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]