Daylight Toolkit Wrappers in Perl

Contents

• Background
• Why Bother?
• Researchers as Hackers
• Solution: A Scripting Languages
• Perl
• What Does This Give Us?
• Was It Worth Doing?
• Summary

Background

• Daylight provides great flexibility with Toolkits
• Programming is often a barrier to use of Toolkits
• Researchers should be able to focus on Toolkits not programming

Why Bother?

• Toolkits make Daylight a great research tool
• Research -> always a new question
• Give the tools to the researchers

Researchers as Hackers

• Researchers shouldn't have to be more than casual programmers
• C and FORTRAN are not the easiest for casual programmers
• Focus should be on using the toolkit

Solution: A Scripting Language

• Easier to learn and use
• Quite powerful these days
• Easy to build systems to hide complexity

Perl: Man's Best Friend

• Easy to learn and use
• Memory Management
• First Class String Handling
• Better Programming Environment
• New Object Oriented Features

What Does This Give Us?

• Raw Toolkits
• Common Function Libraries
• Object-Oriented Tools

Raw Toolkits

• Sample: use Daylight; ... $fieldstream = dt_stream($ditemh, TYP_DATAFIELD); while(($fieldh = dt_next($fieldstream)) != NULL_OB){ ... $value = dt_stringvalue($fieldh); ... } dt_dealloc($fieldstream); print $value;

Common Function Libraries

• Sample: use Daylight; use DaylightAux; ... $varh = dt_chortin($monomertableh, $chortles); $stream = dt_stream($varh, TYP_MULTIMER); while (($multimerh = dt_next($stream)) != NULL_OB) { $smiles = dt_smiles($multimerh); $mw = da_calc_molweight_of_smiles($smiles); print "$smiles $mw\n"; dt_dealloc($multimerh); } ...

Object-Oriented Tools

• Sample: use Daylight; use DaylightObj; use DaylightAux; $db = new ProtosDB_Session; ... $varh = dt_chortin($db->{monomertableh}, $chortles); ...

Was It Worth Doing?

• Even one user makes it worthwhile
• Big gain for occasional programs
• More complex packages can be created

Summary

• Daylight has great tools
• Researchers need direct access to tools and shouldn't have to be programmers
• Perl and other scripting languages are easy to learn and use
• Perl makes Daylight Toolkit programming easier