{
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  "Package": "ChemmineR",
  "Type": "Package",
  "Title": "Cheminformatics Toolkit for R",
  "Version": "3.65.0",
  "Date": "2026-03-12",
  "Author": "Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke",
  "Maintainer": "Thomas Girke <thomas.girke@ucr.edu>",
  "Description": "ChemmineR is a cheminformatics package for analyzing\ndrug-like small molecule data in R. Its latest version contains\nfunctions for efficient processing of large numbers of\nmolecules, physicochemical/structural property predictions,\nstructural similarity searching, classification and clustering\nof compound libraries with a wide spectrum of algorithms. In\naddition, it offers visualization functions for compound\nclustering results and chemical structures.",
  "License": "Artistic-2.0",
  "biocViews": "Cheminformatics, BiomedicalInformatics, Pharmacogenetics,\nPharmacogenomics, MicrotitrePlateAssay, CellBasedAssays,\nVisualization, Infrastructure, DataImport, Clustering,\nProteomics,Metabolomics",
  "URL": "https://github.com/girke-lab/ChemmineR",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "GNU make",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev librsvg2-dev\nlibuv1-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:33:26 UTC",
  "RemoteUrl": "https://github.com/bioc/ChemmineR",
  "RemoteRef": "HEAD",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "biomedicalinformatics",
    "pharmacogenetics",
    "pharmacogenomics",
    "microtitreplateassay",
    "cellbasedassays",
    "visualization",
    "infrastructure",
    "dataimport",
    "clustering",
    "proteomics",
    "metabolomics",
    "cpp"
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  },
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  "_devurl": "https://github.com/girke-lab/chemminer",
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  "_rbuild": "4.6.0",
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/girke-lab/chemminer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addDescriptorType",
    "addNewFeatures",
    "ap",
    "apset2descdb",
    "as.matrix",
    "atomblock",
    "atomblock<-",
    "atomcount",
    "atomcountMA",
    "atomprop",
    "atomsubset",
    "batchByIndex",
    "bondblock",
    "bondblock<-",
    "bonds",
    "browseJob",
    "bufferLines",
    "bufferResultSet",
    "byCluster",
    "canonicalize",
    "canonicalNumbering",
    "cid",
    "cid<-",
    "cluster.sizestat",
    "cluster.visualize",
    "cmp.cluster",
    "cmp.duplicated",
    "cmp.parse",
    "cmp.parse1",
    "cmp.search",
    "cmp.similarity",
    "coerce",
    "conMA",
    "datablock",
    "datablock<-",
    "datablock2ma",
    "datablocktag",
    "db.explain",
    "db.subset",
    "dbTransaction",
    "desc2fp",
    "draw_sdf",
    "DrugBank",
    "DUD",
    "exactMassOB",
    "findCompounds",
    "findCompoundsByName",
    "fingerprintOB",
    "fold",
    "foldCount",
    "forestSizePriorities",
    "fp2bit",
    "fpSim",
    "fptype",
    "fromNNMatrix",
    "genAPDescriptors",
    "generate3DCoords",
    "genParameters",
    "getAllCompoundIds",
    "getAtomAttr",
    "getBondAttr",
    "getCompoundFeatures",
    "getCompoundNames",
    "getCompounds",
    "getIds",
    "grepSDFset",
    "groups",
    "header",
    "header<-",
    "initDb",
    "jarvisPatrick",
    "jarvisPatrick_c",
    "largestComponent",
    "launchCMTool",
    "listCMTools",
    "listFeatures",
    "loadSdf",
    "loadSmiles",
    "makeUnique",
    "maximallyDissimilar",
    "MF",
    "MW",
    "nearestNeighbors",
    "numBits",
    "obmol",
    "openBabelPlot",
    "parBatchByIndex",
    "plot",
    "plotStruc",
    "propOB",
    "pubchemCidToSDF",
    "pubchemFPencoding",
    "pubchemInchi2cid",
    "pubchemInchikey2sdf",
    "pubchemName2CID",
    "pubchemSDFSearch",
    "pubchemSmilesSearch",
    "randomPriorities",
    "read.AP",
    "read.SDFindex",
    "read.SDFset",
    "read.SDFstr",
    "read.SMIset",
    "regenerateCoords",
    "result",
    "rings",
