# Cheminformatic Utils Web Services ChEMBL Chemoinformatic Utils (aka **'ChEMBL Beaker'**) is a set of useful utility web service tools that provide RESTful access to commonly used cheminformatic methods. Many of them utilise the [RDKit cheminformatics library](http://www.rdkit.org/). The ChEMBL Beaker tools can be tested interactively at . They include: * Chemical structure standardisation tools (e.g. check, getParent, standardize; see [Bento et al.](https://github.com/chembl/ChEMBL_Structure_Pipeline)) * Physico-chemical property calculation (e.g. molecular weight, heavy atom count, number of hydrogen bond donors / acceptors, number of aromatic rings, etc) * Chemical structure format converters (e.g. molfile to SMILES, InChI to InChIKey, etc) * Other tools for structural alerts, molecule similarity and molecule display\\ ## Chemical Structure Standardisation | check | Checks a molecule for issues using ChEMBL Structure Pipeline functionality. The input (CTAB) is either a single molfile or an SDF file. | | ----------- | --------------------------------------------------------------------------------------------------------------------------------------- | | exclude | Checks if the structure will be excluded from ChEMBL. The input (CTAB) is either a single molfile or an SDF file. | | getParent | Removes salt/solvates using ChEMBL Structure Pipeline functionality. The input (CTAB) is either a single molfile or an SDF file. | | standardize | Standardises a molecule using ChEMBL Structure Pipeline functionality. The input (CTAB) is either single a molfile or an SDF file. | \\ ## Physico-chemical property calculation | chemblDescriptors | Returns selected physico-chemical descriptors that are available in ChEMBL (except the pKa related ones). The input (CTAB) is either a single molfile or an SDF file. | | ----------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | descriptors | Returns all physico-chemical descriptors calculated by RDKit for a compound. The input (CTAB) is either a single molfile or an SDF file. | \\ ## Chemical structure format converters | canonicalizeSmiles | Converts SMILES to canonical SMILES. This method accepts single or multiple SMILES or \*.smi file. | | ------------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ctab22D | Generates 2D coordinates for a molecule using Schrodinger's coordgen. The input (CTAB) is either a single molfile or an SDF file. | | ctab2inchi | Converts CTAB to an InChI. The input (CTAB) is either a single molfile or an SDF file. | | ctab2inchikey | Converts CTAB to an InChIKey. The input (CTAB) is either a single molfile or an SDF file. | | ctab2smarts | Converts CTAB to SMARTS format. The input (CTAB) is either a single molfile or an SDF file. | | ctab2smiles | Converts CTAB to SMILES format. The input (CTAB) is either a single molfile or an SDF file. | | ctab2svg | Converts CTAB to a SVG vector graphic. The input (CTAB) is either a single molfile or an SDF file. Size is the optional size of image in pixels (default value is 300 px). | | inchi2ctab | Converts InChI to CTAB. This method accepts one or multiple InChIs. | | inchi2inchikey | Converts InChIs to InChIKeys. This method accepts one or multiple InChis. | | inchi2svg | Converts InChI to a SVG vector graphic. This method accepts single or multiple InChIs. Size is the optional size of image in pixels (default value is 300 px). | | molExport | Implements Marvin 4 js MolConvert web service. Converts a compound from one format to another, including Marvin's \*.mrv. | | smarts2Ctab | Converts SMARTS to CTAB. This method accepts single or multiple SMARTS. | | smiles22D | Generate 2D coordinates from SMILES using Schrodinger's coordgen. The input (CTAB) is either a single molfile or an SDF file. | | smiles2ctab | Converts SMILES to CTAB. This method accepts single or multiple SMILES or an \*.smi file. | | smiles2inchi | Converts SMILES to InChI. This method accepts single or multiple SMILES or an \*.smi file. | | smiles2inchikey | Converts SMILES to InChIKey. This method accepts single or multiple SMILES or an \*.smi file. | | smiles2svg | Converts SMILES to a SVG vector graphic. This method accepts single or multiple SMILES or an \*.smi file. Size is the optional size of image in pixels (default value is 300 px). | \\ ## Substructure & similarity & molecule display | cipStereoInfo | Implements Marvin 4 js Stereo Info web service. Marks possible stereocenters, R/S chirality for atoms and cistrans bonds. | | -------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | clean | Implements Marvin 4 js clean2D/3D web service. Recomputes 2D/3D coordinates of given compound. The compound is in Marvin's \*.mrv format. Dim is an optional parameter specifying if 2D or 3D coordinates should be computed. | | highlightCtabFragmentSvg | Converts SMILES to a SVG vector graphic with a highlighted fragment described as SMARTS. SMARTS describes the fragment to be highlighted. The input (CTAB) is either a single molfile or an SDF file. Size is the optional size of image in pixels (default value is 300 px). | | highlightSmilesFragmentSvg | Converts SMILES to a SVG vector graphic with a highlighted fragment described as SMARTS. This method accepts SMARTS and single or multiple SMILES or an \*.smi file. Size is the optional size of image in pixels (default value is 300 px). | | hydrogenize | Implements Marvin 4 js Hydrogenize web service. Adds or removes hydrogen atoms. The compound is in Marvin's \*.mrv format. Dim is an optional parameter specifying if 2D or 3D coordinates should be computed | | Is3D | Checks if a molecule has any 3D coordinates. The input (CTAB) is either a single molfile or an SDF file. | | mcs | Returns the Maximum Common Substructure of a set of compounds. This method accepts compounds in SDF format. | | removeHs | Removes any hydrogens from the graph of a molecule. The input (CTAB) is either a single molfile or an SDF file. | | sdf2SimilarityMapSvg | Generates a similarity map, which is a way to visualise the atomic contributions to the similarity between molecules. This method requires an SDF file containing exactly two molecules. | | smiles2SimilarityMapSvg | Generates a similarity map, which is a way to visualise the atomic contributions to the similarity between molecules. This method requires exactly two SMILES strings | | structuralAlerts | Get structural alerts for a compound. The input (CTAB) is either a single molfile or an SDF file. | ## ChEMBL Beaker Status | status | Provides information about the status of Beaker web services. A response code of 200 means that it is up and running. Returns the ChEMBL Beaker version information. | | ------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |