OEChem Examples¶
The following table lists the currently available OEChem TK examples:
Molecule processing¶
| Program | Description |
|---|---|
| Convert | converting molecule files |
| CatMols | concatenating molecules |
| Parts2Mols | splitting multicomponent molecules |
| MolExtract | extracting molecules by title |
| UniqMol | writing out unique molecules (canonical SMILES) |
| UniqInchi | writing out unique molecules (InChI) |
| RandomizeAtoms | randomizing atoms of molecules |
| CanSmi | generating canonical smiles |
| SizeFilter | filtering molecules by weight or heavy atom count |
| StripSalts | stripping salt |
| RingSubset | extracting rings |
| ExtractScaffold | extracting molecule scaffolds |
| RandomSample | extracting random molecule subset |
| MolChunk | split molecule file into N chunks or chunks of size N |
Molecule alignment¶
| Program | Description |
|---|---|
| MCS3DAlign | aligning molecules by maximum common substructure |
| CliqueAlign | aligning molecules by clique match |
| SMARTSAlign | aligning molecules by SMARTS match |
| RMSD | aligning multi-conformer molecules |
SDF specific¶
| Program | Description |
|---|---|
| SDFModProps | modifying SD tags |
| SDF2CSV | exporting SD data to a csv file |
| CSV2SDF | adding csv data as SD tags |
| sdfrename | renaming molecules by SD field |
| sdfilter | filter molecules by SD data |
Molecule information examples¶
| Program | Description |
|---|---|
| MolCount | counting molecules |
| GetTitles | get molecule titles |
| MolStats | printing simple molecule information |
| RotorCount | printing rotor count distribution |
| MinPath | finding minimum path in a molecule |
| PrintAtomNames | print molecule atom names |
2D coordinate generation examples¶
| Program | Description |
|---|---|
| ExtractRingTemplates | extracting 2D ring templates |
| CreateRingDict | creating 2D ring dictionary |
| AppendRingDict | appending 2D ring dictionary |
| Generate2D | generating 2D coordinates |
Miscellaneous examples¶
| Program | Description |
|---|---|
| OEChemInfo | printing OEChem and format information |
| Anisou | printing anisotropic B-factors |
| Dots | printing dots |
| Options | defining parameters |
Examples
- Convert molecule files
- Concatenating molecules
- Splitting multicomponent molecules
- Extract molecules by title
- Write out unique molecules (canonical SMILES)
- Write out unique molecules (InChI)
- Randomize atoms of molecules
- Generate canonical smiles
- Filter molecules by weight or heavy atom count
- Strip salts
- Extract rings
- Extract molecule scaffolds
- Extract random molecule subset
- Split molecule file
- Performing a reaction
- Library generation
- Perform substructure searches
- Generate database for fast substructure search
- Perform SMARTS search on substructure database file
- Align molecules by maximum common substructure
- Align molecules by clique match
- Align molecules by SMARTS match
- Align multi-conformer molecules
- Modifying SD tags
- Exporting SD data to a csv file
- Adding csv data as SD tags
- Renaming molecules by SD field
- Filter molecules by SD data
- Print OEChem and file format information
- Counting molecules
- Get molecule titles
- Print simple molecule information
- Print rotor count distribution
- Find minimum path in a molecule
- Print molecule atom names
- Extract 2D ring templates
- Create 2D ring dictionary
- Append 2D ring dictionary
- Generate 2D coordinates with user-defined ring templates
- Print anisotropic B-factors
- Print dots
- Define parameters