girke-lab/ChemmineR
Cheminformatics Toolkit for R

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In girke-lab/ChemmineR: Cheminformatics Toolkit for R 

BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

suppressPackageStartupMessages({
    library(ChemmineR)
    library(fmcsR)
    library(ggplot2)
     #library(ChemmineOB)

})

Note: the most recent version of this tutorial can be found here and a short overview slide show here.

Introduction

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 small molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms.

Figure: ChemmineR environment with its add-on packages and selected functionalities

In addition, ChemmineR offers visualization functions for compound clustering results and chemical structures. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. The first version of this package was published in Cao et al. [-@Cao_2008]. Since then many additional utilities and add-on packages have been added to the environment (Figure 2) and many more are under development for future releases [@Backman_2011; @Wang_2013].


Recently Added Features

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Getting Started

Installation

The R software for running ChemmineR can be downloaded from CRAN (http://cran.at.r-project.org/). The ChemmineR package can be installed from R with:

 if (!requireNamespace("BiocManager", quietly=TRUE))
     install.packages("BiocManager")
 BiocManager::install("ChemmineR")
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Loading the Package and Documentation

 library("ChemmineR") # Loads the package

 library(help="ChemmineR") # Lists all functions and classes 
 vignette("ChemmineR") # Opens this PDF manual from R
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Five Minute Tutorial

The following code gives an overview of the most important functionalities provided by ChemmineR. Copy and paste of the commands into the R console will demonstrate their utilities.

Create Instances of SDFset class: 

 data(sdfsample) 
 sdfset <- sdfsample
 sdfset # Returns summary of SDFset 
 sdfset[1:4] # Subsetting of object

