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Exercise 11.1
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Use File::Find and the file test operators to
find the oldest and largest files on the hard drive of your computer.
(You can delete them or store them elsewhere if you're running
short on disk space.)
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Exercise 11.2
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Find all the Perl programs on your computer.
Hint: Use File::Find. What
do all Perl programs have in common?
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Exercise 11.3
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Parse the HEADER, TITLE, and KEYWORDS record types of all PDB files
on your computer. Make a hash with key as a word
from those record types and value as a list of
filenames that contained that word. Save it as a DBM file and build a
query program for it. In the end, you should be able to ask for, say,
sugar, and get a list of all PDB files that contain that word in the
HEADER, TITLE, or KEYWORDS records.
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Exercise 11.4
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Parse out the record types of a PDB file using regular expressions
(as used in Chapter 10) instead of iterating
through an array of input lines (as in this chapter.)
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Exercise 11.5
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Write a program that extracts the secondary structure information
contained in the HELIX, SHEET, and TURN record types of PDB files.
Print out the secondary structure and the primary sequence together,
so that it's easy to see by what secondary structure a given
residue is included. (Consider using a special alphabet for secondary
structure, so that every residue in a helix is represented by H, for
example.)
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Exercise 11.6
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Write a program that finds all PDB files under a given folder and
runs a program (such as stride, or the program
you wrote in Exercise 11.5) that reports on the secondary structure
of each PDB file. Store the results in a DBM file keyed on the
filename.
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Exercise 11.7
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Write a subroutine that, given two strings, prints them out one over
the other, but with line breaks (similar to the
stride program output). Use this subroutine to
print out the strings from Example 11-7.
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Exercise 11-8
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Write a recursive subroutine to determine the size of an array. You
may want to use the pop or
unshift functions. (Ignore the fact that the
scalar @ array returns the size of
@array!)
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Exercise 11.9
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Write a recursive subroutine that extracts the primary amino acid
sequence from the SEQRES record type of a PDB file.
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Exercise 11.10
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(Extra credit) Given an atom and a distance,
find all other atoms in a PDB file that are within that distance of
the atom.
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Exercise 11.11
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(Extra credit) Write a program to find some
correlation between the primary amino acid sequence and the location
of alpha helices.
