Package: ChemmineR 3.59.0
Thomas Girke
ChemmineR: Cheminformatics Toolkit for R
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Authors:
ChemmineR_3.59.0.tar.gz
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ChemmineR.pdf |ChemmineR.html✨
ChemmineR/json (API)
NEWS
| # Install 'ChemmineR' in R: |
| install.packages('ChemmineR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/girke-lab/chemminer/issues
On BioConductor:ChemmineR-3.59.0(bioc 3.21)ChemmineR-3.58.0(bioc 3.20)
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
Last updated 2 months agofrom:ee3bf9e8bb. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 18 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 18 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 18 2024 |
Exports:addDescriptorTypeaddNewFeaturesapapset2descdbas.matrixatomblockatomblock<-atomcountatomcountMAatompropatomsubsetbatchByIndexbondblockbondblock<-bondsbrowseJobbufferLinesbufferResultSetbyClustercanonicalizecanonicalNumberingcidcid<-cluster.sizestatcluster.visualizecmp.clustercmp.duplicatedcmp.parsecmp.parse1cmp.searchcmp.similaritycoerceconMAdatablockdatablock<-datablock2madatablocktagdb.explaindb.subsetdbTransactiondesc2fpdraw_sdfDrugBankDUDexactMassOBfindCompoundsfindCompoundsByNamefingerprintOBfoldfoldCountforestSizePrioritiesfp2bitfpSimfptypefromNNMatrixgenAPDescriptorsgenerate3DCoordsgenParametersgetAllCompoundIdsgetAtomAttrgetBondAttrgetCompoundFeaturesgetCompoundNamesgetCompoundsgetIdsgrepSDFsetgroupsheaderheader<-initDbjarvisPatrickjarvisPatrick_clargestComponentlaunchCMToollistCMToolslistFeaturesloadSdfloadSmilesmakeUniquemaximallyDissimilarMFMWnearestNeighborsnumBitsobmolopenBabelPlotparBatchByIndexplotplotStrucpropOBpubchemCidToSDFpubchemFPencodingpubchemInchi2cidpubchemInchikey2sdfpubchemName2CIDpubchemSDFSearchpubchemSmilesSearchrandomPrioritiesread.APread.SDFindexread.SDFsetread.SDFstrread.SMIsetregenerateCoordsresultringssdf.subsetsdf.visualizesdf2apSDF2apcmpsdf2listsdf2smilessdf2strSDFDataTablesdfidsdfid<-SDFsetSDFset2listSDFset2SDFSDFset2SDF<-sdfstr2listsdfstr2list<-sdfStreamsearchSimsearchStringselectInBatchessetPrioritiesshowsmartsSearchOBsmiles2sdfsplitNumCharstatustoolDetailstrimNeighborsvalidSDFviewwrite.SDFwrite.SDFsplitwrite.SMI
Dependencies:base64encBHBiocGenericsbitopsbslibcachemclicolorspacecrosstalkDBIdigestDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpngpromisesR6rappdirsRColorBrewerRcppRCurlrjsonrlangrmarkdownrsvgsassscalesstringitibbletinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add Descriptor Type | addDescriptorType |
| Add New Features | addNewFeatures |
| Return atom pair component of 'AP/APset' | ap ap-methods |
| Class "AP" | ap,AP-method AP-class show,AP-method |
| Frequent Atom Pairs | apfp |
| Atom pairs stored in 'APset' object | apset |
| Class "APset" | 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 |
| 'APset' to list-style AP database | apset2descdb |
| Return atom block | atomblock atomblock-methods atomblock<- |
| Molecular property functions | atomcount atomcountMA MF MW |
| Standard atomic weights | atomprop |
| Subset SDF/SDFset Objects by Atom Index to Obtain Substructure | atomsubset |
| Batch by Index | batchByIndex |
| Return bond block | bondblock bondblock-methods bondblock<- |
| Bonds, charges and missing hydrogens | bonds |
| Open ChemMine Tools Job in Web Browser | browseJob |
| Buffer File Input | bufferLines |
| Buffer Query Results | bufferResultSet |
| By Cluster | byCluster |
| Canonicalize | canonicalize |
| Canonical Numbering | canonicalNumbering |
| Return compound IDs | cid cid<- |
| generate statistics on sizes of clusters | cluster.sizestat |
| visualize clustering result using multi-dimensional scaling | cluster.visualize |
| cluster compounds using a descriptor database | cmp.cluster |
| quickly detect compound duplication in a descriptor database | cmp.duplicated |
| Parse an SDF file and compute descriptors for all compounds | cmp.parse |
| Parsing an SDF file and calculate the descriptor for one compound | cmp.parse1 |
| Search a descriptor database for compounds similar to query compound | cmp.search |
| Compute similarity between two compounds using their descriptors | cmp.similarity |
| Bond Matrices | conMA |
| Database Connections | DrugBank DUD |
| Return data block | datablock datablock-methods datablock<- datablocktag |
| SDF data blocks to matrix | datablock2ma splitNumChar |
| Explain an atom-pair descriptor or an array of atom-pair descriptors | db.explain |
| Subset a descriptor database and return a sub-database for the selected compounds | db.subset |
| DB Transaction | dbTransaction |
| Fingerprints from descriptor vectors | desc2fp |
| draw_sdf | draw_sdf |
| Exact Mass (Monoisotopic Mass) | exactMassOB |
