The jobs of modelers are filled with tasks that appear trivial but can be surprisingly difficult to carry out in a robust manner. These tasks include, among others, file format conversion, passing SD tag data to Excel spreadsheets, determining RMSD between similar structures, and cleaning up structures pulled from a database. OEChem includes a suite of Python scripts that address Some Common Unfinished Tasks (SCUT). Each of these scripts is useful as is, but can easily be customized to any working environment.

Over 60 simple programs are provided with the OEChem Toolkit, including:

• AdjustCharge - adjusts formal charges on specified atoms
• BitVecTest - manipulates fingerprints, calculates Tanimoto
• Babel - converts data between file formats (SMILES, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, and OEBinary)
• CanSMI - writes canonical SMILES
• Clique - enumerates common substructures
• Flipper - enumerates unspecified stereocenters of SMILES input
• Frag - SMARTS based molecular fragmentation for R-group analysis
• LibGen - generates product library from SMIRKS and reactant list
• MCSS - determines maximum common substructure
• MolCount - counts molecules and conformers
• MolGrep - searches flat files for molecules containing specified substructures
• PDB2Lig - ligand extraction from PDB files
• RMSD - determines minimum RMS distance between two molecules, with proper recognition of automorphism
• SimpleMolCount - reports average number of atoms, bonds and conformers
• Sdf2csv - writes SD tag values into comma separated format suitable for spreadsheets
• TPSA - 2D topology base polar surface area