Formats¶
The CLI reads molecule templates through the io feature and writes the final
packed structure to the path named by the script's output keyword.
The output format is inferred from the output file extension. Input formats can
be inferred from structure-file extensions or set globally with filetype.
| Format | Read | Write | Extension or filetype |
|---|---|---|---|
| PDB | Yes | Yes | .pdb, pdb |
| XYZ | Yes | Yes | .xyz, xyz |
| SDF / MOL | Yes | No | .sdf, .mol, sdf |
| LAMMPS dump | Yes | Yes | .lammpstrj, lammps_dump |
| LAMMPS data | Yes | No | .data, lammps_data |
Example¶
filetype pdb
output packed.xyz
structure water.pdb
number 100
inside box 0. 0. 0. 30. 30. 30.
end structure
The input template is read as PDB because of filetype pdb; the output is
written as XYZ because the output path ends with .xyz.