Type:	Package
Title:	Interface to the 'PubChem' Database for Chemical Data Retrieval
Version:	2.1.4
Date:	2025-03-07
Description:	Provides an interface to the 'PubChem' database via the PUG REST https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest and PUG View https://pubchem.ncbi.nlm.nih.gov/docs/pug-view services. This package allows users to automatically access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types. