INTRODUCTION TO DAYLIGHT

I. Daylight Basics - day one

1. SMILES
• Isomeric SMILES
• Monomer SMILES
• Chuckles and Chortles
• Reaction SMILES
• Atom Map Reaction SMILES
2. SMARTS
• Recursive SMARTS
• Disconnected SMARTS and zero order parentheses
3. SMIRKS (Reaction Transforms)
4. CHARTS (Monomer Query Language)
5. Thor Data Trees (TDTs)
• Datatypes
  • Fingerprints
  • Molecular
  • Mixture
  • Reaction

1. Xview Interface
   • Thor and Merlin clients and servers
   • xvmerlin and xvthor
   • PCModels
     • xvpcmodels
2. Command Line Interface
   • Database Administration
     • sthorman
     • thorfilters
   • PCModels
     • clogp and cmr
   • Printpackage
   • prado, treetops and tablet
   • Clustering Package
   • Rubicon
   • Monomer Package
   • Reaction Package
3. Web Interface
   • DayCGI
   • Java Tools

• Reference Sheet

II. Daylight Administration - day two

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
3. pools and RAM
4. database design

indirect databases
monomer databases
5. creating datatypes
6. creating databases
7. converting to SMILES from other formats
8. automating db admin

starting and stopping servers
MakeDB script
9. reaction databases
10. non-structures in Daylight databases
11. survey of commercial databases

III. Daylight Toolkits - day three

1. Overall capabilities and dependencies of libdt libraries
2. XView Widgets Toolkit
3. Rubicon Toolkit
4. DayCGI Tools
5. Java Tools
6. 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 values (returned strings, etc.)
9. debugging tricks

1. C
2. F77
3. Perl
4. others

1. Debuggers
2. Purify

E. Contrib examples

F. Web development

G. Case studies

1. WinMerlin (Bernd Rohde, Novartis)
2. Stigmata (Norah Shemetulskis, Daylight)
3. mol2smi (Jeremy Yang, Daylight)

Special Topic: Computational Chemistry - State of the Art

Lab Activities - Intro to Daylight

I. Daylight Basics - Languages and Applications

1. SMILES Practice - Compose SMILES, Isomeric SMILES, and Reaction SMILES from depictions, self test by using DayCGI depict tool.  
2. SMARTS Practice - Compose SMARTS for described chemical target substructures / functional groups.  Generate SMARTS highlighted postscript output using the PrintPackage.  Also recursive and disconnected SMARTS.
3. Structural,Non-Structural,Mixture and Reaction Searching - exploratory data analysis techniques with Merlin including Chuckles, Chortles, Charts and Reaction SMILES and SMARTS
4. Thorfilters - thorlookup, thorlist, etc.
5. PCModels - running xvpcmodels, clogp and cmr in various modes.
6. Rubicon - generating 3D coordinates for a TDT file
7. Cluster Package - generating fingerprints and clustering a dataset.
8. DayCGI and MCL - using the web applications, JavaGrins and building MCL scripts with Wizard

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- 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 - and maybe diagnosing a compile/make error; adding to a makefile
4. Creating a development environment - copying a contrib source file and makefile; editing the makefile appropriately; recompiling
5. Debugging - finding memory leaks and other pitfalls
6. Creating a CGI - in /daycgi/, to run one Daylight application
7. Compiling, running, and analyzing some example code:

- rings.c (SMILES)
- look4n.c (SMARTS)
- thorget.c (Thor)
- minimer.c (Merlin)
- mersearch.pl (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)
8. PROJECTS - selected projects of interest to students