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.

AuthorY. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Date of publicationNone
MaintainerThomas Girke <thomas.girke@ucr.edu>
LicenseArtistic-2.0
Version2.26.1
https://github.com/girke-lab/ChemmineR

View on Bioconductor

Man pages

addDescriptorType: Add Descriptor Type

addNewFeatures: Add New Features

ap: Return atom pair component of 'AP/APset'

AP-class: Class "AP"

apfp: Frequent Atom Pairs

apset: Atom pairs stored in 'APset' object

apset2descdb: 'APset' to list-style AP database

APset-class: Class "APset"

atomblock: Return atom block

atomcount: Molecular property functions

atomprop: Standard atomic weights

atomsubset: Subset SDF/SDFset Objects by Atom Index to Obtain...

batchByIndex: Batch by Index

bondblock: Return bond block

bonds: Bonds, charges and missing hydrogens

browseJob: Open ChemMine Tools Job in Web Browser

bufferLines: Buffer File Input

bufferResultSet: Buffer Query Results

byCluster: By Cluster

canonicalize: Canonicalize

canonicalNumbering: Canonical Numbering

cid: Return compound IDs

cluster.sizestat: generate statistics on sizes of clusters

cluster.visualize: visualize clustering result using multi-dimensional scaling

cmp.cluster: cluster compounds using a descriptor database

cmp.duplicated: quickly detect compound duplication in a descriptor database

cmp.parse: Parse an SDF file and compute descriptors for all compounds

cmp.parse1: Parsing an SDF file and calculate the descriptor for one...

cmp.search: Search a descriptor database for compounds similar to query...

cmp.similarity: Compute similarity between two compounds using their...

conMA: Bond Matrices

connections: Database Connections

datablock: Return data block

datablock2ma: SDF data blocks to matrix

db.explain: Explain an atom-pair descriptor or an array of atom-pair...

db.subset: Subset a descriptor database and return a sub-database for...

dbTransaction: DB Transaction

desc2fp: Fingerprints from descriptor vectors

draw_sdf: draw_sdf

exactMassOB: Exact Mass (Monoisotopic Mass)

ExtSDF-class: Class "ExtSDF"

findCompounds: Find Compounds in Database

findCompoundsByName: Find compound by name

fingerprintOB: Fingerprints from OpenBabel

fold: Fold

foldCount: foldCount

fp2bit: Convert base 64 fingerprints to binary

FP-class: Class '"FP"'

FPset-class: Class '"FPset"'

fpSim: Fingerprint Search

fptype: fptype

fromNNMatrix: From Nearest Neighbor Matrix

genAPDescriptors: Generate AP Descriptors

generate3DCoords: Generate 3D Coords

genParameters: Generate Parameters

getAllCompoundIds: Get ALl Compound Ids

getCompoundFeatures: Get Compound Features

getCompoundNames: Get Compound Names

getCompounds: Get Compounds From Database

getIds: Import Compounds from PubChem

grepSDFset: String search in 'SDFset'

groups: Enumeration of Functional Groups and Atom Neighbors

header: Return header block

initDb: Iinitialize SQL Database

jarvisPatrick: Jarvis-Patrick Clustering

jarvisPatrick_c: Jarvis Patrick Clustering in C code

jobToken-class: Class '"jobToken"'

launchCMTool: Launch a Tool on ChemMine Tools

listCMTools: List all available ChemMine Tools

listFeatures: List Features

loadSdf: Load SDF and SMILES Data

makeUnique: Uniquify CMP names

maximallyDissimilar: Maximally Dissimilar

nearestNeighbors: Nearest Neighbors

numBits: numBits

obmol: obmol

parBatchByIndex: Parallel Batch By Index

plotStruc: Plot compound structures

propOB: Properties from OpenBabel

pubchemFPencoding: Enncoding of PubChem Fingerprints

read.AP: Read Atom Pair/Fingerprint Strings

read.SDFindex: Extract Molecules from SD File by Line Index

read.SDFset: SD file to 'SDFset'

read.SDFstr: SD file to 'SDFstr'

read.SMIset: SMILES file to 'SMIset'

regenerateCoords: Re-generate 2D Coordinates

result: Obtain the resulting output data from a ChemMine Tools Job

rings: Ring and Aromaticity Perception

sdf2ap: Atom pair library

SDF2apcmp: 'SDF' to 'list' for AP generation

sdf2list: 'SDF' to 'list'

sdf2smiles: 'SDFset' to 'character' Convert 'SDFset' to SMILES...

sdf2str: 'SDF' to 'SDFstr'

SDF-class: Class "SDF"

sdfid: Return SDF compound IDs

sdfsample: SD file in 'SDFset' object

SDFset2list: 'SDFset' to 'list'

SDFset2SDF: 'SDFset' to list with many 'SDF'

SDFset-class: Class "SDFset"

sdfstr2list: 'SDFstr' to 'list'

