DayPerl2

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• DayPerl2
• You Can Teach an Old Dog New Tricks!

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DayPerl2 Brief History

• Brief History of DayPerl
• Version 1.1, 1996 Alex Wong
• Daylight support Roger Critchlow, Jeremy Yang,
  Margaret Kamphorst, Jack Delany
• Roger did the first swig(1) implementation, which
  supports Perl, Python, Tcl/Tk.

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DayPerl2 Outline

• Overview of the talk
• Features, compare to DayPerl
• Example Molecular modeling
• Example PNG depiction
• Example Molecular graph theory
• Example Thor / Merlin
• Comparison C, PyDaylight

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DayPerl2 What Does It Do?

• Implements the Daylight Toolkit in Perl
• All Daylight Toolkit functions and constants
• Includes a PNG drawing library
• Implemented with swig(1)
• Availability - Tested on
• RedHat Linux 7.2 and 9.0
• Solaris 2.8
• Perl versions 5.6 and 5.8 (Sun and Linux)
• Has compiled on IRIX 6.5, but difficult

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Changes DayPerl to DayPerl2

• Why DayPerl2?
• Uses swig(1) for easier support
• Original DayPerl had illegal perl syntax
• Four major differences
• Constants
• Multiple return values
• "invalid string"
• Depiction library

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Depict Library

• New Feature, built into DayPerl2
• Drawing Library uses libpng
• No patent issues with PNG, worldwide
• Colors
• Antialiasing
• Fixed font, truetype fonts, or old vector font
• Transparent background

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Example 1 Molecular Modeling

• smartsprops.pl
• Simple property calculator
• HBD, HBA, Rotatable Bonds
• example

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Example 2 PNG Depiction

• depicttest.pl
• Illustrates creating a depiction as a PNG image
• example

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Example 3 Molecular Graph

• make_skeleton.pl
• Converts a molecule to all C, single bond (the
  "graph" or "skeleton")
• example

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Example 4 Thor/Merlin

• spresi_reaction_finder.pl
• Finds the ten most-similar compounds to the given
  compound for which a reaction is given in the
  literature
• example

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C man(1) to DayPerl2 syntax

• Add to constants
• C NULL_OBperl NULL_OB
• Drop string lengths
• C dt_alloc_string(len, s)perl dt_alloc_string
  (s)

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C man(1) to DayPerl2 syntax

• Use undef for the "invalid string"
• C dt_alloc_string(0, NULL)
• perl dt_alloc_string(undef)
• Move all return values to left side of ''
• C ok dt_continue(server, status)
• perl (ok, status) dt_continue(server)

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Comparison Other Languages

• C/C
• Perl is MUCH easier
• Writing Perl is 2-10 times faster than C or C
• But ...
• DayPerl2 doesn't protect you against "core dump"
  if you give Toolkit illegal parameters
• DayPerl2 doesn't protect you against memory leaks
  (must call dt_dealloc()).

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Comparison Other Languages

• PyDaylight and Python
• Python PyDaylight is a better solution than
  Perl DayPerl2
• Python is a cleaner language, PyDaylight has nice
  object-oriented features
• However...
• Perl is a great language, and DayPerl2 is a
  "straight-ahead" translation of the Toolkits
• If you're familiar with perl, use DayPerl2, it's
  a very capable combination

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Why Not dayswig?

• For the technical among you...
• Perl has peculiarities that are handled by
  specialized swig(1) rules
• If anyone has time, and more swig(1) expertise
  than me, I'd be happy to team up to try to unify
  DayPerl2's swig rules with dayswig's rules

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DayPerl2

• The Old Dog is Still Alive
• Perl DayPerl2 is still a viable tool for
  writing Daylight Toolkit programs
• Modernized DayPerl2 syntax matches improvements
  in Perl syntax
• He's learned a new trick
• Depictions are very handy for web applications