 sdfset[[1]] # Returns summarized content of one SDF


```r
 view(sdfset[1:4]) # Returns summarized content of many SDFs, not printed here 
 as(sdfset[1:4], "list") # Returns complete content of many SDFs, not printed here

An SDFset is created during the import of an SD file:

 sdfset <- read.SDFset("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/sdfsample.sdf")

Miscellaneous accessor methods for SDFset container:

 header(sdfset[1:4]) # Not printed here

 header(sdfset[[1]])

 atomblock(sdfset[1:4]) # Not printed here 

atomblock(sdfset[[1]])[1:4,] 

bondblock(sdfset[1:4]) # Not printed here 

 bondblock(sdfset[[1]])[1:4,] 

 datablock(sdfset[1:4]) # Not printed here 

 datablock(sdfset[[1]])[1:4]

Assigning compound IDs and keeping them unique: 

 cid(sdfset)[1:4] # Returns IDs from SDFset object
 sdfid(sdfset)[1:4] # Returns IDs from SD file header block
 unique_ids <- makeUnique(sdfid(sdfset))
 cid(sdfset) <- unique_ids

Converting the data blocks in an SDFset to a matrix:

 blockmatrix <- datablock2ma(datablocklist=datablock(sdfset)) # Converts data block to matrix 
 numchar <- splitNumChar(blockmatrix=blockmatrix) # Splits to numeric and character matrix 
 numchar[[1]][1:2,1:2] # Slice of numeric matrix 
 numchar[[2]][1:2,10:11] # Slice of character matrix

Compute atom frequency matrix, molecular weight and formula:

 propma <- data.frame(MF=MF(sdfset), MW=MW(sdfset), atomcountMA(sdfset))
 propma[1:4, ]

Assign matrix data to data block: 

 datablock(sdfset) <- propma 
 datablock(sdfset[1])

String searching in SDFset: 

 grepSDFset("650001", sdfset, field="datablock", mode="subset") # Returns summary view of matches. Not printed here.

 grepSDFset("650001", sdfset, field="datablock", mode="index")

Export SDFset to SD file: 

 write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE)

Plot molecule structure of one or many SDFs: 

 plot(sdfset[1:4], print=FALSE) # Plots structures to R graphics device 

 sdf.visualize(sdfset[1:4]) # Compound viewing in web browser

Figure: Visualization webpage created by calling sdf.visualize.

Structure similarity searching and clustering: 

 apset <- sdf2ap(sdfset) # Generate atom pair descriptor database for searching 

 data(apset) # Load sample apset data provided by library. 
 cmp.search(apset, apset[1], type=3, cutoff = 0.3, quiet=TRUE) # Search apset database with single compound. 

 cmp.cluster(db=apset, cutoff = c(0.65, 0.5), quiet=TRUE)[1:4,] # Binning clustering using variable similarity cutoffs.
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OpenBabel Functions

ChemmineR integrates now a subset of cheminformatics functionalities implemented in the OpenBabel C++ library [@greycite13432; @Cao_2008]. These utilities can be accessed by installing the ChemmineOB package and the OpenBabel software itself. ChemmineR will automatically detect the availability of ChemmineOB and make use of the additional utilities. The following lists the functions and methods that make use of OpenBabel. References are included to locate the sections in the manual where the utility and usage of these functions is described.

Structure format interconversions (see Section Format Inter-Conversions)

convertFormatFile("SML","SDF","mycompound.sml","mycompound.sdf")
sdfset=read.SDFset("mycompound.sdf")

propOB: generates several compound properties. See the man page for a current list of properties computed.

propOB(sdfset[1])

fingerprintOB: generates fingerprints for compounds. The fingerprint name can be anything supported by OpenBabel. See the man page for a current list.

fingerprintOB(sdfset,"FP2")

smartsSearchOB: find matches of SMARTS patterns in compounds

#count rotable bonds
smartsSearchOB(sdfset[1:5],"[!$(*#*)&!D1]-!@[!$(*#*)&!D1]",uniqueMatches=FALSE)

exactMassOB: Compute the monoisotopic (exact) mass of a set of compounds

exactMassOB(sdfset[1:5])

regenerateCoords: Re-compute the 2D coordinates of a compound using Open Babel. This can sometimes improve the quality of the compounds plot. See also the regenCoords option of the plot function.

sdfset2 = regenerateCoords(sdfset[1:5])

plot(sdfset[1], regenCoords=TRUE,print=FALSE)

OpenBabel can also be used to plot compounds directly:

openBabelPlot(sdfset[4],regenCoords=TRUE)

generate3DCoords: Generate 3D coordinates for compounds with only 2D coordinates.

sdf3D = generate3DCoords(sdfset[1])

canonicalize: Compute a canonicalized atom numbering. This allows compounds with the same molecular structure but different atom numberings to be compared properly.

canonicalSdf= canonicalize(sdfset[1])

canonicalNumbering: Return a mapping from the original atom numbering to the canonical atom number.

mapping = canonicalNumbering(sdfset[1])
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Overview of Classes and Functions

The following list gives an overview of the most important S4 classes, methods and functions available in the ChemmineR package. The help documents of the package provide much more detailed information on each utility. The standard R help documents for these utilities can be accessed with this syntax: ?function\_name (e.g. ?cid) and ?class\_name-class (e.g. ?"SDFset-class").

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Molecular Structure Data

Classes

Functions/Methods (mainly for SDFset container, SMIset should be coerced with smiles2sd to SDFset)

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Structure Descriptor Data

Classes

Functions/Methods

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Import of Compounds

SDF Import

The following gives an overview of the most important import/export functionalities for small molecules provided by ChemmineR. The given example creates an instance of the SDFset class using as sample data set the first 100 compounds from this PubChem SD file (SDF): Compound_00650001_00675000.sdf.gz (ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/).

SDFs can be imported with the read.SDFset function:

 sdfset <- read.SDFset("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/sdfsample.sdf") 

 data(sdfsample) # Loads the same SDFset provided by the library 
 sdfset <- sdfsample
 valid <- validSDF(sdfset) # Identifies invalid SDFs in SDFset objects 
 sdfset <- sdfset[valid] # Removes invalid SDFs, if there are any

Import SD file into SDFstr container: 

 sdfstr <- read.SDFstr("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/sdfsample.sdf")

Create SDFset from SDFstr class:

 sdfstr <- as(sdfset, "SDFstr") 
 sdfstr
 as(sdfstr, "SDFset")

SDFs in V3000 format can also be imported, this format will be detected automacially. If you want to also be able to access the extended attributes of this format, you should set extendedAttributes=TRUE on read.SDFset. 

 v3 <- read.SDFset("https://cluster.hpcc.ucr.edu/~tgirke/Documents/R_BioCond/Samples/v3000.sdf",extendedAttributes=TRUE)

This will have the side effect of producing an SDFset composed of ExtSDF objects, which are sub-classes of SDF objects. Not all SDF methods will work on this sub-type currently. 

getAtomAttr(v3[[1]],17,"CHG")
getBondAttr(v3[[1]],10,"CFG")

This example will fetch the value of the atom attribute "CHG" on atom 16, and the value of the bond attribute "CFG" on bond 10.

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SMILES Import

The read.SMIset function imports one or many molecules from a SMILES file and stores them in a SMIset container. The input file is expected to contain one SMILES string per row with tab-separated compound identifiers at the end of each line. The compound identifiers are optional.

Create sample SMILES file and then import it: 

 data(smisample); smiset <- smisample
 write.SMI(smiset[1:4], file="sub.smi") 
 smiset <- read.SMIset("sub.smi")

Inspect content of SMIset: 

 data(smisample) # Loads the same SMIset provided by the library 
 smiset <- smisample
 smiset 
 view(smiset[1:2])

Accessor functions: 

 cid(smiset[1:4]) 
 smi <- as.character(smiset[1:2])

Create SMIset from named character vector:

 as(smi, "SMIset")
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Export of Compounds

SDF Export

Write objects of classes SDFset/SDFstr/SDF to SD file:

 write.SDF(sdfset[1:4], file="sub.sdf")

Writing customized SDFset to file containing ChemmineR signature, IDs from SDFset and no data block: 

 write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE, db=NULL)

Example for injecting a custom matrix/data frame into the data block of an SDFset and then writing it to an SD file:

 props <- data.frame(MF=MF(sdfset), MW=MW(sdfset), atomcountMA(sdfset)) 
 datablock(sdfset) <- props
 write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE)

Indirect export via SDFstr object: 

 sdf2str(sdf=sdfset[[1]], sig=TRUE, cid=TRUE) # Uses default components 
 sdf2str(sdf=sdfset[[1]], head=letters[1:4], db=NULL) # Uses custom components for header and data block

Write SDF, SDFset or SDFstr classes to file: 

 write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE, db=NULL)
 write.SDF(sdfstr[1:4], file="sub.sdf") 
 cat(unlist(as(sdfstr[1:4], "list")), file="sub.sdf", sep="")
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SMILES Export

Write objects of class SMIset to SMILES file with and without compound identifiers: 

 data(smisample); smiset <- smisample # Sample data set 

 write.SMI(smiset[1:4], file="sub.smi", cid=TRUE) write.SMI(smiset[1:4], file="sub.smi", cid=FALSE)
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Format Interconversions

The sdf2smiles and smiles2sdf functions provide format interconversion between SMILES strings (Simplified Molecular Input Line Entry Specification) and SDFset containers.

Convert an SDFset container to a SMILES character string:

 data(sdfsample);
 sdfset <- sdfsample[1] 
 smiles <- sdf2smiles(sdfset) 
 smiles

Convert a SMILES character string to an SDFset container:

 sdf <- smiles2sdf("CC(=O)OC1=CC=CC=C1C(=O)O")
 view(sdf)

