Molekel supports the following file formats through OpenBabel and custom readers/writers.
Note that the main formats used for testing are pdb, xyz, cube, Gaussian and GAMESS output files.
- alc -- Alchemy format
- bgf -- MSI BGF format
- box -- Dock 3.5 Box format
- bs -- Ball and Stick format
- c3d1 -- Chem3D Cartesian 1 format
- c3d2 -- Chem3D Cartesian 2 format
- caccrt -- Cacao Cartesian format
- cache -- CAChe MolStruct format [Write-only]
- cacint -- Cacao Internal format [Write-only]
- car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
- ccc -- CCC format [Read-only]
- cht -- Chemtool format [Write-only]
- cmlr -- CML Reaction format
- com -- Gaussian 98/03 Cartesian Input [Write-only]
- copy -- Copies raw text [Write-only]
- crk2d -- Chemical Resource Kit 2D diagram format
- crk3d -- Chemical Resource Kit 3D format
- csr -- Accelrys/MSI Quanta CSR format [Write-only]
- cssr -- CSD CSSR format [Write-only]
- ct -- ChemDraw Connection Table format
- cube -- Gaussian cube [Read-only] - Supports orthogonal bases only
- dmol -- DMol3 coordinates format
- ent -- Protein Data Bank format
- feat -- Feature format
- fh -- Fenske-Hall Z-Matrix format [Write-only]
- fix -- SMILES FIX format [Write-only]
- fpt -- Fingerprint format [Write-only]
- fract -- Free Form Fractional format
- fs -- FastSearching Index
- g03 -- Gaussian98/03 Output [Read-only]
- g98 -- Gaussian98/03 Output [Read-only]
- gam -- GAMESS Output [Read-only]
- gamin -- GAMESS Input [Write-only]
- gamout -- GAMESS Output [Read-only]
- gau -- Gaussian 98/03 Cartesian Input [Write-only]
- gpr -- Ghemical format
- gr96 -- GROMOS96 format [Write-only]
- hin -- HyperChem HIN format
- inp -- GAMESS Input [Write-only]
- ns -- ShelX format [Read-only]
- jin -- Jaguar input format [Write-only]
- jout -- Jaguar output format [Read-only]
- mdl -- MDL MOL format
- mmd, mmod -- MacroModel format
- mol -- MDL MOL format
- mol2 -- Sybyl Mol2 format
- molden -- Molden input format [Read-only]
- mopcrt -- MOPAC Cartesian format
- mopout -- MOPAC Output format [Read-only]
- mpd -- Sybyl descriptor format [Write-only]
- mpqc -- MPQC output format [Read-only]
- mpqcin -- MPQC simplified input format [Write-only]
- msms -- Michel Sanner'MSMS input format [Write-only]
- nw -- NWChem input format [Write-only]
- nwo -- NWChem output format [Read-only]
- pc -- PubChem format [Read-only]
- pcm -- PCModel format
- pdb -- Protein Data Bank format
- pov -- POV-Ray input format [Write-only]
- pqs -- Parallel Quantum Solutions format
- prep -- Amber Prep format [Read-only]
- qcin -- Q-Chem input format [Write-only]
- qcout -- Q-Chem output format [Read-only]
- report -- Open Babel report format [Write-only]
- res -- ShelX format [Read-only]
- rxn -- MDL RXN format
- sd, sdf -- MDL MOL format
- smi -- SMILES format
- t41 -- ADF Tape41 ASCII format [Read-only]
- test -- Test format [Write-only]
- tmol -- TurboMole Coordinate format
- txyz -- Tinker MM2 format [Write-only]
- unixyz -- UniChem XYZ format
- vmol -- ViewMol format
- xed -- XED format [Write-only]
- xyz -- XYZ cartesian coordinates format
- yob -- YASARA.org YOB format
- zin -- ZINDO input format [Write-only]
- zmatrix -- Z-Matrix input [Read-only]