    "sdf.subset",
    "sdf.visualize",
    "sdf2ap",
    "SDF2apcmp",
    "sdf2list",
    "sdf2smiles",
    "sdf2str",
    "SDFDataTable",
    "sdfid",
    "sdfid<-",
    "SDFset",
    "SDFset2list",
    "SDFset2SDF",
    "SDFset2SDF<-",
    "sdfstr2list",
    "sdfstr2list<-",
    "sdfStream",
    "searchSim",
    "searchString",
    "selectInBatches",
    "setPriorities",
    "show",
    "smartsSearchOB",
    "smiles2sdf",
    "splitNumChar",
    "status",
    "toolDetails",
    "trimNeighbors",
    "validSDF",
    "view",
    "write.SDF",
    "write.SDFsplit",
    "write.SMI"
  ],
  "_datasets": [
    {
      "name": "apfp",
      "title": "Frequent Atom Pairs",
      "object": "apfp",
      "file": "apfp.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "AP",
        "Freq"
      ],
      "rows": 4096,
      "table": true,
      "tojson": true
    },
    {
      "name": "apset",
      "title": "Atom pairs stored in 'APset' object",
      "object": "apset",
      "file": "apset.rda",
      "class": [
        "APset"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "atomprop",
      "title": "Standard atomic weights",
      "object": "atomprop",
      "file": "atomprop.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Number",
        "Name",
        "Symbol",
        "Atomic_weight",
        "Group",
        "Period"
      ],
      "rows": 118,
      "table": true,
      "tojson": true
    },
    {
      "name": "pubchemFPencoding",
      "title": "Enncoding of PubChem Fingerprints",
      "object": "pubchemFPencoding",
      "file": "pubchemFPencoding.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Bit_Position",
        "Bit_Substructure"
      ],
      "rows": 881,
      "table": true,
      "tojson": true
    },
    {
      "name": "sdfsample",
      "title": "SD file in 'SDFset' object",
      "object": "sdfsample",
      "file": "sdfsample.rda",
      "class": [
        "SDFset"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "smisample",
      "title": "SMILES file in 'SMIset' object",
      "object": "smisample",
      "file": "smisample.rda",
      "class": [
        "SMIset"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addDescriptorType",
      "title": "Add Descriptor Type",
      "topics": [
        "addDescriptorType"
      ]
    },
    {
      "page": "addNewFeatures",
      "title": "Add New Features",
      "topics": [
        "addNewFeatures"
      ]
    },
    {
      "page": "ap",
      "title": "Return atom pair component of 'AP/APset'",
      "topics": [
        "ap",
        "ap-methods"
      ]
    },
    {
      "page": "AP-class",
      "title": "Class \"AP\"",
      "topics": [
        "ap,AP-method",
        "AP-class",
        "show,AP-method"
      ]
    },
    {
      "page": "apfp",
      "title": "Frequent Atom Pairs",
      "topics": [
        "apfp"
      ]
    },
    {
      "page": "apset",
      "title": "Atom pairs stored in 'APset' object",
      "topics": [
        "apset"
      ]
    },
    {
      "page": "APset-class",
      "title": "Class \"APset\"",
      "topics": [
        "ap,APset-method",
        "APset-class",
        "c,APset-method",
        "cid,APset-method",
        "cid<-,APset-method",
        "coerce,APset,AP-method",
        "coerce,APset,list-method",
        "coerce,list,APset-method",
        "length,APset-method",
        "show,APset-method",
        "view,APset-method",
        "[,APset-method",
        "[<-,APset-method",
        "[[,APset-method",
        "[[<-,APset-method"
      ]
    },
    {
      "page": "apset2descdb",
      "title": "'APset' to list-style AP database",
      "topics": [
        "apset2descdb"
      ]
    },
    {
      "page": "atomblock",
      "title": "Return atom block",
      "topics": [
        "atomblock",
        "atomblock-methods",
        "atomblock<-"
      ]
    },
    {
      "page": "atomcount",
      "title": "Molecular property functions",
      "topics": [
        "atomcount",
        "atomcountMA",
        "MF",
        "MW"
      ]
    },
    {
