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Cheminformatics

The cdk manager

Basic cheminformatics in Bioclipse is mainly handled by the Chemistry Development Kit (CDK, [1,2,3]) and for this there is the cdk manager.

The cdk manager is one with many features. One is to validate CAS registry numbers, identifiers used by the Chemical Abstract Services:

cdk.isValidCAS("50-00-0")

But let's go to the more interesting functionality around chemical graphs. For example, let's see how we can create molecular structures from a SMILES string:

Script code/FromSMILES.groovy

mol = cdk.fromSMILES("COC")

Normally, structure diagrams are generated without explicit hydrogens. But we can easily add them:

cdk.addExplicitHydrogens(mol)

We can then calculate a number of properties, including the molecular mass\index{molecular mass}, total formal charge, and molecular formula:

cdk.calculateMass(mol)
cdk.totalFormalCharge(mol)
cdk.molecularFormula(mol)

Additionally, we can also inspect some of in the information present in the model:

cdk.has2d(mol)
cdk.has3d(mol)
cdk.isConnected(mol)

The cdk manager is also central to file support. Before we load it, we may want to just check the file format:

cdk.determineFormat(
  "/ACS Drug Disclosures/AZD5423.cml"
)

However, this information is not needed when loading files:

mol = cdk.loadMolecule(
  "/ACS Drug Disclosures/AZD5423.cml"
)

Saving is quite similar, and there are two methods for the two main formats:

cdk.saveCML(mol, "/Test/mol.cml")
cdk.saveMDLMolfile(mol, "/Test/mol.mol")

The cdx manager

The cdx manager is also based on the CDK and exposes functionality more oriented at CDK developers. For example, we can create a String representation of the full data model for debugging purposes:

cdx.debug(mol)

Or we can see the details of the differences between two data models:

cdx.diff(
  cdk.fromSMILES("CC"),
  cdk.fromSMILES("CCC")
)

And we can list the exact atom types for the atoms in a molecule:

Script code/PerceiveCDKAtomTypes.groovy

cdx.perceiveCDKAtomTypes(mol)

Which lists for ethanol:

1:C.sp3
2:C.sp3
3:O.sp3

The inchi manager

The inchi manager makes functionality from the InChI standard available [4,5]. The InChI library is not available as a Java library, but is included as a binary for a selection of platforms and operating systems. This means that we cannot assume the InChI functionality is always available in Bioclipse. Furthermore, we need to load the library:

Script code/LoadInChI.groovy

inchi.load()
inchi.isLoaded()

But when that has succeeded, we can start minting InChIs:

Script code/InChIGenerate.groovy

anInChI = inchi.generate(
  opsin.parseIUPACName("methane")
)

Which returns:

InChI=1S/CH4/h1H4

The returned value is a class called InChI and we can get both the full InChI as well as the InChIKey from it:

Script code/InChIKeyGenerate.groovy

fullInChI = anInChI.getValue()
InChIKey = anInChI.getKey()

The opsin manager

The opsin manager makes functionality from the OPSIN available [6]: convert IUPAC names to chemical structures.

Script code/ParseIUPACName.py

mol = opsin.parseIUPACName(
  "Ethyl [(1R,3aR,4aR,6R,8aR,9S,9aS)-9-" +
  "{(E)-2-[5-(3-fluorophenyl)-2-pyridinyl]vinyl}-" +
  "1-methyl-3-oxododecahydronaphtho[2,3-c]furan-" +
  "6-yl]carbamate"
)

References

  1. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Luttmann E, et al. The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. JCICS. 2003 Feb 11;43(2):493–500. doi:10.1021/CI025584Y (Scholia)
  2. Steinbeck C, Hoppe C, Hoppe C, Kuhn S, Floris M, Guha R, et al. Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Curr Pharm Des [Internet]. 2006 Jun 1;12(17):2111–20. Available from: https://cdk.github.io/cdk-paper-2/ doi:10.2174/138161206777585274 (Scholia)
  3. Willighagen E, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform. 2017 Jun 6;9(1). doi:10.1186/S13321-017-0220-4 (Scholia)
  4. Heller SR, McNaught A, Stein S, Tchekhovskoi D, Pletnev I. InChI - the worldwide chemical structure identifier standard. J Cheminform. 2013;5(1):7. doi:10.1186/1758-2946-5-7 (Scholia)
  5. Spjuth O, Berg A, Adams SE, Willighagen E. Applications of the InChI in cheminformatics with the CDK and Bioclipse. J Cheminform. 2013;5(1):14. doi:10.1186/1758-2946-5-14 (Scholia)
  6. Lowe DM, Lowe DM, Corbett PT, Murray-Rust P, Glen RC. Chemical Name to Structure: OPSIN, an Open Source Solution. JCIM. 2011 Mar 28;51(3):739–53. doi:10.1021/CI100384D (Scholia)