Draw secondary structure (LoopTool)
Base on loopsol by Gary Olsen, University of Illinois, Urbana Illinois.

This function will draw an RNA secondary structure from a proposed
structure.  The secondary structure must be represented as a text sequence
containing only ['s, ]'s, and -'s.  Any column that represents a 5' side
of a helix should have a '[' character, all 3' helix positions should
have a ']' and all others should have a '-' character.

Example:

helix:	---[[[---]]]---
seq:	aaagggaaacccaaa

To represent:

	   aaa
	  g - c
	  g - c
	  g - c
       aaa     aaa

Care must be taken to insure that there are an equal number of ['s and ]'s.

Select the sequence (one at a time) that you wish to draw along with the
Helix sequence before calling this function.  The resulting secondary structure
will be presented in LoopTool.  LoopTool will allow you to manipulate the
helicies, save a given structure to a template file (loop.temp), or print to a
PostScript(tm) file (loopout).

The menus in LoopTool are as follows:
File:
	Save:	Save structure to a template file (loop.temp)

	Print:	Save postscript file (loopout)

	Quit:	Exit LoopTool

Edit:
	Clear constraint:
		Clear all constraints binding the selected bases

	Show constraints:
		Draw lines showing which bases are under positional
		and distance constraints.  This option toggles.

	Distance constraint:
		Set the default constraining mechanism to preserve
		distances between selected bases.  This is the default.

	Positional constrainst:
		Set the default constraining mechanism to preserve
		positional relationships between selected bases.

	Invert helix:
		Reverse the direction of curvature for the selected
		bases.

	Stack Helix:
		Straighten all selected helicies.

View depth:
	For very complicated structures, view depth can reduce the
	amount of the structure displayed. 

Base selection cones in two forms. The first way of selection is Drag
Selection.  Place the pointer over one base, press and drag the mouse
to the last base (5' to 3') that you wish to select, and release.  In this
manner, you will highlight all bases between the first selected and the
last.  You can then go onto use the menu items Clear constraint, Invert
Helix, and Stack helix.

The second form of selection is Anchor and Drag.  You first click and
release on one base to anchor it, and then click and drag a second
base to some new position with respect to the anchored one.  This will
place a "constraint" between those two bases which will change the way that
the structure is drawn.  If the default constraint is set to Distance, then
the distance between the two bases will be reset.  If the default constraint
is set to be Positional, then the relative position of the second base w.r.t.
the first will be set.

Hints:

Constraints are resolved in 5' to 3' clockwise manner.  Anchors should
be set on the most 5' bases.  Not all constraints are allowed, and some
may result in an error "beep" on the console.  Use "Show Constraints" to
get a feel for what you are doing.

Many thanks to Gary Olsen for the layout algorithm, and for the original
source code.