      "page": "atomprop",
      "title": "Standard atomic weights",
      "topics": [
        "atomprop"
      ]
    },
    {
      "page": "atomsubset",
      "title": "Subset SDF/SDFset Objects by Atom Index to Obtain Substructure",
      "topics": [
        "atomsubset"
      ]
    },
    {
      "page": "batchByIndex",
      "title": "Batch by Index",
      "topics": [
        "batchByIndex"
      ]
    },
    {
      "page": "bondblock",
      "title": "Return bond block",
      "topics": [
        "bondblock",
        "bondblock-methods",
        "bondblock<-"
      ]
    },
    {
      "page": "bonds",
      "title": "Bonds, charges and missing hydrogens",
      "topics": [
        "bonds"
      ]
    },
    {
      "page": "browseJob",
      "title": "Open ChemMine Tools Job in Web Browser",
      "topics": [
        "browseJob"
      ]
    },
    {
      "page": "bufferLines",
      "title": "Buffer File Input",
      "topics": [
        "bufferLines"
      ]
    },
    {
      "page": "bufferResultSet",
      "title": "Buffer Query Results",
      "topics": [
        "bufferResultSet"
      ]
    },
    {
      "page": "byCluster",
      "title": "By Cluster",
      "topics": [
        "byCluster"
      ]
    },
    {
      "page": "canonicalize",
      "title": "Canonicalize",
      "topics": [
        "canonicalize"
      ]
    },
    {
      "page": "canonicalNumbering",
      "title": "Canonical Numbering",
      "topics": [
        "canonicalNumbering"
      ]
    },
    {
      "page": "cid",
      "title": "Return compound IDs",
      "topics": [
        "cid",
        "cid<-"
      ]
    },
    {
      "page": "cluster.sizestat",
      "title": "generate statistics on sizes of clusters",
      "topics": [
        "cluster.sizestat"
      ]
    },
    {
      "page": "cluster.visualize",
      "title": "visualize clustering result using multi-dimensional scaling",
      "topics": [
        "cluster.visualize"
      ]
    },
    {
      "page": "cmp.cluster",
      "title": "cluster compounds using a descriptor database",
      "topics": [
        "cmp.cluster"
      ]
    },
    {
      "page": "cmp.duplicated",
      "title": "quickly detect compound duplication in a descriptor database",
      "topics": [
        "cmp.duplicated"
      ]
    },
    {
      "page": "cmp.parse",
      "title": "Parse an SDF file and compute descriptors for all compounds",
      "topics": [
        "cmp.parse"
      ]
    },
    {
      "page": "cmp.parse1",
      "title": "Parsing an SDF file and calculate the descriptor for one compound",
      "topics": [
        "cmp.parse1"
      ]
    },
    {
      "page": "cmp.search",
      "title": "Search a descriptor database for compounds similar to query compound",
      "topics": [
        "cmp.search"
      ]
    },
    {
      "page": "cmp.similarity",
      "title": "Compute similarity between two compounds using their descriptors",
      "topics": [
        "cmp.similarity"
      ]
    },
    {
      "page": "conMA",
      "title": "Bond Matrices",
      "topics": [
        "conMA"
      ]
    },
    {
      "page": "connections",
      "title": "Database Connections",
      "topics": [
        "DrugBank",
        "DUD"
      ]
    },
    {
      "page": "datablock",
      "title": "Return data block",
      "topics": [
        "datablock",
        "datablock-methods",
        "datablock<-",
        "datablocktag"
      ]
    },
    {
      "page": "datablock2ma",
      "title": "SDF data blocks to matrix",
      "topics": [
        "datablock2ma",
        "splitNumChar"
      ]
    },
    {
      "page": "db.explain",
      "title": "Explain an atom-pair descriptor or an array of atom-pair descriptors",
      "topics": [
        "db.explain"
      ]
    },
    {
      "page": "db.subset",
      "title": "Subset a descriptor database and return a sub-database for the selected compounds",
      "topics": [
        "db.subset"
      ]
    },
    {
      "page": "dbTransaction",
      "title": "DB Transaction",
      "topics": [
