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.

Author
Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Date of publication
None
Maintainer
Thomas Girke <thomas.girke@ucr.edu>
License
Artistic-2.0
Version
2.26.1
URLs

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
ChemmineR/vignettes/ChemmineR_cache/html
ChemmineR/vignettes/ChemmineR_cache/html/__packages
ChemmineR/vignettes/ChemmineR_cache/html/ap_dist_matrix_08c23d01350120cdb68ebc7f59dca079.RData
ChemmineR/vignettes/ChemmineR_cache/html/ap_dist_matrix_08c23d01350120cdb68ebc7f59dca079.rdb
ChemmineR/vignettes/ChemmineR_cache/html/ap_dist_matrix_08c23d01350120cdb68ebc7f59dca079.rdx
ChemmineR/vignettes/ChemmineR_cache/html/binningClusterWWW_e9dedc55d1334a82d774fa1881be32c1.RData
ChemmineR/vignettes/ChemmineR_cache/html/binningClusterWWW_e9dedc55d1334a82d774fa1881be32c1.rdb
ChemmineR/vignettes/ChemmineR_cache/html/binningClusterWWW_e9dedc55d1334a82d774fa1881be32c1.rdx
ChemmineR/vignettes/ChemmineR_cache/html/boxplot_3e7bb475e85e3bb60e093a969e967c24.RData
ChemmineR/vignettes/ChemmineR_cache/html/boxplot_3e7bb475e85e3bb60e093a969e967c24.rdb
ChemmineR/vignettes/ChemmineR_cache/html/boxplot_3e7bb475e85e3bb60e093a969e967c24.rdx
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ChemmineR/vignettes/ChemmineR_cache/html/duplicates_82e9ff870b5cd9ffd7c48dcd71407de1.RData
ChemmineR/vignettes/ChemmineR_cache/html/duplicates_82e9ff870b5cd9ffd7c48dcd71407de1.rdb
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ChemmineR/vignettes/ChemmineR_cache/html/fingerprintSearchCMT_e1250cec1b33de05997004d4f16614fa.rdb
ChemmineR/vignettes/ChemmineR_cache/html/fingerprintSearchCMT_e1250cec1b33de05997004d4f16614fa.rdx
ChemmineR/vignettes/ChemmineR_cache/html/fp_hclust_382a97b88d4caae4eb45f73899474e1a.RData
ChemmineR/vignettes/ChemmineR_cache/html/fp_hclust_382a97b88d4caae4eb45f73899474e1a.rdb
ChemmineR/vignettes/ChemmineR_cache/html/fp_hclust_382a97b88d4caae4eb45f73899474e1a.rdx
ChemmineR/vignettes/ChemmineR_cache/html/getIds_b73194a992f0581e3eea2636bff437dc.RData
ChemmineR/vignettes/ChemmineR_cache/html/getIds_b73194a992f0581e3eea2636bff437dc.rdb
ChemmineR/vignettes/ChemmineR_cache/html/getIds_b73194a992f0581e3eea2636bff437dc.rdx
ChemmineR/vignettes/ChemmineR_cache/html/hclust_898157d51633b8dbf2311c6b0918d4ee.RData
ChemmineR/vignettes/ChemmineR_cache/html/hclust_898157d51633b8dbf2311c6b0918d4ee.rdb
ChemmineR/vignettes/ChemmineR_cache/html/hclust_898157d51633b8dbf2311c6b0918d4ee.rdx
ChemmineR/vignettes/ChemmineR_cache/html/heatmap_048d302e841cf9f58d4f5901fc61d059.RData
ChemmineR/vignettes/ChemmineR_cache/html/heatmap_048d302e841cf9f58d4f5901fc61d059.rdb
ChemmineR/vignettes/ChemmineR_cache/html/heatmap_048d302e841cf9f58d4f5901fc61d059.rdx
ChemmineR/vignettes/ChemmineR_cache/html/launchCMTool_bb4cc8a1b2993b63af7362aae854d15c.RData
ChemmineR/vignettes/ChemmineR_cache/html/launchCMTool_bb4cc8a1b2993b63af7362aae854d15c.rdb
ChemmineR/vignettes/ChemmineR_cache/html/launchCMTool_bb4cc8a1b2993b63af7362aae854d15c.rdx
ChemmineR/vignettes/ChemmineR_cache/html/listCMTools_a07c66c1020bd4878bb801cc6e40b005.RData
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ChemmineR/vignettes/ChemmineR_cache/html/listCMTools_a07c66c1020bd4878bb801cc6e40b005.rdx
ChemmineR/vignettes/ChemmineR_cache/html/mds_scatter_3cdf9723ee1a1433ef8432457dfcb58c.RData
ChemmineR/vignettes/ChemmineR_cache/html/mds_scatter_3cdf9723ee1a1433ef8432457dfcb58c.rdb
ChemmineR/vignettes/ChemmineR_cache/html/mds_scatter_3cdf9723ee1a1433ef8432457dfcb58c.rdx
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ChemmineR/vignettes/ChemmineR_cache/html/obDescriptorsCMT_43001ed2d6bf6fde0dfee8721b4e33a1.rdb
ChemmineR/vignettes/ChemmineR_cache/html/obDescriptorsCMT_43001ed2d6bf6fde0dfee8721b4e33a1.rdx
ChemmineR/vignettes/ChemmineR_cache/html/obDescriptorsWWW_cc9e79294516c1d2df4fdff7a3cf78db.RData
ChemmineR/vignettes/ChemmineR_cache/html/obDescriptorsWWW_cc9e79294516c1d2df4fdff7a3cf78db.rdb
ChemmineR/vignettes/ChemmineR_cache/html/obDescriptorsWWW_cc9e79294516c1d2df4fdff7a3cf78db.rdx
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