Add 'addatom' action

[drroe]

6.27.3. Adds the addatom action, which temporarily adds an atom that subsequent actions can use.

  [help addatom]
        aname <name> [elt <element>] [rname <res name>]
        [xyz <X> <Y> <Z>] [mass <mass>] [charge <charge>]
        [outprefix <prefix>] [nobox] [parmout <filename>]
        [parmopts <comma-separated-list>]

This is mostly useful for adding a placeholder “dummy” atom for subsequent actions to use. For example, this can be used in conjunction with the 'mask' command in order to get a list of atoms within a certain distance of a specified point in space. For example, the following input gets a list of atoms within 3.0 Angstroms of coordinates 1, 1, 1:

parm tz2.pdb
trajin tz2.pdb 1 1
addatom aname TEMP rname TMP elt H xyz 1 1 1
mask :TMP<@3.0&!:TMP out tz2.mask.dat name TZ2

Adds a test and updates the manual.

[drroe]

@swails is there any way to update the version of Lyx in ambermd/lyx:latest to 2.4?