        "dbTransaction"
      ]
    },
    {
      "page": "desc2fp",
      "title": "Fingerprints from descriptor vectors",
      "topics": [
        "desc2fp"
      ]
    },
    {
      "page": "draw_sdf",
      "title": "draw_sdf",
      "topics": [
        "draw_sdf"
      ]
    },
    {
      "page": "exactMassOB",
      "title": "Exact Mass (Monoisotopic Mass)",
      "topics": [
        "exactMassOB"
      ]
    },
    {
      "page": "ExtSDF-class",
      "title": "Class \"ExtSDF\"",
      "topics": [
        "ExtSDF-class",
        "getAtomAttr,ExtSDF-method",
        "getBondAttr,ExtSDF-method",
        "show,ExtSDF-method"
      ]
    },
    {
      "page": "findCompounds",
      "title": "Find Compounds in Database",
      "topics": [
        "findCompounds"
      ]
    },
    {
      "page": "findCompoundsByName",
      "title": "Find compound by name",
      "topics": [
        "findCompoundsByName"
      ]
    },
    {
      "page": "fingerprintOB",
      "title": "Fingerprints from OpenBabel",
      "topics": [
        "fingerprintOB"
      ]
    },
    {
      "page": "fold",
      "title": "Fold",
      "topics": [
        "fold"
      ]
    },
    {
      "page": "foldCount",
      "title": "foldCount",
      "topics": [
        "foldCount"
      ]
    },
    {
      "page": "FP-class",
      "title": "Class '\"FP\"'",
      "topics": [
        "as.character,FP-method",
        "as.numeric,FP-method",
        "as.vector,FP-method",
        "c,FP-method",
        "coerce,numeric,FP-method",
        "fold,FP-method",
        "foldCount,FP-method",
        "FP-class",
        "fptype,FP-method",
        "numBits,FP-method",
        "show,FP-method"
      ]
    },
    {
      "page": "fp2bit",
      "title": "Convert base 64 fingerprints to binary",
      "topics": [
        "fp2bit"
      ]
    },
    {
      "page": "FPset-class",
      "title": "Class '\"FPset\"'",
      "topics": [
        "as.character,FPset-method",
        "as.matrix,FPset-method",
        "c,FPset-method",
        "cid,FPset-method",
        "cid<-,FPset-method",
        "coerce,character,FPset-method",
        "coerce,FPset,FP-method",
        "coerce,matrix,FPset-method",
        "fold,FPset-method",
        "foldCount,FPset-method",
        "FPset-class",
        "fptype,FPset-method",
        "length,FPset-method",
        "numBits,FPset-method",
        "show,FPset-method",
        "view,FPset-method",
        "[,FPset-method",
        "[<-,FPset-method",
        "[[,FPset-method"
      ]
    },
    {
      "page": "fpSim",
      "title": "Fingerprint Search",
      "topics": [
        "fpSim"
      ]
    },
    {
      "page": "fptype",
      "title": "fptype",
      "topics": [
        "fptype"
      ]
    },
    {
      "page": "fromNNMatrix",
      "title": "From Nearest Neighbor Matrix",
      "topics": [
        "fromNNMatrix"
      ]
    },
    {
      "page": "genAPDescriptors",
      "title": "Generate AP Descriptors",
      "topics": [
        "genAPDescriptors"
      ]
    },
    {
      "page": "generate3DCoords",
      "title": "Generate 3D Coords",
      "topics": [
        "generate3DCoords"
      ]
    },
    {
      "page": "genParameters",
      "title": "Generate Parameters",
      "topics": [
        "genParameters"
      ]
    },
    {
      "page": "getAllCompoundIds",
      "title": "Get ALl Compound Ids",
      "topics": [
        "getAllCompoundIds"
      ]
    },
    {
      "page": "getAtomAttr",
      "title": "getAtomAttr",
      "topics": [
        "getAtomAttr"
      ]
    },
    {
      "page": "getBondAttr",
      "title": "getBondAttr",
      "topics": [
        "getBondAttr"
      ]
    },
    {
      "page": "getCompoundFeatures",
      "title": "Get Compound Features",
      "topics": [
        "getCompoundFeatures"
      ]
    },
    {
      "page": "getCompoundNames",
      "title": "Get Compound Names",
      "topics": [
        "getCompoundNames"
      ]
    },
    {
      "page": "getCompounds",
      "title": "Get Compounds From Database",
