Daylight Summer School 1999, June 15-17, St. John's College, Santa Fe, NM

Daylight Chemical Information Systems Inc.


A 3 day course

C O U R S E    O U T L I N E

I. Daylight Basics - day one

  A. Languages
  3. Thor Data Trees (TDTs)
  B. Applications
  1. Xview Interface
  2. Command Line Interface
  3. Web Interface
  C. Documentation


II. Daylight Administration - day two

  A. Installation

  2. The Daylight distribution
  3. Daylight environment variables
  4. /etc/services
  5. httpd configuration
  6. Licensing
  B. Servers & Users
  1. dy_passwords.dat
  2. Restricted vs. allowed hosts
  3. "thor" and "thorinfo"
  4. User limits
  5. Thorserver vs. merlinserver
  6. Daytoolserver
  7. Tasks
 C. Customizing
  1. Options
  2. Useful shortcuts
 D. Databases
  1. Installing databases
  2. Configuring databases: caching, holding, passwords, record locking, read-only db's
  3. Pools and RAM
  4. Database design indirect databases, monomer databases, reaction databases, datatypes
  5. Creating datatypes
  6. Creating databases
  7. Converting to SMILES from other formats
  8. Automating db admin: starting and stopping servers, other DB admin tasks
  9. Reaction databases
  10. Non-structures in Daylight databases
  11. Structural standardization
  12. Non-identifier cross references
  13. Survey of commercial databases

Special Topic: Chemistry and the Internet

III. Daylight Toolkits - day three

  A. Overall Capabilities
  1. Dependencies of libdt libraries
  2. XView Widgets Toolkit
  3. Rubicon Toolkit
  4. DayCGI Tools
  5. Java Tools
  6. Reaction Toolkit
  7. Remote Toolkit
B. The Toolkit view
  1. Objects and Handles
  2. Object Types
  3. Streams
  4. Sequences
  5. Properties
  6. dt_parent-age and dt_base
  7. dt_dealloc and Memory Leaks
  8. Persistence of Objects and Returned Values
  9. Debugging Tricks
C. Programming languages
  1. C
  2. F77
  3. Perl
  4. others
D. Programming tools and environments
  1. Debuggers
  2. Purify
E. The functions

F. Contrib examples

G. Web development

H. Case studies

  1. WinMerlin (Bernd Rohde, Novartis)
  2. Stigmata (Norah MacCuish, Daylight)
  3. mol2smi (Jeremy Yang, Daylight)
  4. UC_SELECT (Geoff Skillman, UCSF)
  5. daybase.cgi (Jeremy Yang, Daylight)
  6. Diversity Map (Bernd Rohde, Novartis)
  7. SPURT (Bernd Rohde, Novartis)
  8. Others

I. Special Topics:

  1. CGI-Programming with JavaGRINS - Ragu Bharadwaj

Special Topic: The Future of Computational Chemistry

Lab Activities - Intro to Daylight

I. Daylight Basics - Languages and Applications

  1. SMILES/SMARTS Practice I SMILES Practice II- Compose SMILES, Isomeric SMILES, and Reaction SMILES from depictions, self test by using DayCGI depict tool.
  2. SMARTS Practice II - Compose SMARTS for described chemical target substructures / functional groups.Also recursive and disconnected SMARTS. Generating postscript with SMARTS highlighted using prado from the printpackage.
  3. TDT Retrieval and editing with xvthor-running xvthor and experimenting with its various features.
  4. Structural, Non-Structural, Mixture and Reaction Searching - exploratory data analysis techniques with Merlin including Chuckles, Chortles, Charts and Reaction SMILES and SMARTS
  5. Thorfilters/Sthorman - thorlookup, thorlist, etc. also generating poscript with prado from printpackage
  6. PCModels/PCFilters - running xvpcmodels, clogp and cmr in various modes.
  7. Cluster Package - generating a clustered dataset, jarpat, listclusters, showclusters, etc.
  8. Rubicon - generating 3D coordinates for a TDT file
  9. DayCGI and MCL - using the web applications, JavaGrins, and the daycgi Wizard program to generate an MCL script.

II. Daylight Administration

  1. Installing 4.62 from CDROM - gzip -d and tar
  2. Installing a Database - into $DY_THORDB
  3. Server Security - adding a user or host using sthorman, passwords
  4. Starting and Killing the Servers - several ways: on command line with no log file, with log file, with script; monitoring log file
  5. Loading a Merlin Pool - with merlinload, sthorman
  6. Configuring a Database - auxilliary databases, passwords, file paths, read-only, caching
  7. Configuring a Merlin Pool- selecting datafields for loading
  8. Setting options- via environment variables, dy_profile.opt, dy_sysprofile.opt, and command line
  9. Creating a Database- using sthorman and thormake
  10. Loading a Database- with sthorman and thorload
  11. Building a Database- automating with scripts
  12. Designing a Database- specifying a new datatype
  13. DayCGI Administration-, httpd aliases and script aliases

III. Daylight Toolkits

  1. Compiling cansmi.c- the "hello.c" of Daylight programs
  2. Modifying cansmi.c - to count atoms and bonds in the molecule
  3. Compiling the contrib code- adding a new program to a makefile
  4. Creating a development environment - copying a contrib source file and makefile; editing the makefile appropriately; recompiling
  5. More cansmi.c- reaction toolkit basics
  6. Exploring reaction functionality
  7. Transform Basics - Using and understanding transforms
  8. Creating a CGI - in /daycgi/, to run one Daylight application
  9. Compiling, running, and analyzing some example code:
    - rings.c (SMILES)
    - smartsmatch.c (SMARTS)
    - thorget.c (Thor)
    - minimer.c (Merlin)
    - (Merlin)
    - react.c (Reactions)
    - add2d.c (Depict)
    - chifinger.c (Fingerprint)
    - chor2smi.c (Monomer)
    - depict_usage_1.c (Depict + Xlib)
    - depict_usage_3.c (Depict Widget)
  10. PROJECTS - selected projects of interest to students

Daylight Chemical Information Systems Inc.