Make

The three platform-specific makefiles Makefile.Cygwin, Makefile.Linux, and Makefile.MacOSX handles the small differences in operating systems. The generic Makefile Makefile.generic, which is included by the three platform-specific makefiles, does the bulk of the work. The file Makefile.generic consists of several sections:

• Top Section: This section defines macros for groups of files and dependencies for executables. In particular,
  • make all compiles all programs,
  • make clean removes temporary files,
  • make clobber removes compiled executables,
  • make spotless removes results files.
• PseudoBase: This section provides rules to extract RNA data from pseudobase.fasta, to split the data into RNA sequence and dot-brackets in seq and db formats, and to convert the dot-brackets to base pairs and helices in pkb.bp and pkb.hx formats. It also contains a target pkb for the preparation of experiments.
• HotKnot: This section provides rules to convert the bpseq files precomputed by HotKnot to hotknot.bp and hotknot.hx formats, and a target hot for the preparation of experiments. Note that this section also contains rules to compute RNA secondary structures using HotKnot, but these rules are commented out because HotKnot works on Linux only.
• Delta: This section provides rules to use our folding simulation program and 3D visualization program on individual sequences. Note in particular the three targets result, show, and movie discussed in Download and Install Software.
• Experiments and Analysis: This section includes all the scripts for automating experiments and analysis. Note in particular the targets delta, stop, txt, scr, scatter.pdf, and reconstruct discussed in Repeat Experiments.
• Software Package: This section provides rules for two targets: all.zip is an archive of the complete software package; code.pdf is a single-pdf printout of the complete source code.

The file Makefile.generic contains many shortcuts for typical tasks. For example,

• make PKB00001.seq extracts the sequence PKB00001.seq from pseudobase.fasta.
• make PKB00001.delta.bp uses the folding simulation program to predict base pairs for the sequence PKB00001.seq.
• make PKB00001.delta.hx converts the base pairs to helices.
• make PKB00001.delta.hx2i converts helices to 2-intervals in textual format.

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