When the ChemineOB package is installed these conversions are performed with the OpenBabel Open Source Chemistry Toolbox. Otherwise the functions will fall back to using the ChemMine Tools web service for this operation. The latter will require internet connectivity and is limited to only the first compound given. ChemmineOB provides access to the compound format conversion functions of OpenBabel. Currently, over 160 formats are supported by OpenBabel. The functions convertFormat and convertFormatFile can be used to convert files or strings between any two formats supported by OpenBabel. For example, to convert a SMILES string to an SDF string, one can use the convertFormat function.

 sdfStr <- convertFormat("SMI","SDF","CC(=O)OC1=CC=CC=C1C(=O)O_name")

This will return the given compound as an SDF formatted string. 2D coordinates are also computed and included in the resulting SDF string.

To convert a file with compounds encoded in one format to another format, the convertFormatFile function can be used instead. 

 convertFormatFile("SMI","SDF","test.smiles","test.sdf")

To see the whole list of file formats supported by OpenBabel, one can run from the command-line "obabel -L formats".

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Splitting SD Files

The following write.SDFsplit function allows to split SD Files into any number of smaller SD Files. This can become important when working with very big SD Files. Users should note that this function can output many files, thus one should run it in a dedicated directory!

Create sample SD File with 100 molecules: 

 write.SDF(sdfset, "test.sdf")

Read in sample SD File. Note: reading file into SDFstr is much faster than into SDFset: 

 sdfstr <- read.SDFstr("test.sdf")

Run export on SDFstr object: 

 write.SDFsplit(x=sdfstr, filetag="myfile", nmol=10) # 'nmol' defines the number of molecules to write to each file

Run export on SDFset object: 

 write.SDFsplit(x=sdfset, filetag="myfile", nmol=10)
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Streaming Through Large SD Files

The sdfStream function allows to stream through SD Files with millions of molecules without consuming much memory. During this process any set of descriptors, supported by ChemmineR, can be computed (e.g. atom pairs, molecular properties, etc.), as long as they can be returned in tabular format. In addition to descriptor values, the function returns a line index that gives the start and end positions of each molecule in the source SD File. This line index can be used by the downstream read.SDFindex function to retrieve specific molecules of interest from the source SD File without reading the entire file into R. The following outlines the typical workflow of this streaming functionality in ChemmineR.

Create sample SD File with 100 molecules: 

 write.SDF(sdfset, "test.sdf")

Define descriptor set in a simple function: 

 desc <- function(sdfset) 
 cbind(SDFID=sdfid(sdfset), 
    # datablock2ma(datablocklist=datablock(sdfset)), 
     MW=MW(sdfset),
    groups(sdfset), APFP=desc2fp(x=sdf2ap(sdfset), descnames=1024,
    type="character"), AP=sdf2ap(sdfset, type="character"), rings(sdfset,
    type="count", upper=6, arom=TRUE) )

Run sdfStream with desc function and write results to a file called matrix.xls:

 sdfStream(input="test.sdf", output="matrix.xls", fct=desc, Nlines=1000) # 'Nlines': number of lines to read from input SD File at a time

One can also start reading from a specific line number in the SD file. The following example starts at line number 950. This is useful for restarting and debugging the process. With append=TRUE the result can be appended to an existing file. 

 sdfStream(input="test.sdf", output="matrix2.xls", append=FALSE, fct=desc, Nlines=1000, startline=950)

Select molecules meeting certain property criteria from SD File using line index generated by previous sdfStream step:

 indexDF <- read.delim("matrix.xls", row.names=1)[,1:4] 
 indexDFsub <- indexDF[indexDF$MW < 400, ] # Selects molecules with MW < 400 
 sdfset <- read.SDFindex(file="test.sdf", index=indexDFsub, type="SDFset") # Collects results in 'SDFset' container

Write results directly to SD file without storing larger numbers of molecules in memory: 

 read.SDFindex(file="test.sdf", index=indexDFsub, type="file",
 outfile="sub.sdf")

Read AP/APFP strings from file into APset or FP object: 

 apset <- read.AP(x="matrix.xls", type="ap", colid="AP") 
 apfp <- read.AP(x="matrix.xls", type="fp", colid="APFP")

Alternatively, one can provide the AP/APFP strings in a named character vector: 

 apset <- read.AP(x=sdf2ap(sdfset[1:20], type="character"), type="ap") 
 fpchar <- desc2fp(sdf2ap(sdfset[1:20]), descnames=1024, type="character")
 fpset <- as(fpchar, "FPset")
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Storing Compounds in an SQL Database

As an alternative to sdfStream, there is now also an option to store data in an SQL database, which then allows for fast queries and compound retrieval. The default database is SQLite, but any other SQL database should work with some minor modifications to the table definitions, which are stored in schema/compounds.SQLite under the ChemmineR package directory. Compounds are stored in their entirety in the databases so there is no need to keep any original data files.

Users can define their own set of compound features to compute and store when loading new compounds. Each of these features will be stored in its own, indexed table. Searches can then be performed using these features to quickly find specific compounds. Compounds can always be retrieved quickly because of the database index, no need to scan a large compound file. In addition to user defined features, descriptors can also be computed and stored for each compound.

A new database can be created with the initDb function. This takes either an existing database connection, or a filename. If a filename is given then an SQLite database connection is created. It then ensures that the required tables exist and creates them if not. The connection object is then returned. This function can be called safely on the same connection or database many times and will not delete any data.

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Loading Data

The functions loadSdf and loadSmiles can be used to load compound data from either a file (both) or an SDFset (loadSdf only). The fct parameter should be a function to extract features from the data. It will be handed an SDFset generated from the data being loaded. This may be done in batches, so there is no guarantee that the given SDFSset will contain the whole dataset. This function should return a data frame with a column for each feature and a row for each compound given. The order of the final data frame should be the same as that of the SDFset. The column names will become the feature names. Each of these features will become a new, indexed, table in the database which can be used later to search for compounds.

The descriptors parameter can be a function which computes descriptors. This function will also be given an SDFset object, which may be done in batches. It should return a data frame with the following two columns: "descriptor" and "descriptor_type". The "descriptor" column should contain a string representation of the descriptor, and "descriptor_type" is the type of the descriptor. Our convention for atom pair is "ap" and "fp" for finger print. The order should also be maintained.

When the data has been loaded, loadSdf will return the compound id numbers of each compound loaded. These compound id numbers are computed by the database and are not extracted from the compound data itself. They can be used to quickly retrieve compounds later.

New features can also be added using this function. However, all compounds must have all features so if new features are added to a new set of compounds, all existing features must be computable by the fct function given. If new features are detected, all existing compounds will be run through fct in order to compute the new features for them as well.

For example, if dataset X is loaded with features F1 and F2, and then at a later time we load dataset Y with new feature F3, the fct function used to load dataset Y must compute and return features F1, F2, and F3. loadSdf will call fct with both datasets X and Y so that all features are available for all compounds. If any features are missing an error will be raised. If just new features are being added, but no new compounds, use the addNewFeatures function.

In this example, we create a new database called "test.db" and load it with data from an SDFset. We also define fct to compute the molecular weight, "MW", and the number of rings and aromatic rings. The rings function actually returns a data frame with columns "RINGS" and "AROMATIC", which will be merged into the data frame being created which will also contain the "MW" column. These will be the names used for these features and must be used when searching with them. Finally, the new compound ids are returned and stored in the "ids" variable.

 data(sdfsample)

 #create and initialize a new SQLite database 
 conn <- initDb("test.db")

 # load data and compute 3 features: molecular weight, with the MW function, 
 # and counts for RINGS and AROMATIC, as computed by rings, which 
 # returns a data frame itself. 
 ids<-loadSdf(conn,sdfsample, function(sdfset) 
                     data.frame(rings(sdfset,type="count",upper=6, arom=TRUE)) ) 

 #list features in the database:
 print(listFeatures(conn))
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Updates

By default the loadSdf / loadSmiles functions will detect duplicate compound entries and only insert one of them. This means it is safe to run these functions on the same data set several times and you won't end up with duplicates. This allows the functions to be re-run in the event that a previous run on a dataset does not complete. Duplicate compounds are detected by compouting the MD5 checksum on the textual representation of it.