      "topics": [
        "getCompounds"
      ]
    },
    {
      "page": "getIds",
      "title": "Import Compounds from PubChem",
      "topics": [
        "getIds"
      ]
    },
    {
      "page": "grepSDFset",
      "title": "String search in 'SDFset'",
      "topics": [
        "grepSDFset"
      ]
    },
    {
      "page": "groups",
      "title": "Enumeration of Functional Groups and Atom Neighbors",
      "topics": [
        "groups"
      ]
    },
    {
      "page": "header",
      "title": "Return header block",
      "topics": [
        "header",
        "header-methods",
        "header<-"
      ]
    },
    {
      "page": "initDb",
      "title": "Iinitialize SQL Database",
      "topics": [
        "initDb"
      ]
    },
    {
      "page": "jarvisPatrick",
      "title": "Jarvis-Patrick Clustering",
      "topics": [
        "jarvisPatrick"
      ]
    },
    {
      "page": "jarvisPatrick_c",
      "title": "Jarvis Patrick Clustering in C code",
      "topics": [
        "jarvisPatrick_c"
      ]
    },
    {
      "page": "jobToken-class",
      "title": "Class '\"jobToken\"'",
      "topics": [
        "jobToken-class",
        "show,jobToken-method"
      ]
    },
    {
      "page": "largestComponent",
      "title": "Largest Component",
      "topics": [
        "largestComponent"
      ]
    },
    {
      "page": "launchCMTool",
      "title": "Launch a Tool on ChemMine Tools",
      "topics": [
        "launchCMTool"
      ]
    },
    {
      "page": "listCMTools",
      "title": "List all available ChemMine Tools",
      "topics": [
        "listCMTools"
      ]
    },
    {
      "page": "listFeatures",
      "title": "List Features",
      "topics": [
        "listFeatures"
      ]
    },
    {
      "page": "loadSdf",
      "title": "Load SDF and SMILES Data",
      "topics": [
        "loadSdf",
        "loadSmiles"
      ]
    },
    {
      "page": "makeUnique",
      "title": "Uniquify CMP names",
      "topics": [
        "makeUnique"
      ]
    },
    {
      "page": "maximallyDissimilar",
      "title": "Maximally Dissimilar",
      "topics": [
        "maximallyDissimilar"
      ]
    },
    {
      "page": "nearestNeighbors",
      "title": "Nearest Neighbors",
      "topics": [
        "nearestNeighbors"
      ]
    },
    {
      "page": "numBits",
      "title": "numBits",
      "topics": [
        "numBits"
      ]
    },
    {
      "page": "obmol",
      "title": "obmol",
      "topics": [
        "obmol",
        "obmol-methods"
      ]
    },
    {
      "page": "openBabelPlot",
      "title": "Plot compound structures",
      "topics": [
        "openBabelPlot"
      ]
    },
    {
      "page": "parBatchByIndex",
      "title": "Parallel Batch By Index",
      "topics": [
        "parBatchByIndex"
      ]
    },
    {
      "page": "plotStruc",
      "title": "Plot compound structures",
      "topics": [
        "plot",
        "plotStruc"
      ]
    },
    {
      "page": "propOB",
      "title": "Properties from OpenBabel",
      "topics": [
        "propOB"
      ]
    },
    {
      "page": "pubchemCidToSDF",
      "title": "Import Compounds from PubChem",
      "topics": [
        "pubchemCidToSDF"
      ]
    },
    {
      "page": "pubchemFPencoding",
      "title": "Enncoding of PubChem Fingerprints",
      "topics": [
        "pubchemFPencoding"
      ]
    },
    {
      "page": "pubchemInchi2cid",
      "title": "Query pubchem by InChI sttrings and return CIDs",
      "topics": [
        "pubchemInchi2cid"
      ]
    },
    {
      "page": "pubchemInchikey2sdf",
      "title": "Query pubchem by InChIKeys sttrings and get SDF back",
      "topics": [
        "pubchemInchikey2sdf"
      ]
    },
    {
      "page": "pubchemName2CID",
      "title": "Translate compound name to pubchem compound id",
      "topics": [
        "pubchemName2CID"
      ]
    },
    {
      "page": "pubchemSDFSearch",
      "title": "PubChem Similarity (Fingerprint) Search",
      "topics": [
        "pubchemSDFSearch"
      ]
