Returns the list of unique atom types names. Returns the number of atom types as determined from the type property. bondorder bond order parameter (default: 1) bondtype bond type name (default: unknown) This also results in performance differences in commands operating on the two groups. Bond information is treated and stored differently from angles, dihedrals, and impropers in VMD, since bond information is used for visualization and the others not. The following flags can be added to subsequently documented operations on bonds. sel atom selection function or text (default: 'all') For operations on bonds, angles, dihedrals, and impropers selections will be applied in such a way that only topological data where all atoms are contained in the selection. The -sel transparently handles both, previously defined selection functions or selection texts, as arguments. They will select the molecule to which the operation should be applied to and also the set of atoms. The following flags can be passed on to all subsequent topo commands. All command lines start with the topo keyword and then take a subcommand name to determine the actual functionality that is requested. This is modeled after the example of the internal mol or molinfo commands, or the pbc command from the PBCTools package to provide a somewhat consistent interface to the functionality. This is the middleware part of the package that provides abstract operations on top of the low-level API.

more powerful and easy to use script commands that make combine multiple low lever commands in a way to solve common tasks conveniently and efficiently.įinally topotools also contains some utilities and applications for more complex operations like combining multiple molecules (=different files) or multiple selections into one new molecule, or building larger systems by replicating a given unitcell. The topotools packages is supposed to provide a middleware, i.e.

The underlying Tcl script API in VMD itself had been designed to be minimalistic, since most operations are not computationally demanding and could be programmed with scripting. Of course write support is also possible. This is especially useful for file formats, where additional input from the user is required, for example reading LAMMPS format 'data' (=topology) files, where the 'style' of the Atoms section cannot be deduced from the data. In combination with the new command mol new atoms it is now also possible to do many operations directly that previously required writing and manipulating temporary files and reading them back into VMD, or even write complete molecule or simulation data readers in Tcl script. The focus lies hereby on being able to perform many operations manually or scripted and thus being less focused on and optimized for biomolecules like psfgen.

This now allows to do a large variety of modifications to topology data or even building topologies from scratch. not only bonds, but also angle, dihedral, and improper definitions as well as their force field type labels (if available). Starting with VMD version 1.8.7 it is now possible to store the complete topology information, i.e.

Vmd topotools