• conda 安装
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conda install -c conda-forge openbabel

obabel
# Open Babel 3.1.0 -- Nov  2 2021 -- 08:43:45
  • 查看支持的格式
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obabel -L
# charges
# descriptors
# fingerprints
# forcefields
# formats
# loaders
# ops

obabel -L formats | head
# acesin -- ACES input format [Write-only]
# acesout -- ACES output format [Read-only]
# acr -- ACR format [Read-only]
# adf -- ADF cartesian input format [Write-only]
# adfband -- ADF Band output format [Read-only]
# adfdftb -- ADF DFTB output format [Read-only]
# adfout -- ADF output format [Read-only]
# alc -- Alchemy format
# aoforce -- Turbomole AOFORCE output format [Read-only]

  • 格式转换

    例如将mol2转为pdbqt格式

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ls *mol2
# MOL000006.mol2 MOL000098.mol2

#单个文件格式转换
obabel -imol2 MOL000006.mol2 -opdbqt -O MOL000006.pdbqt

#批量转换
ls *mol2 | while read id; do obabel -imol2 $id -opdbqt -O ${id%.*}.pdbqt; done

obabel -L formats: All supported format

abinit – ABINIT Output Format [Read-only] acesin – ACES input format [Write-only] acesout – ACES output format [Read-only] acr – ACR format [Read-only] adf – ADF cartesian input format [Write-only] adfband – ADF Band output format [Read-only] adfdftb – ADF DFTB output format [Read-only] adfout – ADF output format [Read-only] alc – Alchemy format aoforce – Turbomole AOFORCE output format [Read-only] arc – Accelrys/MSI Biosym/Insight II CAR format [Read-only] ascii – ASCII format [Write-only] axsf – XCrySDen Structure Format [Read-only] bgf – MSI BGF format box – Dock 3.5 Box format bs – Ball and Stick format c09out – Crystal 09 output format [Read-only] c3d1 – Chem3D Cartesian 1 format c3d2 – Chem3D Cartesian 2 format cac – CAChe MolStruct format [Write-only] caccrt – Cacao Cartesian format cache – CAChe MolStruct format [Write-only] cacint – Cacao Internal format [Write-only] can – Canonical SMILES format car – Accelrys/MSI Biosym/Insight II CAR format [Read-only] castep – CASTEP format [Read-only] ccc – CCC format [Read-only] cdjson – ChemDoodle JSON cdx – ChemDraw binary format [Read-only] cdxml – ChemDraw CDXML format cht – Chemtool format [Write-only] cif – Crystallographic Information File ck – ChemKin format cml – Chemical Markup Language cmlr – CML Reaction format cof – Culgi object file format com – Gaussian Input [Write-only] confabreport – Confab report format [Write-only] CONFIG – DL-POLY CONFIG CONTCAR – VASP format CONTFF – MDFF format copy – Copy raw text [Write-only] crk2d – Chemical Resource Kit diagram(2D) 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 cub – Gaussian cube format cube – Gaussian cube format dallog – DALTON output format [Read-only] dalmol – DALTON input format dat – Generic Output file format [Read-only] dmol – DMol3 coordinates format dx – OpenDX cube format for APBS ent – Protein Data Bank format exyz – Extended XYZ cartesian coordinates format fa – FASTA format fasta – FASTA format fch – Gaussian formatted checkpoint file format [Read-only] fchk – Gaussian formatted checkpoint file format [Read-only] fck – Gaussian formatted checkpoint file format [Read-only] feat – Feature format fh – Fenske-Hall Z-Matrix format [Write-only] fhiaims – FHIaims XYZ format fix – SMILES FIX format [Write-only] fps – FPS text fingerprint format (Dalke) [Write-only] fpt – Fingerprint format [Write-only] fract – Free Form Fractional format fs – Fastsearch format fsa – FASTA format g03 – Gaussian Output [Read-only] g09 – Gaussian Output [Read-only] g16 – Gaussian Output [Read-only] g92 – Gaussian Output [Read-only] g94 – Gaussian Output [Read-only] g98 – Gaussian Output [Read-only] gal – Gaussian Output [Read-only] gam – GAMESS Output [Read-only] gamess – GAMESS Output [Read-only] gamin – GAMESS Input gamout – GAMESS Output [Read-only] gau – Gaussian Input [Write-only] gjc – Gaussian