Supported file formats

sire supports reading and writing to many common molecular file formats. You can print the list of supported formats using

>>> print(sr.supported_formats())

## Parser dcd ##
Supports files: DCD
DCD coordinate/velocity binary trajectory files based on charmm / namd / x-plor format.
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## Parser gro87 ##
Supports files: gro, g87
Gromacs Gro87 structure format files.
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## Parser grotop ##
Supports files: top, grotop, gtop
Gromacs Topology format files.
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## Parser mol2 ##
Supports files: mol2
Sybyl Mol2 format files.
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## Parser pdb ##
Supports files: pdb
Protein Data Bank (PDB) format files.
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## Parser pdbx ##
Supports files: pdbx, cif
Protein Data Bank PDBx/mmCIF format files.
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## Parser prm7 ##
Supports files: prm7, prm, top7, top, prmtop7, prmtop
Amber topology/parameter format files supported from Amber 7 upwards.
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## Parser psf ##
Supports files: psf
Charmm PSF format files.
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## Parser rst ##
Supports files: rst, crd, trj, traj
Amber coordinate/velocity binary (netcdf) restart/trajectory files supported since Amber 9, now default since Amber 16.
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## Parser rst7 ##
Supports files: rst7, rst, crd7, crd
Amber coordinate/velocity text (ascii) restart files supported from Amber 7 upwards.
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## Parser sdf ##
Supports files: sdf, mol
Structure Data File (SDF) format files.
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## Parser traj ##
Supports files: traj, trj, crd
Amber trajectory (ascii) coordinate or velocity files supported from Amber 7 upwards.
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## Parser trr ##
Supports files: trr
Gromacs TRR (XDR file) coordinate / velocity / force trajectory file
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## Parser xtc ##
Supports files: xtc
Gromacs XTC (XDR file) compressed coordinate trajectory file
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Symmetric Input / Output

One of our design principles is that molecular file input and output is symmetrical. This means that sire can read in and write out the same amount of information from a file (i.e. it can always read what it writes).

Another design principle is that information should not be lost. As much as possible, sire will load and preserve all molecular-level information it can read from a molecular file.