Formats¶
The CLI reads each molecule template with the molrs reader of its format
(molrs::io::read_pdb, read_xyz, …) and writes the final packed structure
with the molrs writer of the output's format to the path named by the
script's output keyword. molrs names every door after its format and picks
none for the caller, so the choice below — filetype, else the file name —
is the .inp grammar's, held once in molpack::script::StructureFormat;
reading and writing each format is molrs's.
The output format is inferred from the output file name. Input formats can be
inferred from structure-file names or set globally with filetype, which
accepts a format name or any of its extensions.
| Format | Read | Write | File names / filetype |
|---|---|---|---|
| PDB | Yes | Yes | .pdb, .ent; pdb |
| XYZ / extended XYZ | Yes | Yes | .xyz, .extxyz; xyz |
| SDF / MOL | Yes | No | .sdf, .mol; sdf |
| MOL2 | Yes | Yes | .mol2; mol2 |
| GROMACS GRO | Yes | Yes | .gro; gro |
| CIF | Yes | Yes | .cif; cif |
| VASP POSCAR | Yes | Yes | .poscar, .vasp, POSCAR*, CONTCAR*; poscar |
| XSF | Yes | Yes | .xsf; xsf |
| Gaussian cube | Yes | Yes | .cube, .cub; cube |
| AMBER inpcrd | Yes | No | .inpcrd, .rst7, .restrt, .crd; inpcrd |
| LAMMPS data | Yes | Yes | .data, .lmp; lammps_data |
| LAMMPS dump | Yes (first snapshot) | Yes | .lammpstrj, .dump; lammps_dump |
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.