SDFstr-class: Class "SDFstr"

sdfStream: Streaming through large SD files

sdf.subset: Subset a SDF and return SDF segements for selected compounds

sdf.visualize: Visualize an SDFset online using ChemMine Tools

searchSim: PubChem Similarity (Fingerprint) Search

searchString: PubChem Similarity (Fingerprint) SMILES Search

selectInBatches: Select in Batches

setPriorities: Set Priorities

smartsSearchOB: SMARTS Search OB

SMI-class: Class '"SMI"'

smiles2sdf: Convert SMILES ('character') to 'SDFset'

smisample: SMILES file in 'SMIset' object

SMIset-class: Class '"SMIset"'

status: Get Status of a ChemMine Tools Job

toolDetails: Detailed instructions for each ChemMine Tools web tool

trimNeighbors: Trim Neighbors

validSDF: Validity check of SDFset

view: Viewing of complex objects

write.SDF: SDF export function

write.SDFsplit: SDF split function

write.SMI: SMI export function

Files in this package

ChemmineR/DESCRIPTION
ChemmineR/NAMESPACE
ChemmineR/R
ChemmineR/R/AllClasses.R ChemmineR/R/ChemmineR.R ChemmineR/R/chemmine_tools.R ChemmineR/R/cluster.R ChemmineR/R/compound_db.R ChemmineR/R/draw_sdf.R ChemmineR/R/postgresql.R ChemmineR/R/pvalue.R ChemmineR/R/sim.R
ChemmineR/README
ChemmineR/README.md
ChemmineR/build
ChemmineR/build/vignette.rds
ChemmineR/data
ChemmineR/data/apfp.rda
ChemmineR/data/apset.rda
ChemmineR/data/atomprop.rda
ChemmineR/data/atomprop.txt
ChemmineR/data/pubchemFPencoding.rda
ChemmineR/data/sdfsample.rda
ChemmineR/data/smisample.rda
ChemmineR/inst
ChemmineR/inst/CITATION
ChemmineR/inst/NEWS.Rd
ChemmineR/inst/doc
ChemmineR/inst/doc/ChemmineR.R
ChemmineR/inst/doc/ChemmineR.Rmd
ChemmineR/inst/doc/ChemmineR.html
ChemmineR/inst/schema
ChemmineR/inst/schema/compounds.RPostgreSQL
ChemmineR/inst/schema/compounds.SQLite
ChemmineR/inst/unitTests
ChemmineR/inst/unitTests/sample.mol
ChemmineR/inst/unitTests/sample.sdf
ChemmineR/inst/unitTests/singleMolecule.sdf
ChemmineR/inst/unitTests/test_classes.R
ChemmineR/inst/unitTests/test_clustering.R
ChemmineR/inst/unitTests/test_db.R
ChemmineR/inst/unitTests/test_general.R
ChemmineR/man
ChemmineR/man/AP-class.Rd ChemmineR/man/APset-class.Rd ChemmineR/man/ExtSDF-class.Rd ChemmineR/man/FP-class.Rd ChemmineR/man/FPset-class.Rd ChemmineR/man/SDF-class.Rd ChemmineR/man/SDF2apcmp.Rd ChemmineR/man/SDFset-class.Rd ChemmineR/man/SDFset2SDF.Rd ChemmineR/man/SDFset2list.Rd ChemmineR/man/SDFstr-class.Rd ChemmineR/man/SMI-class.Rd ChemmineR/man/SMIset-class.Rd ChemmineR/man/addDescriptorType.Rd ChemmineR/man/addNewFeatures.Rd ChemmineR/man/ap.Rd ChemmineR/man/apfp.Rd ChemmineR/man/apset.Rd ChemmineR/man/apset2descdb.Rd ChemmineR/man/atomblock.Rd ChemmineR/man/atomcount.Rd ChemmineR/man/atomprop.Rd ChemmineR/man/atomsubset.Rd ChemmineR/man/batchByIndex.Rd ChemmineR/man/bondblock.Rd ChemmineR/man/bonds.Rd ChemmineR/man/browseJob.Rd ChemmineR/man/bufferLines.Rd ChemmineR/man/bufferResultSet.Rd ChemmineR/man/byCluster.Rd ChemmineR/man/canonicalNumbering.Rd ChemmineR/man/canonicalize.Rd ChemmineR/man/cid.Rd ChemmineR/man/cluster.sizestat.Rd ChemmineR/man/cluster.visualize.Rd ChemmineR/man/cmp.cluster.Rd ChemmineR/man/cmp.duplicated.Rd ChemmineR/man/cmp.parse.Rd ChemmineR/man/cmp.parse1.Rd ChemmineR/man/cmp.search.Rd ChemmineR/man/cmp.similarity.Rd ChemmineR/man/conMA.Rd ChemmineR/man/connections.Rd ChemmineR/man/datablock.Rd