INTRODUCTION TO DAYLIGHT

A 3 day course

• Class schedule
• Files for course
• Orientation and disclaimers
• Documentation/reference list
• SUMnet hosts table

I. Daylight Basics - day one

1. SMILES
   • Simple forms
   • SMILES syntax rules
   • Isomeric SMILES
   • Canonical SMILES
   • Reaction SMILES
2. SMARTS
   • Simple forms
   • SMARTS syntax rules
   • Atom and bond primitives, operators
   • Recursive SMARTS (vectors)
3. SMIRKS (Reaction Transforms)
4. Thor Data Trees (TDTs)
   • Datatypes
   • Root identifiers
   • Cross-reference identifiers
   • Non-identifiers (data)
5. Fingerprints

1. X-clients Interface
   • Thor and Merlin clients and servers (xvmerlin and xvthor)
   • PCModels (xvpcmodels)
2. Command Line Interface
   • Database Administration (sthorman, thorfilters)
   • PCFilters (clogp and cmr)
   • Printpackage (prado, treetops and tablet)
   • Clustering Package (nearneighbors, jarpat, etc.)
   • Rubicon (rubicon, autorules)
3. Web Interface
   • JavaGrins
   • DayCGI
4. Special Topic: The Daylight/Oracle Chemistry Cartridge and Documentation

• Documentation/reference list

II. Daylight Administration - day two

  A. Installation

1. FTP, WWW, CDROMs
2. The Daylight distribution
3. Daylight environment variables
4. /etc/services
5. httpd configuration
6. Licensing

1. dy_passwords.dat
2. Restricted vs. allowed hosts
3. "thor" and "thorinfo"
4. User limits
5. Thorserver vs. merlinserver
6. Daytoolserver
7. Tasks

1. Options
2. Useful shortcuts

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: Cheminformatics Present and Future

III. Daylight Toolkits - day three

1. Dependencies of libdt libraries
2. XView Widgets Toolkit
3. Rubicon Toolkit
4. DayCGI Tools
5. Java Tools
6. Reaction Toolkit
7. Remote Toolkit

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

1. C
2. F77
3. Perl
4. Python
5. Java
6. others

1. Debuggers
2. Purify

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. 3rd Party GUI's and Other Applications
   • Modgraph Registry System
   • MSI Diversity Explorer, Cerius, etc.
   • CambridgeSoft ChemDraw
   • Others
2. CGI-Programming with JavaGRINS - Ragu Bharadwaj

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, and Reaction Searching - exploratory data analysis techniques with Merlin including 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.
10. Oracle Cartridge - using SQLPLUS or a JDBC interface to explore the oracle cartridge

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- dcgi_env.sh, 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 1 - Using and understanding transforms with react.cgi
8. Transform Basics 2 - Using and understanding transforms with trantest2.c and enumerate.c
9. Creating a CGI - in /daycgi/, to run one Daylight application
10. Compiling, running, and analyzing some example code:
    - rings.c (SMILES)
    - smartsmatch.c (SMARTS)
    - thorget.c (Thor)
    - minimer.c (Merlin)
    - mersearch.pl (Merlin)
    - react.c (Reactions)
    - add2d.c (Depict)
    - chifinger.c (Fingerprint)
    - simatrix.c (Fingerprint)
    - mol2smi.c (SMILES)
    - add_clogp.c (Program Object)
    - depict_usage_1.c (Depict + Xlib)
    - depict_usage_3.c (Depict Widget)
11. PROJECTS - selected projects of interest to students