CHEMDRAW NUMBER ATOMS MANUAL
References are included to locate the sections in the manual where the utility and usage of these functions is described. The following lists the functions and methods that make use of OpenBabel. ChemmineR will automatically detect the availability of ChemmineOB and make use of the additional utilities.
CHEMDRAW NUMBER ATOMS SOFTWARE
These utilities can be accessed by installing the ChemmineOB package and the OpenBabel software itself. Sdf.visualize(sdfset) # Compound viewing in web browserĬhemmineR integrates now a subset of cheminformatics functionalities implemented in the OpenBabel C++ library (O’Boyle, Morley, and Hutchison 2008 Cao et al. Plot molecule structure of one or many SDFs: plot(sdfset, print=FALSE) # Plots structures to R graphics device grepSDFset("650001", sdfset, field="datablock", mode="index") # 1 1 1 1 1 1 1 1 1Įxport SDFset to SD file: write.SDF(sdfset, file="sub.sdf", sig=TRUE)
String searching in SDFset: grepSDFset("650001", sdfset, field="datablock", mode="subset") # Returns summary view of matches. # 650002 "C18H23N5O3" "CN1C2=C(C(=O)NC1=O)N(C(=N2)NCCCO)CCCC3=CC=CC=C3"Ĭompute atom frequency matrix, molecular weight and formula: propma <- ame(MF=MF(sdfset), MW=MW(sdfset), atomcountMA(sdfset)) # 650002 650002 1 numchar] # Slice of character matrix # PUBCHEM_MOLECULAR_FORMULA PUBCHEM_OPENEYE_CAN_SMILES Numchar] # Slice of numeric matrix # PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED Numchar <- splitNumChar(blockmatrix=blockmatrix) # Splits to numeric and character matrix # 4 3 25 1 0 0 0 0 datablock(sdfset) # Not printed here datablock(sdfset]) # PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED PUBCHEM_CACTVS_COMPLEXITYĪssigning compound IDs and keeping them unique: cid(sdfset) # Returns IDs from SDFset object # "CMP1" "CMP2" "CMP3" "CMP4" sdfid(sdfset) # Returns IDs from SD file header block # "650001" "650002" "650003" "650004" unique_ids <- makeUnique(sdfid(sdfset)) # "No duplicates detected!" cid(sdfset) <- unique_idsĬonverting the data blocks in an SDFset to a matrix: blockmatrix <- datablock2ma(datablocklist=datablock(sdfset)) # Converts data block to matrix Miscellaneous accessor methods for SDFset container: header(sdfset) # Not printed here header(sdfset]) # Molecule_Name Source # "7" "." view(sdfset) # Returns summarized content of many SDFs, not printed hereĪs(sdfset, "list") # Returns complete content of many SDFs, not printed hereĪn SDFset is created during the import of an SD file: sdfset <- read.SDFset("") # PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED PUBCHEM_CACTVS_COMPLEXITY Copy and paste of the commands into the R console will demonstrate their utilities.Ĭreate Instances of SDFset class: data(sdfsample)
CHEMDRAW NUMBER ATOMS CODE
The following code gives an overview of the most important functionalities provided by ChemmineR. Mismatch tolerant maximum common substructure (MCS) search algorithmįast and memory efficient fingerprint search support using atom pair or PubChem fingerprints Streaming functionality for processing millions of molecules on a laptop Integration of a subset of OpenBabel functionalities via new ChemmineOB add-on package (Cao et al. Improved SMILES support via new SMIset object class and SMILES import/export functions Since then many additional utilities and add-on packages have been added to the environment (Figure 2) and many more are under development for future releases (Backman, Cao, and Girke 2011 Wang et al. The first version of this package was published in Cao et al. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. In addition, ChemmineR offers visualization functions for compound clustering results and chemical structures. Figure: ChemmineR environment with its add-on packages and selected functionalities