It can also update existing compounds with new versions of the same compound. To enable this, set updateByName to true. It will then consider two compounds with the same name to be the same, even if the definition is different. Then, if the name of a compound exists in the database and it is trying to insert another compound with the same name, it will overwrite the existing compound. It will also drop and re-compute all associated descriptors and features for the new compound (assuming the required functions for descriptor and feature computation are available at the time the update is performed).

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Duplicate Descriptors

It is often the case when loading a large set of compounds that several compounds will produce the same descriptor. ChemmineR detects this case and only stores one copy of the descriptor for every compound it is for. This feature saves some space and some time for processes that need to be applied to every descriptor. It also highlights a new problem. If you have a descriptor in hand and you want to find a single compound to represent it, which compound should be used if the descriptor was produced from multiple compounds? To address this problem, ChemmineR allows you to set priority values for each compound-descriptor mapping. Then, in contexts where a single compound is required, the highest priority compound will be chosen. Highest priority corresponds to the lowest numerical value. So mapping with priority 0 would be used first.

To set these priorities there is the function setPriorities. It takes a function, priorityFn, for computing these priority values. The setPriorities function should be run after loading a complete set of data. It will find each group of compounds which share the same descriptor and call the given function, priorityFn, with the compound_id numbers of the group. This function should then assign priorities to each compound-descriptor pair, however it wishes.

One built in priority function is forestSizePriorities. This simply prefers compounds with fewer disconnected components over compounds with more dissconnected components.

setPriorities(conn,forestSizePriorities)
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Searching

Compounds can be searched for using the findCompounds function. This function takes a connection object, a vector of feature names used in the tests, and finally, a vector of tests that must all pass for a compound to be included in the result set. Each test should be a boolean expression. For example: c("MW <= 400","RINGS \> 3") would return all compounds with a molecular weight of 400 or less and more than 3 rings, assuming these features exist in the database. The syntax for each test is '\<feature name\> \<SQL operator\> \<value\>'. If you know SQL you can go beyond this basic syntax. These tests will simply be concatenated together with "AND" in-between them and tacked on the end of a WHERE clause of an SQL statement. So any SQL that will work in that context is fine. The function will return a list of compound ids, the actual compounds can be fetched with getCompounds. If just the names are needed, the getCompoundNames function can be used. Compounds can also be fetched by name using the findCompoundsByName function.

In this example we search for compounds with 0 or 1 rings:

results = findCompounds(conn,"rings",c("rings <= 1"))
message("found ",length(results))

If more than one test is given, only compounds which satisfy all tests are found. So if we wanted to further restrict our search to compounds with 2 or more aromatic rings we could do:

results = findCompounds(conn,c("rings","aromatic"),c("rings<=2","aromatic >= 2"))
message("found ",length(results))

Remember that any feature used in some test must be listed in the second argument.

String patterns can also be used. So if we wanted to match a substring of the molecular formula, say to find compounds with 21 carbon atoms, we could do:

results = findCompounds(conn,"formula",c("formula like '%C21%'"))
message("found ",length(results))

The "like" operator does a pattern match. There are two wildcard operators that can be used with this operator. The "%" will match any stretch of characters while the "?" will match any single character. So the above expression would match a formula like "C21H28N4O6".

Valid comparison operators are:

The boolean operators "AND" and "OR" can also be used to create more complex expressions within a single test.

If you just want to fetch every compound in the database you can use the getAllCompoundIds function:

allIds = getAllCompoundIds(conn)
message("found ",length(allIds))
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Using Search Results

Once you have a list of compound ids from the findCompounds function, you can either fetch the compound names, or the whole set of compounds as an SDFset. 

#get the names of the compounds:
names = getCompoundNames(conn,results)

#if the name order is important set keepOrder=TRUE 
#It will take a little longer though
names = getCompoundNames(conn,results,keepOrder=TRUE) 


# get the whole set of compounds
compounds = getCompounds(conn,results)
#in order:
compounds = getCompounds(conn,results,keepOrder=TRUE)
#write results directly to a file:
compounds = getCompounds(conn,results,filename=file.path(tempdir(),"results.sdf"))

Using the getCompoundFeatures function, you can get a set of feature values as a data frame:

getCompoundFeatures(conn,results[1:5],c("rings","aromatic"))

#write results directly to a CSV file (reduces memory usage):
getCompoundFeatures(conn,results[1:5],c("rings","aromatic"),filename="features.csv")

#maintain input order in output:
print(results[1:5])
getCompoundFeatures(conn,results[1:5],c("rings","aromatic"),keepOrder=TRUE)
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Pre-Built Databases

We have pre-built SQLite databases for the Drug Bank and DUD datasets. They can be found in the ChemmineDrugs annotation package. Connections to these databases can be fetched from the functions DrugBank and DUD to get the corresponding database. Any of the above functions can then be used to query the database.

The DUD dataset was downloaded from here. A description can be found here.

The Drug Bank data set is version 4.1. It can be downloaded here

The following features are included:

The DUD database additionally includes:

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Working with SDF/SDFset Classes

Several methods are available to return the different data components of SDF/SDFset containers in batches. The following examples list the most important ones. To save space their content is not printed in the manual. 

 view(sdfset[1:4]) # Summary view of several molecules 

 length(sdfset) # Returns number of molecules 
 sdfset[[1]] # Returns single molecule from SDFset as SDF object 

 sdfset[[1]][[2]] # Returns atom block from first compound as matrix

 sdfset[[1]][[2]][1:4,] 
 c(sdfset[1:4], sdfset[5:8]) # Concatenation of several SDFsets

The grepSDFset function allows string matching/searching on the different data components in SDFset. By default the function returns a SDF summary of the matching entries. Alternatively, an index of the matches can be returned with the setting mode="index". 

 grepSDFset("650001", sdfset, field="datablock", mode="subset") # To return index, set mode="index")

Utilities to maintain unique compound IDs: 

 sdfid(sdfset[1:4]) # Retrieves CMP IDs from Molecule Name field in header block. 
 cid(sdfset[1:4]) # Retrieves CMP IDs from ID slot in SDFset. 
 unique_ids <- makeUnique(sdfid(sdfset)) # Creates unique IDs by appending a counter to duplicates. 
 cid(sdfset) <- unique_ids # Assigns uniquified IDs to ID slot

Subsetting by character, index and logical vectors: 

 view(sdfset[c("650001", "650012")])
 view(sdfset[4:1])
 mylog <- cid(sdfset)
 view(sdfset[mylog])

Accessing SDF/SDFset components: header, atom, bond and data blocks: 

 atomblock(sdf); sdf[[2]];
 sdf[["atomblock"]] # All three methods return the same component

 header(sdfset[1:4]) 
 atomblock(sdfset[1:4])
 bondblock(sdfset[1:4]) 
 datablock(sdfset[1:4])  
 header(sdfset[[1]])
 atomblock(sdfset[[1]]) 
 bondblock(sdfset[[1]]) 
 datablock(sdfset[[1]])

Replacement Methods: 

 sdfset[[1]][[2]][1,1] <- 999 
 atomblock(sdfset)[1] <- atomblock(sdfset)[2] 
 datablock(sdfset)[1] <- datablock(sdfset)[2]

Assign matrix data to data block: 

 datablock(sdfset) <- as.matrix(iris[1:100,])
 view(sdfset[1:4])

Class coercions from SDFstr to list, SDF and SDFset: 

 as(sdfstr[1:2], "list") as(sdfstr[[1]], "SDF")
 as(sdfstr[1:2], "SDFset")

Class coercions from SDF to SDFstr, SDFset, list with SDF sub-components: 

 sdfcomplist <- as(sdf, "list") sdfcomplist <-
 as(sdfset[1:4], "list"); as(sdfcomplist[[1]], "SDF") sdflist <-
 as(sdfset[1:4], "SDF"); as(sdflist, "SDFset") as(sdfset[[1]], "SDFstr")
 as(sdfset[[1]], "SDFset")

Class coercions from SDFset to lists with components consisting of SDF or sub-components: 

 as(sdfset[1:4], "SDF") as(sdfset[1:4], "list") as(sdfset[1:4], "SDFstr")
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Molecular Property Functions (Physicochemical Descriptors)

Several methods and functions are available to compute basic compound descriptors, such as molecular formula (MF), molecular weight (MW), and frequencies of atoms and functional groups. In many of these functions, it is important to set addH=TRUE in order to include/add hydrogens that are often not specified in an SD file.

 propma <- atomcountMA(sdfset, addH=FALSE) 
 boxplot(propma, col="blue", main="Atom Frequency") 

 boxplot(rowSums(propma), main="All Atom Frequency")

Data frame provided by library containing atom names, atom symbols, standard atomic weights, group and period numbers: 

