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. The ChEMBL Beaker tools can be tested interactively at https://www.ebi.ac.uk/chembl/api/utils/docs. They include:

• Chemical structure standardisation tools (e.g. check, getParent, standardize; see Bento et al.)

• 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.