Input [Write-only] gjf – Gaussian Input [Write-only] got – GULP format [Read-only] gpr – Ghemical format gr96 – GROMOS96 format [Write-only] gro – GRO format gukin – GAMESS-UK Input gukout – GAMESS-UK Output gzmat – Gaussian Z-Matrix Input hin – HyperChem HIN format HISTORY – DL-POLY HISTORY [Read-only] inchi – InChI format inchikey – InChIKey [Write-only] inp – GAMESS Input ins – ShelX format [Read-only] jin – Jaguar input format jout – Jaguar output format [Read-only] k – Compare molecules using InChI [Write-only] lmpdat – The LAMMPS data format [Write-only] log – Generic Output file format [Read-only] lpmd – LPMD format mcdl – MCDL format mcif – Macromolecular Crystallographic Info MDFF – MDFF format mdl – MDL MOL format ml2 – Sybyl Mol2 format mmcif – Macromolecular Crystallographic Info mmd – MacroModel format mmod – MacroModel format mna – Multilevel Neighborhoods of Atoms (MNA) [Write-only] mol – MDL MOL format mol2 – Sybyl Mol2 format mold – Molden format molden – Molden format molf – Molden format molreport – Open Babel molecule report [Write-only] moo – MOPAC Output format [Read-only] mop – MOPAC Cartesian format mopcrt – MOPAC Cartesian format mopin – MOPAC Internal mopout – MOPAC Output format [Read-only] mp – Molpro input format [Write-only] mpc – MOPAC Cartesian format mpd – MolPrint2D format [Write-only] mpo – Molpro output format [Read-only] mpqc – MPQC output format [Read-only] mpqcin – MPQC simplified input format [Write-only] mrv – Chemical Markup Language msi – Accelrys/MSI Cerius II MSI format [Read-only] msms – M.F. Sanner’s MSMS input format [Write-only] nul – Outputs nothing [Write-only] nw – NWChem input format [Write-only] nwo – NWChem output format [Read-only] orca – ORCA output format [Read-only] orcainp – ORCA input format [Write-only] out – Generic Output file format [Read-only] outmol – DMol3 coordinates format output – Generic Output file format [Read-only] paint – Painter format [Write-only] pc – PubChem format [Read-only] pcjson – PubChem JSON pcm – PCModel Format pdb – Protein Data Bank format pdbqt – AutoDock PDBQT format png – PNG 2D depiction pointcloud – Point cloud on VDW surface [Write-only] pos – POS cartesian coordinates format [Read-only] POSCAR – VASP format POSFF – MDFF format pov – POV-Ray input format [Write-only] pqr – PQR format pqs – Parallel Quantum Solutions format prep – Amber Prep format [Read-only] pwscf – PWscf 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] rinchi – RInChI [Write-only] rsmi – Reaction SMILES format rxn – MDL RXN format sd – MDL MOL format sdf – MDL MOL format siesta – SIESTA format [Read-only] smi – SMILES format smiles – SMILES format smy – SMILES format using Smiley parser [Read-only] stl – STL 3D-printing format [Write-only] svg – SVG 2D depiction [Write-only] sy2 – Sybyl Mol2 format t41 – ADF TAPE41 format [Read-only] tdd – Thermo format text – Read and write raw text therm – Thermo format tmol – TurboMole Coordinate format txt – Title format txyz – Tinker XYZ format unixyz – UniChem XYZ format VASP – VASP format vmol – ViewMol format wln – Wiswesser Line Notation [Read-only] xed – XED format [Write-only] xml – General XML format [Read-only] xsf – XCrySDen Structure Format [Read-only] xtc – XTC format [Read-only] xyz – XYZ cartesian coordinates format yob – YASARA.org YOB format zin – ZINDO input format [Write-only]

obabel -L fingerprints

ECFP0 Extended-Connectivity Fingerprints (ECFPs) ECFP10 Extended-Connectivity Fingerprints (ECFPs) ECFP2 Extended-Connectivity Fingerprints (ECFPs) ECFP4 Extended-Connectivity Fingerprints (ECFPs) ECFP6 Extended-Connectivity Fingerprints (ECFPs) ECFP8 Extended-Connectivity Fingerprints (ECFPs) FP2 Indexes linear fragments up to 7 atoms. FP3 SMARTS patterns specified in the file patterns.txt FP4 SMARTS patterns specified in the file SMARTS_InteLigand.txt MACCS SMARTS patterns specified in the file MACCS.txt