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 | Searching | 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
Package: ChemmineR 3.65.0
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_3.65.0.tar.gz
ChemmineR_3.65.0.zip(r-4.7)ChemmineR_3.65.0.zip(r-4.6)ChemmineR_3.65.0.zip(r-4.5)
ChemmineR_3.65.0.tgz(r-4.6-x86_64)ChemmineR_3.65.0.tgz(r-4.6-arm64)ChemmineR_3.65.0.tgz(r-4.5-x86_64)ChemmineR_3.65.0.tgz(r-4.5-arm64)
ChemmineR_3.65.0.tar.gz(r-4.7-arm64)ChemmineR_3.65.0.tar.gz(r-4.7-x86_64)ChemmineR_3.65.0.tar.gz(r-4.6-arm64)ChemmineR_3.65.0.tar.gz(r-4.6-x86_64)
ChemmineR_3.65.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ChemmineR/json (API)
| # 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
Datasets:
On BioConductor:ChemmineR-3.65.0(bioc 3.24)ChemmineR-3.64.0(bioc 3.23)
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
Last updated from:0e099c2464. Checks:4 ERROR, 8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 309 | ||
| linux-devel-arm64 | WARNING | 321 | ||
| linux-devel-x86_64 | WARNING | 373 | ||
| source / vignettes | OK | 313 | ||
| linux-release-arm64 | WARNING | 368 | ||
| linux-release-x86_64 | WARNING | 414 | ||
| macos-release-arm64 | WARNING | 198 | ||
| macos-release-x86_64 | WARNING | 332 | ||
| macos-oldrel-arm64 | WARNING | 173 | ||
| macos-oldrel-x86_64 | WARNING | 623 | ||
| windows-devel | ERROR | 274 | ||
| windows-release | ERROR | 218 | ||
| windows-oldrel | ERROR | 243 | ||
| wasm-release | OK | 149 |
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:base64encBHBiocGenericsbitopsbslibcachemclicpp11crosstalkDBIdigestDTevaluatefarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimeotelpngpromisesR6rappdirsRColorBrewerRcppRCurlrjsonrlangrmarkdownrsvgS7sassscalesstringitinytexvctrsviridisLitewithrxfunyaml
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 |
