Moltemplate

fixed a python3-specific bug in ttree.py causing expressions containing ".." (like "atom:../A") to sometimes cause an uncaught exception. Example:

MoleculeTypeA {
write_once("In Settings") {
atom:../A
}
}
MoleculeTypeB {
}

These kinds of expressions should work again now. (The A leaf node should be created in "/" now.)

updated the manual. updated dump2data.py. fixed a bug reading triclinic boundary conditions from PDB files that affects some versions of awk. Corrected the README file for the EFF example.

Previous versions of **genpoly_modify_lt.py** would crash when told to make 0 modifications. The current version handles this edge case more gracefully. Several examples and README files were also updated.

fixed a bug in COMPASS and "msifrc2lt.py" causing low priority dihedrals and impropers to occasionally override high priority ones

Summary:
This release contains infrastructure improvements for parsing text, as well as bug fixes for the COMPASS force field as well as the "msifrc2lt.py" converter script.

Infrastructure:
1) Greater consistency with the way wildcards and regular expressions are handled. All rules for generating angles, dihedrals, impropers, and looking up bond types and charge-by-bonds, as well as all pair_coeff, bond_coeff, angle_coeff, dihedral_coeff, and improper_coeffs can accept wildcards and regular expressions (eg "atom:re.c[1-6]") . (NOTE: Regular expressions have not been tested yet, but the infrastructure for supporting them is finally there.)
2) Counter variables ($ and ) can no longer contain , or () characters. (In the future, this will make it much easier to create source code for programming languages. Note to self: The +-=/. characters are still allowed. The / and . characters are used for path resolution and should never be forbidden.)

COMPASS: The "msifrc2lt.py" script has been (hopefully) fixed and is now able to convert the COMPASS force field files again. This made it possible to fix 2 bugs in the "compass_published.lt" force field file: 1) wildcards are now given low priority instead of high priority, and 2) non-hybrid bond, angle, dihedral, improper, and pair styles are used by default (for KOKKOS compatibility). Also: Commas were removed from the atom type names (and replaced with ~ characters).

This fixed a unit test failure I was having after introducing v2.17.9.