fixed a minor bug in genpoly_lt.py

It was not behaving correctly when invoked using the "-box" argument. (The minimum X,Y,Z coordinates were not allowed to exceed 0.)

fixed a bug in "interpolate_curve.py"

The bug was preventing the correct scaling of coordinates when using "interpolate_curve.py". (This bug has no effect unless the "scale" parameter was used.)

fixed a bug preventing wildcards in _coeff commands

Fixed a bug that prevented wildcards in _coeff commands from being interpreted correctly in some files generated moltemplate. Currently, they are ignored unless they appear in the "In Settings" section (<-->"system.in.settings") file. Now all files generated by moltemplate are screened for wildcards in _coeff commands.

fixed a serious bug in cleanup_moltemplate.sh

This is a disturbing and potentially serious bug that causes "cleanup_moltemplate.sh" to alter the order of improper atoms for all force fields, (including GAFF, GAFF2, OPLSAA, and COMPASS). It is unlikely but also possible it could have caused improper interactions to be incorrectly identified as redundant and deleted. Thanks to bhargavchava97 (again) for catching this!

AMBER GAFF bugfix (credit: bhargavchava97)

Important correction to AMBER GAFF and GAFF2 force fields (improper interactions). Prior to this version, molecules built using AMBER force fields (GAFF and GAFF2) would contain redundant improper interactions. This might cause these molecules to be unrealistically stiff. Currently the improper interactions generated by moltemplate now agree with improper interactions generated by AmberTools/Antechamber. (Details: I can't guarantee that the order that the atoms appear in each improper is equivalent, but at least the number of improper interactions is correct, the central atom is correct, and the atoms involved are correct.) This bug fix was contributed by bhargavchava97(github user). THANKS!

added the amberfrcmod2lt.sh converter for AMBER FRCMOD files

Added the "amberfrcmod2lt.sh script for converting user-supplied FRCMOD files into moltemplate LT files that can be used with gaff.lt and gaff2.lt. I will eventually have to document all of the scripts in this directory for them to be useful to end users. (On my to-do list.) I also corrected some some of the error messages in genpoly_lt.py.

error checking now understands "pair_coeff @{atom:b1}*@{atom:b3}" commands

syntax error checking no longer crashes when it encounters @{atom:b1}*@{atom:b3} style ranges specifiers in pair_coeff commands (or "Pair Coeffs" sections from data files).
(Note: I have only tested input scripts with "pair_coeff" commands that use this syntax. Hopefully data files with "Pair Coeffs" also work.)

fixed 2 bugs and 1 example

The bugs effected some python environments, and also users who use atom_style ellipsoid. (Thanks to LunarLanding, Clemens Possel, and Johannes Haataja!)

added a small feature to dump2data.py (moltemplate.sh is not effected)

added the "-type", "-mol", "-id" arguments to dump2data.py, to enable users to be able to select atoms based on type, id, or molecule-id. (I'm not sure if this small feature justifies a version update.)

fixed .matrix(), added features to genpoly_lt.py

-Fixed a bug in the ".matrix()" and ".quatT()" coordinate transforms.
-Added the "-orientations", "-quaternions", and "-helix-angles" arguments
to genpoly_lt.py.
-Updated the documentation.
(I doubt these are popular features, hence I don't think anyone will notice.)