The following list gives an overview of the most important S4 classes, methods and functions available in the ChemmineR package. The help documents of the package provide much more detailed information on each utility. The standard R help documents for these utilities can be accessed with this syntax: ?function\_name (e.g. ?cid) and ?class\_name-class (e.g. ?"SDFset-class").

Molecular Structure Data

Classes

  • SDFstr: intermediate string class to facilitate SD file import; not important for end user

  • SDF: container for single molecule imported from an SD file

  • SDFset: container for many SDF objects; most important structure container for end user

  • SMI: container for a single SMILES string

  • SMIset: container for many SMILES strings

Functions/Methods (mainly for SDFset container, SMIset should be coerced with smiles2sd to SDFset)

  • Accessor methods for SDF/SDFset

    • Object slots: cid, header, atomblock, bondblock, datablock (sdfid, datablocktag)

    • Summary of SDFset: view

    • Matrix conversion of data block: datablock2ma, splitNumChar

    • String search in SDFset: grepSDFset

  • Coerce one class to another

    • Standard syntax as(..., "...") works in most cases. For details see R help with ?"SDFset-class".

  • Utilities

    • Atom frequencies: atomcountMA, atomcount

    • Molecular weight: MW

    • Molecular formula: MF

    • …

  • Compound structure depictions

    • R graphics device: plot, plotStruc

    • Online: cmp.visualize

Structure Descriptor Data

Classes

  • AP: container for atom pair descriptors of a single molecule

  • APset: container for many AP objects; most important structure descriptor container for end user

  • FP: container for fingerprint of a single molecule

  • FPset: container for fingerprints of many molecules, most important structure descriptor container for end user

Functions/Methods

  • Create AP/APset instances

    • From SDFset: sdf2ap

    • From SD file: cmp.parse

    • Summary of AP/APset: view, db.explain

  • Accessor methods for AP/APset

    • Object slots: ap, cid

  • Coerce one class to another

    • Standard syntax as(..., "...") works in most cases. For details see R help with ?"APset-class".

  • Structure Similarity comparisons and Searching

    • Compute pairwise similarities : cmp.similarity, fpSim

    • Search APset database: cmp.search, fpSim

  • AP-based Structure Similarity Clustering

    • Single-linkage binning clustering: cmp.cluster

    • Visualize clustering result with MDS: cluster.visualize

    • Size distribution of clusters: cluster.sizestat

  • Folding

    • Fold a descriptor with fold
    • Query the number of times a descriptor has been folded: foldCount
    • Query the number of bits in a descriptor: numBits
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