 data(atomprop)
 atomprop[1:4,]

Compute MW and formula: 

 MW(sdfset[1:4], addH=FALSE)
 MF(sdfset[1:4], addH=FALSE)

Enumerate functional groups: 

 groups(sdfset[1:4], groups="fctgroup", type="countMA")

Combine MW, MF, charges, atom counts, functional group counts and ring counts in one data frame: 

 propma <- data.frame(MF=MF(sdfset, addH=FALSE), MW=MW(sdfset, addH=FALSE),
                             Ncharges=sapply(bonds(sdfset, type="charge"), length),
                             atomcountMA(sdfset, addH=FALSE), 
                             groups(sdfset, type="countMA"), 
                             rings(sdfset, upper=6, type="count", arom=TRUE))
 propma[1:4,]

The following shows an example for assigning the values stored in a matrix (e.g. property descriptors) to the data block components in an SDFset. Each matrix row will be assigned to the corresponding slot position in the SDFset.

 datablock(sdfset) <- propma # Works with all SDF components 
 datablock(sdfset)[1:4] 
 test <- apply(propma[1:4,], 1, function(x) 
 data.frame(col=colnames(propma), value=x))

The data blocks in SDFs contain often important annotation information about compounds. The datablock2ma function returns this information as matrix for all compounds stored in an SDFset container. The splitNumChar function can then be used to organize all numeric columns in a numeric matrix and the character columns in a character matrix as components of a list object. 

 datablocktag(sdfset, tag="PUBCHEM_NIST_INCHI")
 datablocktag(sdfset,
 tag="PUBCHEM_OPENEYE_CAN_SMILES")

Convert entire data block to matrix: 

 blockmatrix <- datablock2ma(datablocklist=datablock(sdfset)) # Converts data block to matrix 
 numchar <- splitNumChar(blockmatrix=blockmatrix) # Splits matrix to numeric matrix and character matrix 
 numchar[[1]][1:4,]; numchar[[2]][1:4,]
 # Splits matrix to numeric matrix and character matrix
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Bond Matrices

Bond matrices provide an efficient data structure for many basic computations on small molecules. The function conMA creates this data structure from SDF and SDFset objects. The resulting bond matrix contains the atom labels in the row/column titles and the bond types in the data part. The labels are defined as follows: 0 is no connection, 1 is a single bond, 2 is a double bond and 3 is a triple bond. 

 conMA(sdfset[1:2],
 exclude=c("H")) # Create bond matrix for first two molecules in sdfset

 conMA(sdfset[[1]], exclude=c("H")) # Return bond matrix for first molecule 
 plot(sdfset[1], atomnum = TRUE, noHbonds=FALSE , no_print_atoms = "", atomcex=0.8) # Plot its structure with atom numbering 
 rowSums(conMA(sdfset[[1]], exclude=c("H"))) # Return number of non-H bonds for each atom
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Charges and Missing Hydrogens

The function bonds returns information about the number of bonds, charges and missing hydrogens in SDF and SDFset objects. It is used by many other functions (e.g. MW, MF, atomcount, atomcuntMA and plot) to correct for missing hydrogens that are often not specified in SD files. 

 bonds(sdfset[[1]], type="bonds")[1:4,]
 bonds(sdfset[1:2], type="charge")
 bonds(sdfset[1:2], type="addNH")
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Ring Perception and Aromaticity Assignment

The function rings identifies all possible rings in one or many molecules (here sdfset[1]) using the exhaustive ring perception algorithm from Hanser et al. [-@Hanser_1996]. In addition, the function can return all smallest possible rings as well as aromaticity information.

The following example returns all possible rings in a list. The argument upper allows to specify an upper length limit for rings. Choosing smaller length limits will reduce the search space resulting in shortened compute times. Note: each ring is represented by a character vector of atom symbols that are numbered by their position in the atom block of the corresponding SDF/SDFset object. 

 ringatoms <- rings(sdfset[1], upper=Inf, type="all", arom=FALSE, inner=FALSE)

For visual inspection, the corresponding compound structure can be plotted with the ring bonds highlighted in color: 

 atomindex <- as.numeric(gsub(".*_", "", unique(unlist(ringatoms))))
 plot(sdfset[1], print=FALSE, colbonds=atomindex)

Alternatively, one can include the atom numbers in the plot:

 plot(sdfset[1], print=FALSE, atomnum=TRUE, no_print_atoms="H")

Aromaticity information of the rings can be returned in a logical vector by setting arom=TRUE: 

 rings(sdfset[1], upper=Inf, type="all", arom=TRUE, inner=FALSE)

Return rings with no more than 6 atoms that are also aromatic:

 rings(sdfset[1], upper=6, type="arom", arom=TRUE, inner=FALSE)

Count shortest possible rings and their aromaticity assignments by setting type=count and inner=TRUE. The inner (smallest possible) rings are identified by first computing all possible rings and then selecting only the inner rings. For more details, consult the help documentation with ?rings.

 rings(sdfset[1:4], upper=Inf, type="count", arom=TRUE, inner=TRUE)
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Rendering Chemical Structure Images

R Graphics Device

A new plotting function for compound structures has been added to the package recently. This function uses the native R graphics device for generating compound depictions. At this point this function is still in an experimental developmental stage but should become stable soon.

If you have ChemmineOB available you can use the regenCoords option to have OpenBabel regenerate the coordinates for the compound. This can sometimes produce better looking plots.

Plot compound Structures with R's graphics device: 

 data(sdfsample)
 sdfset <- sdfsample
 plot(sdfset[1:4], regenCoords=TRUE,print=FALSE) # 'print=TRUE' returns SDF summaries

Customized plots: 

 plot(sdfset[1:4], griddim=c(2,2), print_cid=letters[1:4], print=FALSE, 
        noHbonds=FALSE)

In the following plot, the atom block position numbers in the SDF are printed next to the atom symbols (atomnum = TRUE). For more details, consult help documentation with ?plotStruc or ?plot. 

 plot(sdfset["CMP1"], atomnum = TRUE, noHbonds=F , no_print_atoms = "",
        atomcex=0.8, sub=paste("MW:", MW(sdfsample["CMP1"])), print=FALSE)

Substructure highlighting by atom numbers: 

 plot(sdfset[1], print=FALSE, colbonds=c(22,26,25,3,28,27,2,23,21,18,8,19,20,24))
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Data Tables

Compound images and data can also be viewed in a web browser. This allows you to page through the table, as well as filter the results using the search box. Results can be sorted on any column by clicking on the column title. Compound images are rendered as SVGs, so you can zoom in on them to see more details.

data(sdfsample)
SDFDataTable(sdfsample[1:5])

Online with ChemMine Tools

Alternatively, one can visualize compound structures with a standard web browser using the online ChemMine Tools service.

Plot structures using web service ChemMine Tools: 

 sdf.visualize(sdfset[1:4])

Figure: Visualization webpage created by calling sdf.visualize.

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Similarity Comparisons and Searching

Maximum Common Substructure (MCS) Searching

The ChemmineR add-on package fmcsR provides support for identifying maximum common substructures (MCSs) and flexible MCSs among compounds. The algorithm can be used for pairwise compound comparisons, structure similarity searching and clustering. The manual describing this functionality is available here and the associated publication is Wang et al. [-@Wang_2013]. The following gives a short preview of some functionalities provided by the fmcsR package. 

 library(fmcsR)
 data(fmcstest) # Loads test sdfset object 
 test <- fmcs(fmcstest[1], fmcstest[2], au=2, bu=1) # Searches for MCS with mismatches 
 plotMCS(test) # Plots both query compounds with MCS in color
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AP/APset Classes for Storing Atom Pair Descriptors

The function sdf2ap computes atom pair descriptors for one or many compounds [@Carhart_1985; @Chen_2002]. It returns a searchable atom pair database stored in a container of class APset, which can be used for structural similarity searching and clustering. As similarity measure, the Tanimoto coefficient or related coefficients can be used. An APset object consists of one or many AP entries each storing the atom pairs of a single compound. Note: the deprecated cmp.parse function is still available which also generates atom pair descriptor databases, but directly from an SD file. Since the latter function is less flexible it may be discontinued in the future.

Generate atom pair descriptor database for searching: 

 ap <- sdf2ap(sdfset[[1]]) # For single compound
 ap 

 apset <- sdf2ap(sdfset)
 # For many compounds. 

view(apset[1:4])

Return main components of APset objects: 

 cid(apset[1:4]) # Compound IDs 
 ap(apset[1:4]) # Atom pair
 descriptors 
 db.explain(apset[1]) # Return atom pairs in human readable format

Coerce APset to other objects: 

 apset2descdb(apset) # Returns old list-style AP database 
 tmp <- as(apset, "list") # Returns list 
 as(tmp, "APset") # Converts list back to APset
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Large SDF and Atom Pair Databases

When working with large data sets it is often desirable to save the SDFset and APset containers as binary R objects to files for later use. This way they can be loaded very quickly into a new R session without recreating them every time from scratch.

Save and load of SDFset and APset containers: 

 save(sdfset, file = "sdfset.rda", compress = TRUE) 
 load("sdfset.rda") save(apset, file = "apset.rda", compress = TRUE)
 load("apset.rda")
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Pairwise Compound Comparisons with Atom Pairs

