Add ability to write axes, take user specified base pairs, and report all hydrogen bonds to nastruct

[drroe]

Version 6.19.6.

Contains several enhancements to the nastruct action. Should address #1036.

First, formally adds the ability to write base, base pair, and base pair step axes to trajectory files:

    [axesout <file> [axesoutarg <arg> ...] [axesparmout <file>]]
    [bpaxesout <file> [bpaxesoutarg <arg> ...] [bpaxesparmout <file>]]
    [stepaxesout <file> [stepaxesoutarg <arg> ...] [stepaxesparmout <file>]]
    [axisnameo <name>] [axisnamex <name>] [axisnamey <name>] [axisnamez <name>]

The axes can be written to any trajectory format cpptraj can write. For example:

parm ../adh026.3.pdb
trajin ../adh026.3.pdb 
nastruct axesout axes.bases.pdb axesoutarg noter \
         bpaxesout axes.bp.mol2

Adds the ability to specify base pairing directly. Should help in cases where base pair determination is difficult, or user wants to omit certain base pairs:

        specifiedbp pairs <b1>-<b2>,...

For example:

nastruct NA naout dna resmap DCP:C resmap D3C:C calcnohb allhb \
  specifiedbp pairs 2-14,3-15,4-16,5-17,6-18,7-19,8-20,9-21,10-22,11-23,12-24

Also adds the ability to report the total number of all detected hydrogen bonds via the new allhb keyword, instead of only Watson-Crick-Franklin hydrogen bonds (the default).

Adds tests and updates the manual.

[AmberJenkins]

The PGI build in Jenkins failed.