    },
    {
      "page": "pubchemSmilesSearch",
      "title": "PubChem Similarity (Fingerprint) SMILES Search",
      "topics": [
        "pubchemSmilesSearch"
      ]
    },
    {
      "page": "read.AP",
      "title": "Read Atom Pair/Fingerprint Strings",
      "topics": [
        "read.AP"
      ]
    },
    {
      "page": "read.SDFindex",
      "title": "Extract Molecules from SD File by Line Index",
      "topics": [
        "read.SDFindex"
      ]
    },
    {
      "page": "read.SDFset",
      "title": "SD file to 'SDFset'",
      "topics": [
        "read.SDFset"
      ]
    },
    {
      "page": "read.SDFstr",
      "title": "SD file to 'SDFstr'",
      "topics": [
        "read.SDFstr"
      ]
    },
    {
      "page": "read.SMIset",
      "title": "SMILES file to 'SMIset'",
      "topics": [
        "read.SMIset"
      ]
    },
    {
      "page": "regenerateCoords",
      "title": "Re-generate 2D Coordinates",
      "topics": [
        "regenerateCoords"
      ]
    },
    {
      "page": "result",
      "title": "Obtain the resulting output data from a ChemMine Tools Job",
      "topics": [
        "result"
      ]
    },
    {
      "page": "rings",
      "title": "Ring and Aromaticity Perception",
      "topics": [
        "rings"
      ]
    },
    {
      "page": "SDF-class",
      "title": "Class \"SDF\"",
      "topics": [
        "atomblock,SDF-method",
        "atomcount,SDF-method",
        "bondblock,SDF-method",
        "coerce,character,SDF-method",
        "coerce,list,SDF-method",
        "coerce,SDF,character-method",
        "coerce,SDF,list-method",
        "coerce,SDF,SDFset-method",
        "coerce,SDF,SDFstr-method",
        "datablock,SDF-method",
        "datablocktag,SDF-method",
        "header,SDF-method",
        "obmol,SDF-method",
        "plot,SDF-method",
        "SDF-class",
        "sdf2list,SDF-method",
        "sdf2str,SDF-method",
        "sdfid,SDF-method",
        "show,SDF-method",
        "[,SDF-method",
        "[<-,SDF-method",
        "[[,SDF-method",
        "[[<-,SDF-method"
      ]
    },
    {
      "page": "sdf.subset",
      "title": "Subset a SDF and return SDF segements for selected compounds",
      "topics": [
        "sdf.subset"
      ]
    },
    {
      "page": "sdf.visualize",
      "title": "Visualize an SDFset online using ChemMine Tools",
      "topics": [
        "sdf.visualize"
      ]
    },
    {
      "page": "sdf2ap",
      "title": "Atom pair library",
      "topics": [
        "sdf2ap"
      ]
    },
    {
      "page": "SDF2apcmp",
      "title": "'SDF' to 'list' for AP generation",
      "topics": [
        "SDF2apcmp"
      ]
    },
    {
      "page": "sdf2list",
      "title": "'SDF' to 'list'",
      "topics": [
        "sdf2list"
      ]
    },
    {
      "page": "sdf2smiles",
      "title": "'SDFset' to 'character' Convert 'SDFset' to SMILES ('character')",
      "topics": [
        "sdf2smiles",
        "sdf2smilesOB"
      ]
    },
    {
      "page": "sdf2str",
      "title": "'SDF' to 'SDFstr'",
      "topics": [
        "sdf2str",
        "sdf2str-methods"
      ]
    },
    {
      "page": "SDFDataTable",
      "title": "SDF Data Table",
      "topics": [
        "SDFDataTable"
      ]
    },
    {
      "page": "sdfid",
      "title": "Return SDF compound IDs",
      "topics": [
        "sdfid"
      ]
    },
    {
      "page": "sdfsample",
      "title": "SD file in 'SDFset' object",
      "topics": [
        "sdfsample"
      ]
    },
    {
      "page": "SDFset-class",
      "title": "Class \"SDFset\"",
      "topics": [
        "atomblock,SDFset-method",
        "atomblock<-,SDFset-method",
        "atomcount,SDFset-method",
        "bondblock,SDFset-method",
        "bondblock<-,SDFset-method",
        "c,SDFset-method",
        "cid,SDFset-method",
        "cid<-,SDFset-method",
        "coerce,list,SDFset-method",
        "coerce,SDFset,list-method",
        "coerce,SDFset,SDF-method",
        "coerce,SDFset,SDFstr-method",
        "datablock,SDFset-method",
