fixed a small bug in mol22lt.py

The "--charges" argument for mol22lt.py should be working now.

I forgot to mention that the AMBER "gaff.lt" and "gaff2.lt" files were also recently updated today (in moltemplate v2.20.8). This should help a lot of people who use GAFF or GAFF2.

I also made some minor improvements to the
mol22lt.py documentation

initial (alpha) attempt at MOL2 file conversion

The new converter program (mol22lt.py) converts MOL2 files to moltemplate (LT) files. This program has not been widely tested and probably fails on some MOL2 files. But the program appears to be useful in some cases.

I fear it is possible I have misinterpreted the MOL2 file format when I wrote this converter. Once I this feature has been tested on a wider variety of MOL2 files, I'll post another version update.

bugfix: stop deleting the "system.in" file

This is a very minor update, but I thought it was important. Some people edit that file, and their work was getting erased.
Thanks again to Jordan Dialpuri for catching this bug.

renamed the "system.in" file to "run.in.EXAMPLE"

I also removed the "moltemplate_manual.pdf" file because it was causing the .git directory to grow in size rapidly as I made frequent changes to this large binary file.

Thanks to Jordan Dialpuri for the suggestion!

fixed a bug when using "@{atom:NAME}" syntax

fixed a bug that occurs when @{atom:NAME} syntax is used inside pair_coeff commands. (The explicit use of {} brackets was sometimes failing.)

Thanks to Otello Roscioni (MaterialX, LTD, https://materialx.co.uk) for reporting the bug!

updated the LOPLS force field file ("loplsaa.lt")

The new version of "loplsaa.lt" includes much more clear atom type descriptions (for the atoms described in the 2015 LOPLS paper, at least).

I also removed some (hopefully) unnecessary and confusing atom types (such as 81LL, 118L, 718LL).

The moltemplate.sh program has not been modified, but I updated the version info anyway. (I had to change the version number of the project in order to be able to upload a new version to pypi.)

Please let me know if I have made any mistakes in the process.
-Andrew

speed improvement when using wildcards or DREIDING

The changes in this commit can significantly increase the speed of moltemplate.sh when the user's LT files contain wildcard characters ('*' characters) in any of the LAMMPS coeffs or coeff commands. In particular, simulations using the DREIDING force field ("dreiding.lt", which uses wildcard characters frequently) should be faster to prepare. Some coarse-grained force fields also make frequent use of wildcard characters.

fixed serious bug in "bond type" count in data files

Fixed a serious bug (the number of bond types in the generated data files are incorrect). LAMMPS would crash when run using data files generated by moltemplate. This bug was caused by a typo introduced in version v2.20.0 on 2022-1-11.

fixed a bug parsing blank lines with whitespace

Fixed a bug introduced in the previous version (v2.20.0) causing moltemplate to misinterpret blank lines containing nothing but white space (spaces or tabs). Thanks to github user conandolley103 (Tue Le) for reporting this bug!

improved ltemplify.py (whitespace) compatibility and improved dump2data.py and raw2data.py

1. Improved compatibility with ltemplify.py. This required adding better support in moltemplate.sh for atom types and names containing whitespace (which ltemplify.py frequently generates).
2. Improved performance and behavior of dump2data.py and raw2data.py.

This update might break some people's LT files.