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

Daylight Worksheet - Compiling, running, analyzing, and modifying more example code

The following example programs are a diverse set representing many of the toolkits and their functions. By experimenting with these, much can be learned about the toolkit. You may wish to focus on those areas of particular interest.

$DY_ROOT/contrib/src/c/smiles/rings.c (SMILES)
Description: finds ringsystems
Suggested experiments: Determine when ringsystem substituents are part of the ringsystem (e.g., double-bonded substituents). Modify and improve this behavior.

$DY_ROOT/contrib/src/c/smarts/smartsmatch.c (SMARTS)
Description: Match SMARTS pattern against input SMILES.
Suggested experiments: Modify the matched part of the molecule in some way and write out the new smiles. Your own reaction toolkit!

$DY_ROOT/contrib/src/c/thor/thorget.c (Thor)
Description: Looks up data in a database from input identifiers.
Suggested experiments: Try looking up some datatrees using primary id (e.g., $SMI), and using a cross-reference id (e.g., $NAM). Modify the program to lookup data using a predefined list of possible identifier datatypes. Next modify the program to query the database and find out all the identifier datatypes and use all of them for any lookup.

$DY_ROOT/contrib/src/c/merlin/minimer.c (Merlin)
Description: Minimal Merlin client.
Suggested experiments: Add some functionality so it's less minimal.

$DY_ROOT/contrib/src/perl/examples/ (Merlin)
Description: DayPerl version of a serial interactive Merlin client.
Suggested experiments: Try all the features. What is missing? Add a search type, or another missing feature.

$DY_ROOT/contrib/src/c/depict/add2d.c (Depict)
Description: Generates 2D data and adds it to an input TDT.
Suggested experiments: View some of the output using depict2d.cgi.

$DY_ROOT/contrib/src/c/fingerprint/chifinger.c (Fingerprint)
Description: Generate chiral fingerprints.
Suggested experiments: Try the program and verify that stereochemistry affects the FPs by inspection. Add a feature to the program so that the Tanimoto similarity of different stereoisomers can be calculated.

$DY_ROOT/contrib/src/c/fingerprint/simatrix.c (Fingerprint)
Description: Generates a similarity matrix for input SMILES.
Suggested experiments: Add Tversky-similarity capability.

$DY_ROOT/contrib/src/convert/mdl/mol2smi.c (SMILES)
Description: Convert MDL SD/MOL files to SMILES/TDT format.
Suggested experiments: Test using various SD/MOL files with varying options.

$DY_ROOT/contrib/src/c/progob/add_clogp.c (Program Object)
Description: Calculate ClogP using clogptalk and add to TDTs.
Suggested experiments:

$DY_ROOT/contrib/src/c/widgets/depict_usage_1.c (Depict + Xlib)
Suggested experiments:

$DY_ROOT/contrib/src/c/widgets/depict_usage_3.c (Depict Widget)
Suggested experiments:

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