| Class "ExtSDF" | ExtSDF-class getAtomAttr,ExtSDF-method getBondAttr,ExtSDF-method show,ExtSDF-method |
| Find Compounds in Database | findCompounds |
| Find compound by name | findCompoundsByName |
| Fingerprints from OpenBabel | fingerprintOB |
| Fold | fold |
| foldCount | foldCount |
| Class '"FP"' | 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 |
| Convert base 64 fingerprints to binary | fp2bit |
| Class '"FPset"' | 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 |
| Fingerprint Search | fpSim |
| fptype | fptype |
| From Nearest Neighbor Matrix | fromNNMatrix |
| Generate AP Descriptors | genAPDescriptors |
| Generate 3D Coords | generate3DCoords |
| Generate Parameters | genParameters |
| Get ALl Compound Ids | getAllCompoundIds |
| getAtomAttr | getAtomAttr |
| getBondAttr | getBondAttr |
| Get Compound Features | getCompoundFeatures |
| Get Compound Names | getCompoundNames |
| Get Compounds From Database | getCompounds |
| Import Compounds from PubChem | getIds |
| String search in 'SDFset' | grepSDFset |
| Enumeration of Functional Groups and Atom Neighbors | groups |
| Return header block | header header-methods header<- |
| Iinitialize SQL Database | initDb |
| Jarvis-Patrick Clustering | jarvisPatrick |
| Jarvis Patrick Clustering in C code | jarvisPatrick_c |
| Class '"jobToken"' | jobToken-class show,jobToken-method |
| Largest Component | largestComponent |
| Launch a Tool on ChemMine Tools | launchCMTool |
| List all available ChemMine Tools | listCMTools |
| List Features | listFeatures |
| Load SDF and SMILES Data | loadSdf loadSmiles |
| Uniquify CMP names | makeUnique |
| Maximally Dissimilar | maximallyDissimilar |
| Nearest Neighbors | nearestNeighbors |
| numBits | numBits |
| obmol | obmol obmol-methods |
| Plot compound structures | openBabelPlot |
| Parallel Batch By Index | parBatchByIndex |
| Plot compound structures | plot plotStruc |
| Properties from OpenBabel | propOB |
| Import Compounds from PubChem | pubchemCidToSDF |
| Enncoding of PubChem Fingerprints | pubchemFPencoding |
| Query pubchem by InChI sttrings and return CIDs | pubchemInchi2cid |
| Query pubchem by InChIKeys sttrings and get SDF back | pubchemInchikey2sdf |
| Translate compound name to pubchem compound id | pubchemName2CID |
| PubChem Similarity (Fingerprint) Search | pubchemSDFSearch |
| PubChem Similarity (Fingerprint) SMILES Search | pubchemSmilesSearch |
| Read Atom Pair/Fingerprint Strings | read.AP |
| Extract Molecules from SD File by Line Index | read.SDFindex |
| SD file to 'SDFset' | read.SDFset |
| SD file to 'SDFstr' | read.SDFstr |
| SMILES file to 'SMIset' | read.SMIset |
| Re-generate 2D Coordinates | regenerateCoords |
| Obtain the resulting output data from a ChemMine Tools Job | result |
| Ring and Aromaticity Perception | rings |
| Class "SDF" | 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 |
| Subset a SDF and return SDF segements for selected compounds | sdf.subset |
| Visualize an SDFset online using ChemMine Tools | sdf.visualize |
| Atom pair library | sdf2ap |
| 'SDF' to 'list' for AP generation | SDF2apcmp |
| 'SDF' to 'list' | sdf2list |
| 'SDFset' to 'character' Convert 'SDFset' to SMILES ('character') | sdf2smiles sdf2smilesOB |
| 'SDF' to 'SDFstr' | sdf2str sdf2str-methods |
| SDF Data Table | SDFDataTable |
| Return SDF compound IDs | sdfid |
| SD file in 'SDFset' object | sdfsample |
| Class "SDFset" | 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 |
| 'SDFset' to 'list' | SDFset2list SDFset2list-methods |
| 'SDFset' to list with many 'SDF' | SDFset2SDF SDFset2SDF-methods SDFset2SDF<- |
| Class "SDFstr" | 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 |
| 'SDFstr' to 'list' | sdfstr2list sdfstr2list-methods sdfstr2list<- |
| Streaming through large SD files | sdfStream |
| PubChem Similarity (Fingerprint) Search | searchSim |
| PubChem Similarity (Fingerprint) SMILES Search | searchString |
| Select in Batches | selectInBatches |
| Set Priorities | forestSizePriorities randomPriorities setPriorities |
| SMARTS Search OB | smartsSearchOB |
| Class '"SMI"' | as.character,SMI-method coerce,character,SMI-method show,SMI-method SMI-class |
| Convert SMILES ('character') to 'SDFset' | smiles2sdf smiles2sdfOB |
| SMILES file in 'SMIset' object | smisample |
| Class '"SMIset"' | 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 |
| Get Status of a ChemMine Tools Job | status |
| Detailed instructions for each ChemMine Tools web tool | toolDetails |
| Trim Neighbors | trimNeighbors |
| Validity check of SDFset | validSDF |
| Viewing of complex objects | view view-methods |
| SDF export function | write.SDF |
| SDF split function | write.SDFsplit |
| SMI export function | write.SMI |