        "datablock<-,SDFset-method",
        "datablocktag,SDFset-method",
        "header,SDFset-method",
        "header<-,SDFset-method",
        "length,SDFset-method",
        "obmol,SDFset-method",
        "plot,SDFset-method",
        "sdfid,SDFset-method",
        "SDFset",
        "SDFset-class",
        "SDFset2list,SDFset-method",
        "SDFset2SDF,SDFset-method",
        "SDFset2SDF<-,SDFset-method",
        "show,SDFset-method",
        "view,SDFset-method",
        "[,SDFset-method",
        "[<-,SDFset-method",
        "[[,SDFset-method",
        "[[<-,SDFset-method"
      ]
    },
    {
      "page": "SDFset2list",
      "title": "'SDFset' to 'list'",
      "topics": [
        "SDFset2list",
        "SDFset2list-methods"
      ]
    },
    {
      "page": "SDFset2SDF",
      "title": "'SDFset' to list with many 'SDF'",
      "topics": [
        "SDFset2SDF",
        "SDFset2SDF-methods",
        "SDFset2SDF<-"
      ]
    },
    {
      "page": "SDFstr-class",
      "title": "Class \"SDFstr\"",
      "topics": [
        "coerce,character,SDFstr-method",
        "coerce,list,SDFstr-method",
        "coerce,SDFstr,list-method",
        "coerce,SDFstr,SDFset-method",
        "length,SDFstr-method",
        "SDFstr-class",
        "sdfstr2list,SDFstr-method",
        "sdfstr2list<-,SDFstr-method",
        "show,SDFstr-method",
        "[,SDFstr-method",
        "[<-,SDFstr-method",
        "[[,SDFstr-method",
        "[[<-,SDFstr-method"
      ]
    },
    {
      "page": "sdfstr2list",
      "title": "'SDFstr' to 'list'",
      "topics": [
        "sdfstr2list",
        "sdfstr2list-methods",
        "sdfstr2list<-"
      ]
    },
    {
      "page": "sdfStream",
      "title": "Streaming through large SD files",
      "topics": [
        "sdfStream"
      ]
    },
    {
      "page": "searchSim",
      "title": "PubChem Similarity (Fingerprint) Search",
      "topics": [
        "searchSim"
      ]
    },
    {
      "page": "searchString",
      "title": "PubChem Similarity (Fingerprint) SMILES Search",
      "topics": [
        "searchString"
      ]
    },
    {
      "page": "selectInBatches",
      "title": "Select in Batches",
      "topics": [
        "selectInBatches"
      ]
    },
    {
      "page": "setPriorities",
      "title": "Set Priorities",
      "topics": [
        "forestSizePriorities",
        "randomPriorities",
        "setPriorities"
      ]
    },
    {
      "page": "smartsSearchOB",
      "title": "SMARTS Search OB",
      "topics": [
        "smartsSearchOB"
      ]
    },
    {
      "page": "SMI-class",
      "title": "Class '\"SMI\"'",
      "topics": [
        "as.character,SMI-method",
        "coerce,character,SMI-method",
        "show,SMI-method",
        "SMI-class"
      ]
    },
    {
      "page": "smiles2sdf",
      "title": "Convert SMILES ('character') to 'SDFset'",
      "topics": [
        "smiles2sdf",
        "smiles2sdfOB"
      ]
    },
    {
      "page": "smisample",
      "title": "SMILES file in 'SMIset' object",
      "topics": [
        "smisample"
      ]
    },
    {
      "page": "SMIset-class",
      "title": "Class '\"SMIset\"'",
      "topics": [
        "as.character,SMIset-method",
        "c,SMIset-method",
        "cid,SMIset-method",
        "cid<-,SMIset-method",
        "coerce,character,SMIset-method",
        "coerce,list,SMIset-method",
        "coerce,SMIset,SMI-method",
        "length,SMIset-method",
        "show,SMIset-method",
        "SMIset-class",
        "view,SMIset-method",
        "[,SMIset-method",
        "[<-,SMIset-method",
        "[[,SMIset-method"
      ]
    },
    {
      "page": "status",
      "title": "Get Status of a ChemMine Tools Job",
      "topics": [
        "status"
      ]
    },
    {
      "page": "toolDetails",
      "title": "Detailed instructions for each ChemMine Tools web tool",
      "topics": [
        "toolDetails"
      ]
    },
    {
      "page": "trimNeighbors",
      "title": "Trim Neighbors",
      "topics": [
        "trimNeighbors"
      ]
    },