The cmp.similarity function computes the atom pair similarity between two compounds using the Tanimoto coefficient as similarity measure. The coefficient is defined as c/(a+b+c), which is the proportion of the atom pairs shared among two compounds divided by their union. The variable c is the number of atom pairs common in both compounds, while a and b are the numbers of their unique atom pairs. 

 cmp.similarity(apset[1],
 apset[2])
 cmp.similarity(apset[1], apset[1])
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Similarity Searching with Atom Pairs

The cmp.search function searches an atom pair database for compounds that are similar to a query compound. The following example returns a data frame where the rows are sorted by the Tanimoto similarity score (best to worst). The first column contains the indices of the matching compounds in the database. The argument cutoff can be a similarity cutoff, meaning only compounds with a similarity value larger than this cutoff will be returned; or it can be an integer value restricting how many compounds will be returned. When supplying a cutoff of 0, the function will return the similarity values for every compound in the database. 

 cmp.search(apset,
 apset["650065"], type=3, cutoff = 0.3, quiet=TRUE)

Alternatively, the function can return the matches in form of an index or a named vector if the type argument is set to 1 or 2, respectively. 

 cmp.search(apset, apset["650065"], type=1, cutoff = 0.3, quiet=TRUE)
 cmp.search(apset, apset["650065"], type=2, cutoff = 0.3, quiet=TRUE)
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FP/FPset Classes for Storing Fingerprints

The FPset class stores fingerprints of small molecules in a matrix-like representation where every molecule is encoded as a fingerprint of the same type and length. The FPset container acts as a searchable database that contains the fingerprints of many molecules. The FP container holds only one fingerprint. Several constructor and coerce methods are provided to populate FP/FPset containers with fingerprints, while supporting any type and length of fingerprints. For instance, the function desc2fp generates fingerprints from an atom pair database stored in an APset, and as(matrix, "FPset") and as(character, "FPset") construct an FPset database from objects where the fingerprints are represented as matrix or character objects, respectively.

Show slots of FPset class: 

 showClass("FPset")

Instance of FPset class: 

 data(apset) 
 fpset <- desc2fp(apset)
 view(fpset[1:2])

FPset class usage: 

 fpset[1:4] # behaves like a list 
 fpset[[1]] # returns FP object 
 length(fpset) # number of compounds ENDCOMMENT
 cid(fpset) # returns compound ids 
 fpset[10] <- 0 # replacement of 10th fingerprint to all zeros 
 cid(fpset) <- 1:length(fpset) # replaces compound ids 
 c(fpset[1:4], fpset[11:14]) # concatenation of several FPset objects

Construct FPset class form matrix:

 fpma <- as.matrix(fpset) # coerces FPset to matrix 
 as(fpma, "FPset")

Construct FPset class form character vector: 

 fpchar <- as.character(fpset) # coerces FPset to character strings 
 as(fpchar, "FPset") # construction of FPset class from character vector

Compound similarity searching with FPset:

 fpSim(fpset[1], fpset, method="Tanimoto", cutoff=0.4, top=4)

Folding fingerprints:

 fold(fpset) # fold each FP once
 fold(fpset, count=2) #fold each FP twice
 fold(fpset, bits=128) #fold each FP down to 128 bits
 fold(fpset[[1]])  # fold an individual FP

 fptype(fpset) # get type of FPs
 numBits(fpset) # get the number of bits of each FP
 foldCount(fold(fpset)) # the number of times an FP or FPset has been folded
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Atom Pair Fingerprints

Atom pairs can be converted into binary atom pair fingerprints of fixed length. Computations on this compact data structure are more time and memory efficient than on their relatively complex atom pair counterparts. The function desc2fp generates fingerprints from descriptor vectors of variable length such as atom pairs stored in APset or list containers. The obtained fingerprints can be used for structure similarity comparisons, searching and clustering.

Create atom pair sample data set: 

 data(sdfsample)
 sdfset <- sdfsample[1:10] 
 apset <- sdf2ap(sdfset)

Compute atom pair fingerprint database using internal atom pair selection containing the 4096 most common atom pairs identified in DrugBank's compound collection. For details see ?apfp. The following example uses from this set the 1024 most frequent atom pairs: 

 fpset <- desc2fp(apset, descnames=1024, type="FPset")

Alternatively, one can provide any custom atom pair selection. Here, the 1024 most common ones in apset: 

 fpset1024 <- names(rev(sort(table(unlist(as(apset, "list")))))[1:1024]) 
 fpset <- desc2fp(apset, descnames=fpset1024, type="FPset")

A more compact way of storing fingerprints is as character values:

 fpchar <- desc2fp(x=apset,
 descnames=1024, type="character") fpchar <- as.character(fpset)

Converting a fingerprint database to a matrix and vice versa:

 fpma <- as.matrix(fpset)
 fpset <- as(fpma, "FPset")

Similarity searching and returning Tanimoto similarity coefficients:

 fpSim(fpset[1], fpset, method="Tanimoto")

Under method one can choose from several predefined similarity measures including Tanimoto (default), Euclidean, Tversky or Dice. Alternatively, one can pass on custom similarity functions. 

 fpSim(fpset[1], fpset, method="Tversky", cutoff=0.4, top=4, alpha=0.5, beta=1)

Example for using a custom similarity function: 

 myfct <- function(a, b, c, d) c/(a+b+c+d)
 fpSim(fpset[1], fpset, method=myfct)

Clustering example: 

 simMAap <- sapply(cid(apfpset), function(x) fpSim(x=apfpset[x], apfpset, sorted=FALSE)) 
 hc <- hclust(as.dist(1-simMAap), method="single")
 plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=TRUE)
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Fingerprint E-values

The fpSim function can also return Z-scores, E-values, and p-values if given a set of score distribution parameters. These parameters can be computed over an fpSet with the genParameters function.

    params <- genParameters(fpset)

This function will compute all pairwise distances between the given fingerprints and then fit a Beta distribution to the resulting Tanimoto scores, conditioned on the number of set bits in each fingerprint. For large data sets where you would not want to compute all pairwise distances, you can set what fraction to sample with the sampleFraction argument. This step only needs to be done once for each database of fpSet objects. Alternatively, if you have a large database of fingerprints, or you believe that the parameters computed on a single database are more generally applicable, you can use the resulting parameters for other databases as well.

Once you have a set of parameters, you can pass them to fpSim with the parameters argument. 

    fpSim(fpset[[1]], fpset, top=10, parameters=params)

This will then return a data frame with the similarity, Z-score, E-value, and p-value. You can change which value will be used as a cutoff and to sort by by setting the argument scoreType to one of these scores. In this way you could set an E-value cutoff of 0.04 for example.

    fpSim(fpset[[1]], fpset, cutoff=0.04, scoreType="evalue", parameters=params)
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Pairwise Compound Comparisons with PubChem Fingerprints

The fpSim function computes the similarity coefficients (e.g. Tanimoto) for pairwise comparisons of binary fingerprints. For this data type, c is the number of "on-bits" common in both compounds, and a and b are the numbers of their unique "on-bits". Currently, the PubChem fingerprints need to be provided (here PubChem's SD files) and cannot be computed from scratch in ChemmineR. The PubChem fingerprint specifications can be loaded with data(pubchemFPencoding).

Convert base 64 encoded PubChem fingerprints to character vector, matrix or FPset object: 

 cid(sdfset) <- sdfid(sdfset)
 fpset <- fp2bit(sdfset, type=1) 
 fpset <- fp2bit(sdfset, type=2) 
 fpset <- fp2bit(sdfset, type=3) 
 fpset

Pairwise compound structure comparisons: 

 fpSim(fpset[1], fpset[2])
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Similarity Searching with PubChem Fingerprints

Similarly, the fpSim function provides search functionality for PubChem fingerprints: 

 fpSim(fpset["650065"], fpset, method="Tanimoto", cutoff=0.6, top=6)
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Visualize Similarity Search Results

The cmp.search function allows to visualize the chemical structures for the search results. Similar but more flexible chemical structure rendering functions are plot and sdf.visualize described above. By setting the visualize argument in cmp.search to TRUE, the matching compounds and their scores can be visualized with a standard web browser. Depending on the visualize.browse argument, an URL will be printed or a webpage will be opened showing the structures of the matching compounds.

View similarity search results in R's graphics device:

 cid(sdfset) <-
 cid(apset) # Assure compound name consistency among objects. 

 plot(sdfset[names(cmp.search(apset, apset["650065"], type=2, cutoff=4, quiet=TRUE))], print=FALSE)

View results online with Chemmine Tools: 

 similarities <- cmp.search(apset, apset[1], type=3, cutoff = 10)
 sdf.visualize(sdfset[similarities[,1]])
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Clustering

Clustering Identical or Very Similar Compounds

Often it is of interest to identify very similar or identical compounds in a compound set. The cmp.duplicated function can be used to quickly identify very similar compounds in atom pair sets, which will be frequently, but not necessarily, identical compounds.

Identify compounds with identical AP sets: 

 cmp.duplicated(apset, type=1)[1:4] # Returns AP duplicates as logical vector 
