Supported formats

List of supported formats

This page list the supported formats in chemfiles, with a link to the format specification. For each format, it is also indicated which kind of data can be read or written with ✓ for ‘yes’ and ✗ for ‘no’. Even if chemfiles can read some type of data from a file, this does not mean that all files of this format will contain this type of data.

The Extension column gives the extension used when trying to detect the format. If your file does not have this extension, you can also use the string in the Format column as a parameter to the chemfiles::Trajectory constructor to manually specify which format to use.

Format	Extension	Read	Write	Memory	Positions	Velocities	UnitCell	Atoms	Bonds	Residues
Amber Restart	.ncrst	✓	✓	✗	✓	✓	✓	✗	✗	✗
Amber NetCDF	.nc	✓	✓	✗	✓	✓	✓	✗	✗	✗
CIF	.cif	✓	✓	✓	✓	✗	✓	✓	✗	✗
CML	.cml	✓	✓	✓	✓	✓	✓	✓	✓	✗
CSSR	.cssr	✓	✓	✓	✓	✗	✓	✓	✓	✗
DCD	.dcd	✓	✓	✗	✓	✗	✓	✗	✗	✗
GRO	.gro	✓	✓	✓	✓	✓	✓	✓	✗	✓
LAMMPS	.lammpstrj	✓	✓	✓	✓	✓	✓	✓	✗	✗
LAMMPS Data	✗	✓	✓	✓	✓	✓	✓	✓	✓	✓
mmCIF	.mmcif	✓	✓	✓	✓	✗	✓	✓	✓	✓
MMTF	.mmtf	✓	✓	✓	✓	✗	✓	✓	✓	✓
MOL2	.mol2	✓	✓	✓	✓	✗	✓	✓	✓	✓
Molden	.molden	✓	✗	✗	✓	✗	✗	✓	✗	✗
PDB	.pdb	✓	✓	✓	✓	✗	✓	✓	✓	✓
PSF	.psf	✓	✗	✗	✗	✗	✗	✓	✓	✗
SDF	.sdf	✓	✓	✓	✓	✗	✗	✓	✓	✗
SMI	.smi	✓	✓	✓	✗	✗	✗	✓	✓	✓
Tinker	.arc	✓	✓	✓	✓	✗	✓	✓	✓	✗
TNG	.tng	✓	✗	✗	✓	✓	✓	✓	✓	✓
TRJ	.trj	✓	✗	✗	✓	✗	✗	✗	✗	✗
TPR	.tpr	✓	✗	✗	✓	✓	✓	✓	✓	✓
TRR	.trr	✓	✓	✗	✓	✓	✓	✗	✗	✗
XTC	.xtc	✓	✓	✗	✓	✗	✓	✗	✗	✗
XYZ	.xyz	✓	✓	✓	✓	✗	✓	✓	✗	✗

• LAMMPS format corresponds to trajectory files written by the LAMMPS dump command.

• LAMMPS Data format corresponds to LAMMPS data files, as read by the LAMMPS read_data command.

Note

in-memory IO

Additionally, some formats support reading and writing directly to memory, without going through a file. At this time, all text based files (excluding those backed by the Molfiles plugin) support both reading and writing directly to memory. The MMTF format supports reading from a memory buffer, but does not support writing. It is also possible to read a compressed GZ or XZ file directly to memory buffer, but writing compressed files is not supported.

Asking for a new format

If you want to use chemfiles with a format which is not yet implemented, you may easily add it by yourself if you know some C++. See the src/formats/XYZ.cpp file for example. The list of planned formats can be found here. If you can not find your favorite format in this list, you can open an issue with a description of the format, or even better a link to the format specification.