    {
      "page": "validSDF",
      "title": "Validity check of SDFset",
      "topics": [
        "validSDF"
      ]
    },
    {
      "page": "view",
      "title": "Viewing of complex objects",
      "topics": [
        "view",
        "view-methods"
      ]
    },
    {
      "page": "write.SDF",
      "title": "SDF export function",
      "topics": [
        "write.SDF"
      ]
    },
    {
      "page": "write.SDFsplit",
      "title": "SDF split function",
      "topics": [
        "write.SDFsplit"
      ]
    },
    {
      "page": "write.SMI",
      "title": "SMI export function",
      "topics": [
        "write.SMI"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ChemmineR/raw/HEAD/README.md",
  "_rundeps": [
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    "BH",
    "BiocGenerics",
    "bitops",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
    "crosstalk",
    "DBI",
    "digest",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "otel",
    "png",
    "promises",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "rjson",
    "rlang",
    "rmarkdown",
    "rsvg",
    "S7",
    "sass",
    "scales",
    "stringi",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "ChemmineR.Rmd",
      "filename": "ChemmineR.html",
      "title": "ChemmineR: Cheminformatics Toolkit for R",
      "author": "Authors: Kevin Horan, Yiqun Cao, Tyler Backman, Thomas Girke",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "Installation",
        "Loading the Package and Documentation",
        "Five Minute Tutorial",
        "OpenBabel Functions",
        "Overview of Classes and Functions",
        "Molecular Structure Data",
        "Structure Descriptor Data",
        "Import of Compounds",
        "SDF Import",
        "SMILES Import",
        "Export of Compounds",
        "SDF Export",
        "SMILES Export",
        "Format Interconversions",
        "Splitting SD Files",
        "Streaming Through Large SD Files",
        "Storing Compounds in an SQL Database",
        "Loading Data",
        "Updates",
        "Duplicate Descriptors",
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        "Using Search Results",
        "Pre-Built Databases",
        "Working with SDF/SDFset Classes",
        "Molecular Property Functions (Physicochemical Descriptors)",
        "Bond Matrices",
        "Charges and Missing Hydrogens",
        "Ring Perception and Aromaticity Assignment",
        "Rendering Chemical Structure Images",
        "R Graphics Device",
        "Data Tables",
        "Online with ChemMine Tools",
        "Similarity Comparisons and Searching",
        "Maximum Common Substructure (MCS) Searching",
        "AP/APset Classes for Storing Atom Pair Descriptors",
        "Large SDF and Atom Pair Databases",
        "Pairwise Compound Comparisons with Atom Pairs",
        "Similarity Searching with Atom Pairs",
        "FP/FPset Classes for Storing Fingerprints",
        "Atom Pair Fingerprints",
        "Fingerprint E-values",
        "Pairwise Compound Comparisons with PubChem Fingerprints",
        "Similarity Searching with PubChem Fingerprints",
        "Visualize Similarity Search Results",
        "Clustering",
        "Clustering Identical or Very Similar Compounds",
        "Binning Clustering",
        "Jarvis-Patrick Clustering",
        "Multi-Dimensional Scaling (MDS)",
        "Clustering with Other Algorithms",
        "Searching PubChem",
        "Get Compound SDF from PubChem by Id",
        "Get Compound SDF from PubChem by InChIkey",
        "Get Compound CID from PubChem by InChI",
        "Search a SMILES Query in PubChem",
        "Search an SDF Query in PubChem",
        "ChemMine Tools R Interface",
        "Launch a Job",
        "View Job Result in Browser",
        "Version Information",
        "Funding",
        "References"
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      "created": "2014-03-24 18:41:39",
      "modified": "2022-03-25 13:34:47",
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