ChemmineR/man/datablock2ma.Rd ChemmineR/man/db.explain.Rd ChemmineR/man/db.subset.Rd ChemmineR/man/dbTransaction.Rd ChemmineR/man/desc2fp.Rd ChemmineR/man/draw_sdf.Rd ChemmineR/man/exactMassOB.Rd ChemmineR/man/findCompounds.Rd ChemmineR/man/findCompoundsByName.Rd ChemmineR/man/fingerprintOB.Rd ChemmineR/man/fold.Rd ChemmineR/man/foldCount.Rd ChemmineR/man/fp2bit.Rd ChemmineR/man/fpSim.Rd ChemmineR/man/fptype.Rd ChemmineR/man/fromNNMatrix.Rd ChemmineR/man/genAPDescriptors.Rd ChemmineR/man/genParameters.Rd ChemmineR/man/generate3DCoords.Rd ChemmineR/man/getAllCompoundIds.Rd ChemmineR/man/getCompoundFeatures.Rd ChemmineR/man/getCompoundNames.Rd ChemmineR/man/getCompounds.Rd ChemmineR/man/getIds.Rd ChemmineR/man/grepSDFset.Rd ChemmineR/man/groups.Rd ChemmineR/man/header.Rd ChemmineR/man/initDb.Rd ChemmineR/man/jarvisPatrick.Rd ChemmineR/man/jarvisPatrick_c.Rd ChemmineR/man/jobToken-class.Rd ChemmineR/man/launchCMTool.Rd ChemmineR/man/listCMTools.Rd ChemmineR/man/listFeatures.Rd ChemmineR/man/loadSdf.Rd ChemmineR/man/makeUnique.Rd ChemmineR/man/maximallyDissimilar.Rd ChemmineR/man/nearestNeighbors.Rd ChemmineR/man/numBits.Rd ChemmineR/man/obmol.Rd ChemmineR/man/parBatchByIndex.Rd ChemmineR/man/plotStruc.Rd ChemmineR/man/propOB.Rd ChemmineR/man/pubchemFPencoding.Rd ChemmineR/man/read.AP.Rd ChemmineR/man/read.SDFindex.Rd ChemmineR/man/read.SDFset.Rd ChemmineR/man/read.SDFstr.Rd ChemmineR/man/read.SMIset.Rd ChemmineR/man/regenerateCoords.Rd ChemmineR/man/result.Rd ChemmineR/man/rings.Rd ChemmineR/man/sdf.subset.Rd ChemmineR/man/sdf.visualize.Rd ChemmineR/man/sdf2ap.Rd ChemmineR/man/sdf2list.Rd ChemmineR/man/sdf2smiles.Rd ChemmineR/man/sdf2str.Rd ChemmineR/man/sdfStream.Rd ChemmineR/man/sdfid.Rd ChemmineR/man/sdfsample.Rd ChemmineR/man/sdfstr2list.Rd ChemmineR/man/searchSim.Rd ChemmineR/man/searchString.Rd ChemmineR/man/selectInBatches.Rd ChemmineR/man/setPriorities.Rd ChemmineR/man/smartsSearchOB.Rd ChemmineR/man/smiles2sdf.Rd ChemmineR/man/smisample.Rd ChemmineR/man/status.Rd ChemmineR/man/toolDetails.Rd ChemmineR/man/trimNeighbors.Rd ChemmineR/man/validSDF.Rd ChemmineR/man/view.Rd ChemmineR/man/write.SDF.Rd ChemmineR/man/write.SDFsplit.Rd ChemmineR/man/write.SMI.Rd
ChemmineR/profiling
ChemmineR/profiling/test_fpSim.R
ChemmineR/profiling/test_parsing.R
ChemmineR/runSwig.sh
ChemmineR/src
ChemmineR/src/DisjointSets.cpp
ChemmineR/src/DisjointSets.h
ChemmineR/src/Makevars
ChemmineR/src/cluster.cc
ChemmineR/src/cstrsplit.cc
ChemmineR/src/debug.h
ChemmineR/src/desc.cc
ChemmineR/src/desc.h
ChemmineR/src/fingerprints.cc
ChemmineR/src/formats.cc
ChemmineR/src/molecule.cc
ChemmineR/src/molecule.h
ChemmineR/src/r_wrap.cc
ChemmineR/src/script.cc
ChemmineR/src/script.h
ChemmineR/src/similarity.cc
ChemmineR/swig.i
ChemmineR/tests
ChemmineR/tests/runTests.R
ChemmineR/vignettes
ChemmineR/vignettes/ChemmineR.Rmd
ChemmineR/vignettes/ChemmineR.Rmd_bootstrap
ChemmineR/vignettes/ChemmineR.Rnw.orig
ChemmineR/vignettes/ChemmineR_cache
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ChemmineR/vignettes/ChemmineR_cache/html/__packages
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ChemmineR/vignettes/header.html
ChemmineR/vignettes/html.template_bootstrap
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ChemmineR/vignettes/visualizescreenshot.png

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