 cmp.duplicated(apset, type=2)[1:4,] # Returns AP duplicates as data frame

Plot the structure of two pairs of duplicates: 

 plot(sdfset[c("650059","650060", "650065", "650066")], print=FALSE)

Remove AP duplicates from SDFset and APset objects: 

 apdups <- cmp.duplicated(apset, type=1)
 sdfset[which(!apdups)]; apset[which(!apdups)]

Alternatively, one can identify duplicates via other descriptor types if they are provided in the data block of an imported SD file. For instance, one can use here fingerprints, InChI, SMILES or other molecular representations. The following examples show how to enumerate by identical InChI strings, SMILES strings and molecular formula, respectively.

 count <- table(datablocktag(sdfset,
 tag="PUBCHEM_NIST_INCHI"))
 count <- table(datablocktag(sdfset, tag="PUBCHEM_OPENEYE_CAN_SMILES")) 
 count <- table(datablocktag(sdfset, tag="PUBCHEM_MOLECULAR_FORMULA")) 
 count[1:4]
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Binning Clustering

Compound libraries can be clustered into discrete similarity groups with the binning clustering function cmp.cluster. The function accepts as input an atom pair (APset) or a fingerprint (FPset) descriptor database as well as a similarity threshold. The binning clustering result is returned in form of a data frame. Single linkage is used for cluster joining. The function calculates the required compound-to-compound distance information on the fly, while a memory-intensive distance matrix is only created upon user request via the save.distances argument (see below).

Because an optimum similarity threshold is often not known, the cmp.cluster function can calculate cluster results for multiple cutoffs in one step with almost the same speed as for a single cutoff. This can be achieved by providing several cutoffs under the cutoff argument. The clustering results for the different cutoffs will be stored in one data frame.

One may force the cmp.cluster function to calculate and store the distance matrix by supplying a file name to the save.distances argument. The generated distance matrix can be loaded and passed on to many other clustering methods available in R, such as the hierarchical clustering function hclust (see below).

If a distance matrix is available, it may also be supplied to cmp.cluster via the use.distances argument. This is useful when one has a pre-computed distance matrix either from a previous call to cmp.cluster or from other distance calculation subroutines.

Single-linkage binning clustering with one or multiple cutoffs:

 clusters <- cmp.cluster(db=apset, cutoff = c(0.7, 0.8, 0.9), quiet = TRUE)
 clusters[1:12,]

Clustering of FPset objects with multiple cutoffs. This method allows to call various similarity methods provided by the fpSim function. For details consult ?fpSim. 

 fpset <- desc2fp(apset)
 clusters2 <- cmp.cluster(fpset, cutoff=c(0.5, 0.7, 0.9), method="Tanimoto", quiet=TRUE)
 clusters2[1:12,]

Sames as above, but using Tversky similarity measure: 

 clusters3 <- cmp.cluster(fpset, cutoff=c(0.5, 0.7, 0.9), 
                                  method="Tversky", alpha=0.3, beta=0.7, quiet=TRUE)

Return cluster size distributions for each cutoff: 

 cluster.sizestat(clusters, cluster.result=1)
 cluster.sizestat(clusters, cluster.result=2)
 cluster.sizestat(clusters, cluster.result=3)

Enforce calculation of distance matrix: 

 clusters <- cmp.cluster(db=apset, cutoff = c(0.65, 0.5, 0.3),
 save.distances="distmat.rda") # Saves distance matrix to file "distmat.rda" in current working directory. 
 load("distmat.rda") # Loads distance matrix.
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Jarvis-Patrick Clustering

The Jarvis-Patrick clustering algorithm is widely used in cheminformatics [@greycite13371]. It requires a nearest neighbor table, which consists of j nearest neighbors for each item (e.g. compound). The nearest neighbor table is then used to join items into clusters when they meet the following requirements: (a) they are contained in each other's neighbor list and (b) they share at least k nearest neighbors. The values for j and k are user-defined parameters. The jarvisPatrick function implemented in ChemmineR takes a nearest neighbor table generated by nearestNeighbors, which works for APset and FPset objects. This function takes either the standard Jarvis-Patrick j parameter (as the numNbrs parameter), or else a cutoff value, which is an extension to the basic algorithm that we have added. Given a cutoff value, the nearest neighbor table returned contains every neighbor with a similarity greater than the cutoff value, for each item. This allows one to generate tighter clusters and to minimize certain limitations of this method, such as false joins of completely unrelated items when operating on small data sets. The trimNeighbors function can also be used to take an existing nearest neighbor table and remove all neighbors whose similarity value is below a given cutoff value. This allows one to compute a very relaxed nearest neighbor table initially, and then quickly try different refinements later.

In case an existing nearest neighbor matrix needs to be used, the fromNNMatrix function can be used to transform it into the list structure that jarvisPatrick requires. The input matrix must have a row for each compound, and each row should be the index values of the neighbors of compound represented by that row. The names of each compound can also be given through the names argument. If not given, it will attempt to use the rownames of the given matrix.

The jarvisPatrick function also allows one to relax some of the requirements of the algorithm through the mode parameter. When set to "a1a2b", then all requirements are used. If set to "a1b", then (a) is relaxed to a unidirectional requirement. Lastly, if mode is set to "b", then only requirement (b) is used, which means that all pairs of items will be checked to see if (b) is satisfied between them. The size of the clusters generated by the different methods increases in this order: "a1a2b" < "a1b" < "b". The run time of method "a1a2b" follows a close to linear relationship, while it is nearly quadratic for the much more exhaustive method "b". Only methods "a1a2b" and "a1b" are suitable for clustering very large data sets (e.g. >50,000 items) in a reasonable amount of time.

An additional extension to the algorithm is the ability to set the linkage mode. The linkage parameter can be one of "single", "average", or "complete", for single linkage, average linkage and complete linkage merge requirements, respectively. In the context of Jarvis-Patrick, average linkage means that at least half of the pairs between the clusters under consideration must meet requirement (b). Similarly, for complete linkage, all pairs must requirement (b). Single linkage is the normal case for Jarvis-Patrick and just means that at least one pair must meet requirement (b).

The output is a cluster vector with the item labels in the name slot and the cluster IDs in the data slot. There is a utility function called byCluster, which takes out cluster vector output by jarvisPatrick and transforms it into a list of vectors. Each slot of the list is named with a cluster id and the vector contains the cluster members. By default the function excludes singletons from the output, but they can be included by setting excludeSingletons=FALSE`.

Load/create sample APset and FPset:

 data(apset) 
 fpset <- desc2fp(apset)

Standard Jarvis-Patrick clustering on APset and FPset objects: 

 jarvisPatrick(nearestNeighbors(apset,numNbrs=6), k=5, mode="a1a2b")
 #Using "APset" 

 jarvisPatrick(nearestNeighbors(fpset,numNbrs=6), k=5, mode="a1a2b")
 #Using "FPset"

The following example runs Jarvis-Patrick clustering with a minimum similarity cutoff value (here Tanimoto coefficient). In addition, it uses the much more exhaustive "b" method that generates larger cluster sizes, but significantly increased the run time. For more details, consult the corresponding help file with ?jarvisPatrick. 

 cl<-jarvisPatrick(nearestNeighbors(fpset,cutoff=0.6,
 method="Tanimoto"), k=2 ,mode="b")
 byCluster(cl)

Output nearest neighbor table (matrix): 

 nnm <- nearestNeighbors(fpset,numNbrs=6)
 nnm$names[1:4] 
 nnm$ids[1:4,] 
 nnm$similarities[1:4,]

Trim nearest neighbor table: 

 nnm <- trimNeighbors(nnm,cutoff=0.4) 
 nnm$similarities[1:4,]

Perform clustering on precomputed nearest neighbor table: 

 jarvisPatrick(nnm, k=5,mode="b")

Using a user defined nearest neighbor matrix: 

 nn <- matrix(c(1,2,2,1),2,2,dimnames=list(c('one','two'))) 
 nn
 byCluster(jarvisPatrick(fromNNMatrix(nn),k=1))
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Multi-Dimensional Scaling (MDS)

To visualize and compare clustering results, the cluster.visualize function can be used. The function performs Multi-Dimensional Scaling (MDS) and visualizes the results in form of a scatter plot. It requires as input an APset, a clustering result from cmp.cluster, and a cutoff for the minimum cluster size to consider in the plot. To help determining a proper cutoff size, the cluster.sizestat function is provided to generate cluster size statistics.

MDS clustering and scatter plot: 

 cluster.visualize(apset, clusters, size.cutoff=2, quiet = TRUE) # Color codes clusters with at least two members. 
 cluster.visualize(apset, clusters, quiet = TRUE) # Plots all items.

Create a 3D scatter plot of MDS result: 

 library(scatterplot3d) 
 coord <- cluster.visualize(apset, clusters, size.cutoff=1, dimensions=3, quiet=TRUE) 
 scatterplot3d(coord)

Interactive 3D scatter plot with Open GL (graphics not evaluated here):

 library(rgl) rgl.open(); offset <- 50;
 par3d(windowRect=c(offset, offset, 640+offset, 640+offset)) 
 rm(offset)
 rgl.clear() 
 rgl.viewpoint(theta=45, phi=30, fov=60, zoom=1)
 spheres3d(coord[,1], coord[,2], coord[,3], radius=0.03, color=coord[,4], alpha=1, shininess=20) 
 aspect3d(1, 1, 1) 
