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:Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke

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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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

apfp - Frequent Atom Pairs
apset - Atom pairs stored in 'APset' object
atomprop - Standard atomic weights
pubchemFPencoding - Enncoding of PubChem Fingerprints
sdfsample - SD file in 'SDFset' object
smisample - SMILES file in 'SMIset' object

On BioConductor:ChemmineR-3.59.0(bioc 3.21)ChemmineR-3.58.0(bioc 3.20)

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics

9.34 score 13 stars 13 packages 228 scripts 1.4k downloads 39 mentions 139 exports 68 dependencies

Last updated 20 days agofrom:ee3bf9e8bb. Checks:ERROR: 2 WARNING: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 18 2024
R-4.5-win-x86_64	ERROR	Nov 18 2024
R-4.5-linux-x86_64	WARNING	Nov 18 2024
R-4.4-win-x86_64	WARNING	Nov 18 2024
R-4.4-mac-x86_64	WARNING	Nov 18 2024
R-4.4-mac-aarch64	WARNING	Nov 18 2024
R-4.3-win-x86_64	WARNING	Nov 18 2024
R-4.3-mac-x86_64	WARNING	Nov 18 2024
R-4.3-mac-aarch64	WARNING	Nov 18 2024

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

Dependencies:base64enc BH BiocGenerics bitops bslib cachem cli colorspace crosstalk DBI digest DT evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpuv isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig png promises R6 rappdirs RColorBrewer Rcpp RCurl rjson rlang rmarkdown rsvg sass scales stringi tibble tinytex utf8 vctrs viridisLite withr xfun yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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

Package: ChemmineR 3.59.0

ChemmineR: Cheminformatics Toolkit for R

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