................................

STHORMAN needs to be connected to a server.

Enter machine the server is running on: ("localhost") 
Enter port (service) of server: ("thor")
Enter username: ("thor")
Enter server username's password:


Connected to new server.
Current service:  localhost:thor

SERVER MENU (TOP LEVEL MENU):
1) Connect to a new server
2) List server's version
3) List current users
4) Change server security...
5) Databases...
6) Send message to users...
7) Evict user...
0) Quit
Enter menu selection (or '?'): 5

DATABASE MENU:
 1) List known databases
 2) Change database search-path...
 3) Get database information...
 4) Create   a database...
 5) Load     a database
 6) Dump     a database
 7) Crunch   a database
 8) Change   a database's configuration...
 9) Destroy  a database
10) Send message to users of a database...
11) Evict users of a database...
 0) Go back to server menu
Enter menu selection (or '?'): 4

DATABASE CREATION MENU:
1) Create a datatypes database
2) Create a indirect-reference database
3) Create a monomer-table database
4) Create a regular database
0) Go back to database menu
Enter menu selection (or '?'): 4

Enter name of regular database to create: $DY_THORDB/test

Existing datatypes databases:
  1) %lt;other>
  2)  /usr/local/daylight/demodb/asinex00demo_datatypes
  3)  /usr/local/daylight/demodb/bioscr00demo_datatypes
  4)  /usr/local/daylight/demodb/chemsynth97demo_datatypes
  5)  /usr/local/daylight/demodb/m4x10bound_datatypes
  6)  /usr/local/daylight/demodb/maybridge00demo_datatypes
  7)  /usr/local/daylight/demodb/medchem00demo_datatypes
  8)  /usr/local/daylight/demodb/mix97demo_datatypes
  9)  /usr/local/daylight/demodb/nci96demo_datatypes
  10)  /usr/local/daylight/demodb/spresi95demo_datatypes
  11)  /usr/local/daylight/demodb/spresirxn98demo_datatypes
  12)  /usr/local/daylight/demodb/wdi00demo_datatypes
  13)  /usr/local/daylight/thordb/acd012_datatypes
  14)  /usr/local/daylight/thordb/medchem02_datatypes
  15)  /usr/local/daylight/thordb/wdi021_datatypes
Enter number of existing datatypes database: 12

Existing indirect-reference databases:
  1) %lt;other>
  2) %lt;none>
  3)  /usr/local/daylight/demodb/chemsynth97demo_indirect
  4)  /usr/local/daylight/demodb/medchem00demo_indirect
  5)  /usr/local/daylight/demodb/spresi95demo_indirect
  6)  /usr/local/daylight/demodb/spresirxn98demo_indirect
  7)  /usr/local/daylight/thordb/medchem02_indirect
Enter number of existing indirect database: 2

Existing monomer-table databases:
  1) %lt;other>
  2) %lt;none>
  3)  /usr/local/daylight/demodb/mix97demo_monomers
Enter number of existing monomer-table database: 2
Enter size for primary hash-table: 200
Enter size for cross-reference hash-table: 200
Enter  new READ password:

Verify new READ password:

Enter  new WRITE password:

Verify new WRITE password:

Enter  new EXECUTIVE password:

Verify new EXECUTIVE password:


The executive password for a database is needed to change passwords.
No executive password has been specified; anybody can change any password.
Is this ok? ("yes")

Database ............................ $DY_THORDB/test
Database type ....................... regular
Datatypes database .................. /usr/local/daylight/thordb/wdi00demo_datatypes.THOR
Indirect reference database ......... %lt;none>
Monomer-definitions database ........ %lt;none>
Primary hash-table size ............. 200
Cross-ref. hash-table size .......... 200

Create above database? ("yes")

Database created.

Create a database using thormake.
% thormake $DY_THORDB/test2 200 200 -DATATYPES_DATABASE wdi00demo_datatypes

Delete the databases.
% thordestroy $DY_THORDB/test % thordestroy $DY_THORDB/test2

Daylight Chemical Information Systems Inc.
support@daylight.com