 axes3d(col='black')
 title3d("", "", "", "", "", col='black')
 bg3d("white") # To save a snapshot of the graph, one can use the command rgl.snapshot("test.png").
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Clustering with Other Algorithms

ChemmineR allows the user to take advantage of the wide spectrum of clustering utilities available in R. An example on how to perform hierarchical clustering with the hclust function is given below.

Create atom pair distance matrix:

 dummy <- cmp.cluster(db=apset, cutoff=0, save.distances="distmat.rda", quiet=TRUE) 
 load("distmat.rda")

Hierarchical clustering with hclust: 

 hc <- hclust(as.dist(distmat), method="single") 
 hc[["labels"]] <- cid(apset) # Assign correct item labels 
 plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=T)

Instead of atom pairs one can use PubChem's fingerprints for clustering:

 simMA <- sapply(cid(fpset), function(x) fpSim(fpset[x], fpset, sorted=FALSE))
 hc <- hclust(as.dist(1-simMA), method="single") 
 plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=TRUE)

Plot dendrogram with heatmap (here similarity matrix): 

 library(gplots) 
 heatmap.2(1-distmat, Rowv=as.dendrogram(hc), Colv=as.dendrogram(hc), 
              col=colorpanel(40, "darkblue", "yellow", "white"), 
              density.info="none", trace="none")
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Searching PubChem

Get Compound SDF from PubChem by Id

The function pubchemCidToSDF (alias getIds) accepts one or more numeric PubChem compound ids and downloads the corresponding compounds from PubChem Power User Gateway (PUG) returning results in an SDFset container.

Fetch 2 compounds from PubChem:

 compounds <- pubchemCidToSDF(c(111,123))
 compounds
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Get Compound SDF from PubChem by InChIkey

The function pubchemInchikey2sdf accepts one or more character PubChem compound InChIkey(s) and downloads the corresponding compounds from PubChem's Power User Gateway (PUG). This returns the results in a list of two items. The first item is the SDFset container of all successful queries. The second item is a named numeric vector. This vector records whether an InChIkey has a successful return. If the InChIkey query is successful, a non-zero number is returned as the index of where it exists in the SDFset object for this InChIkey. If failed, 0 is returned.

inchikeys <- c(
"ZFUYDSOHVJVQNB-FZERPYLPSA-N",
"KONGRWVLXLWGDV-BYGOPZEFSA-N",
"AANKDJLVHZQCFG-WLIQWNBFSA-N",
"SNFRINMTRPQQLE-JQWAAABSSA-N"
)
# You should only have 2 SDF returned, 2 other not found
inchikey_query <- pubchemInchikey2sdf(inchikeys)
inchikey_query$sdf_set

# successful queries
inchikey_query_index <- inchikey_query$sdf_index[inchikey_query$sdf_index != 0]

# get CID of these queries
inchikey_query_cid <- cid(inchikey_query$sdf_set[inchikey_query_index])
names(inchikey_query_cid) <- names(inchikey_query_index)
inchikey_query_cid
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Get Compound CID from PubChem by InChI

The function pubchemInchi2cid accepts one or more character PubChem compound InChI string(s) and downloads the corresponding compound CID from PubChem Power User Gateway (PUG) returning results in a named numeric vector. Successful requests will have empty names, requests with invalid InChI strings will have name "invalid" and requests with valid InChI but not found in PubChem will have name "not_found". Both "invalid" and "not_found" queries will have CID 0 as return.

PubChem API allows users to only query one InChI a time, so this function sends one PubChem API request per InChI. For courtesy reasons, the rate is limited to 1 query per second. It is not recommended to parallelize this function. 

# first two are valid, third has no result, last is invalid 
inchis <- c(
 "InChI=1S/C15H26O/c1-9(2)11-6-5-10(3)15-8-7-14(4,16)13(15)12(11)15/h9-13,16H,5-8H2,1-4H3/t10-,11+,12-,13+,14+,15-/m1/s1", 
 "InChI=1S/C3H8/c1-3-2/h3H2,1-2H3", 
 "InChI=1S/C15H20Br2O2/c1-2-12(17)13-7-3-4-8-14-15(19-13)10-11(18-14)6-5-9-16/h3-4,6,9,11-15H,2,7-8,10H2,1H3/t5-,11-,12+,13+,14-,15-/m1/s1",
 "InChI=abc"
)
pubchemInchi2cid(inchis)
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Search a SMILES Query in PubChem

The function searchString accepts one SMILES string (Simplified Molecular Input Line Entry Specification) and performs a >0.95 similarity PubChem fingerprint search, returning the hits in an SDFset container. The ChemMine Tools web service is used as an intermediate, to translate queries from plain HTTP POST to a PubChem Power User Gateway (PUG) query.

Search a SMILES string on PubChem:

compounds <- searchString("CC(=O)OC1=CC=CC=C1C(=O)O") 
compounds
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Search an SDF Query in PubChem

The function searchSim performs a PubChem similarity search just like searchString, but accepts a query in an SDFset container. If the query contains more than one compound, only the first is searched.

Search an SDFset container on PubChem:

 data(sdfsample); 
 sdfset <- sdfsample[1] 
 compounds <- searchSim(sdfset) 
 compounds
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ChemMine Tools R Interface

ChemMine Web Tools is an online service for analyzing and clustering small molecules. It provides numerous cheminformatics tools which can be used directly on the website, or called remotely from within R. When called within R jobs are sent remotely to a queue on a compute cluster at UC Riverside, which is a free service offered to ChemmineR users. The website is free and open to all users and is available at http://chemmine.ucr.edu. When new tools are added to the service, they automatically become availiable within ChemmineR without updating your local R package.

List all available tools:

listCMTools()

# cache results from previous code chunk
# NOTE: this must match the code in the previous code chunk but will be
#   hidden. Delete cacheFileName to rebuild the cache from web data.
cacheFileName <- "listCMTools.RData"
if(! file.exists(cacheFileName)){
    toolList <- listCMTools()
    save(list=c("toolList"), file=cacheFileName)
}
load(cacheFileName)
toolList

Show options and description for a tool. This also provides an example function call which can be copied verbatim, and changed as necessary:

toolDetails("Fingerprint Search")

# cache results from previous code chunk
# NOTE: this must match the code in the previous code chunk but will be
#   hidden. Delete cacheFileName to rebuild the cache from web data.
cacheFileName <- "toolDetails.RData"
if(! file.exists(cacheFileName)){
    .serverURL <- "http://chemmine.ucr.edu/ChemmineR/"
    library(RCurl)
    response <- postForm(paste(.serverURL, "toolDetails", sep = ""), tool_name = "Fingerprint Search")[[1]]
    save(list=c("response"), file=cacheFileName)
}
load(cacheFileName)
cat(response)
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Launch a Job

When a job is launched it returns a job token which refers to the running job on the UC Riverside cluster. You can check the status of a job or obtain the results as follows. If result is called on a job that is still running, it will loop internally until the job is completed, and then return the result.

Launch the tool pubchemID2SDF to obtain the structure for PubChem cid 2244:

job1 <- launchCMTool("pubchemID2SDF", 2244)
status(job1)
result1 <- result(job1)

Use the previous result to search PubChem for similar compounds:

job2 <- launchCMTool('Fingerprint Search', result1, 'Similarity Cutoff'=0.95, 'Max Compounds Returned'=200)
result2 <- result(job2)
job3 <- launchCMTool("pubchemID2SDF", result2)
result3 <- result(job3)

Compute OpenBabel descriptors for these search results:

job4 <- launchCMTool("OpenBabel Descriptors", result3)
result4 <- result(job4)
result4[1:10,] # show first 10 lines of result

# cache results from previous code chunk
# NOTE: this must match the code in the previous code chunk but will be
#   hidden. Delete cacheFileName to rebuild the cache from web data.
cacheFileName <- "launchCMTool.RData"
if(! file.exists(cacheFileName)){
    job1 <- launchCMTool("pubchemID2SDF", 2244)
    status(job1)
    result1 <- result(job1)
    job2 <- launchCMTool('Fingerprint Search', result1, 'Similarity Cutoff'=0.95, 'Max Compounds Returned'=200)
    result2 <- result(job2)
    job3 <- launchCMTool("pubchemID2SDF", result2)
    result3 <- result(job3)
    job4 <- launchCMTool("OpenBabel Descriptors", result3)
    result4 <- result(job4)
    save(list=c("result4"), file=cacheFileName)
}
load(cacheFileName)
result4[1:10,]
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View Job Result in Browser

The function browseJob launches a web browser to view the results of a job online, just as if they had been run from the ChemMine Tools website itself. If you also want the result data within R, you must first call the result object from within R before calling browseJob. Once browseJob has been called on a job token, the results are no longer accessible within R.

If you have an account on ChemMine Tools and would like to save the web results from your job, you must first login to your account within the default web browser on your system before you launch browseJob. The job will then be assigned automatically to the currently logged in account.

View OpenBabel descriptors online:

browseJob(job4)

Perform binning clustering and visualize result online:

job5 <- launchCMTool("Binning Clustering", result3, 'Similarity Cutoff'=0.9)
browseJob(job5)
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Version Information

 sessionInfo()
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Funding

This software was developed with funding from the National Science Foundation: ABI-0957099, 2010-0520325 and IGERT-0504249.

References



girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.

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