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