Daylight Summer School 1998, July 28-30, St. John's College, Santa Fe, NM

Daylight Chemical Information Systems Inc.


A 3 day course

Files for course

C O U R S E    O U T L I N E

I. Daylight Basics - day one

  A. Languages
  1. Dave's Stuff...

  4. 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. Non-identifier cross references
  12. Survey of commercial databases

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 Shemetulskis, Daylight)
  3. mol2smi (Jeremy Yang, Daylight)
  4. UC_SELECT (Geoff Skillman, UCSF)
  5. thorget.cgi (Jeremy Yang, Daylight)
  6. Diversity Map (Bernd Rohde, Novartis)
  7. SPURT (Bernd Rohde, Novartis)
  8. Others

I. Special Topics:

  1. Reaction Toolkit Programming - Jack Delany

  2. Integrating JavaGRINS - Ragu Bharadwaj

  3. Daylight at Vertex - Pat Walters and Matt Stahl (Vertex)

Special Topic: Computational Chemistry - State of the Art

The present and future of chemical computing from a Daylight perspective.  Planning for the next generation of computational tools -- to go boldly, not fearfully, where no computational chemist has gone before.

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 4.61 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. Creating a CGI - in /daycgi/, to run one Daylight application
  6. Compiling, running, and analyzing some example code:
    - rings.c (SMILES)
    - look4n.c (SMARTS)
    - thorget.c (Thor)
    - minimer.c (Merlin)
    - (Merlin)
    - tranfilter.c (Reactions)
    - smi_to_2d.c (Depict)
    - chifinger.c (Fingerprint)
    - chor2smi.c (Monomer)
    - depict_usage_1.c (Depict + Xlib)
    - depict_usage_3.c (Depict Widget)
  7. PROJECTS - selected projects of interest to students