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and [first|last|step] options for readvarxyz
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This PR adds read/write support for LAMMPS molecule templates to topotools.
readlammpsmol:
Read in atom coordinates, properties, bond, angle, dihedral and other related topology info from a molecule template file, i.e. a file suitable for the molecule command. This can be used to check a molecule template for its validity (e.g. for fixes that utilize molecule templates), or for manipulations from within VMD. This subcommand creates a new molecule in VMD and returns its molecule id or -1 in case of failure. The -sel parameter is currently ignored.
writelammpsmol:
Write out atom coordinates, properties, bond, angle, dihedral and other related topology info stored inside VMD to a molecule template file, i.e. a file suitable for the molecule command. Using the optional 'typelabels' flag will trigger writing a molecule template file with typelabel support requiring LAMMPS version 15Sep2022 or later. By default a traditional molecule template with numerical types will be written. This way VMD can be used to build LAMMPS input with Tcl scripting and convert existing inputs from other MD codes to be used in LAMMPS. Only data that is present will be written.
This PR also adds [first|last|step] options for readvarxyz, similar to other topotools commands.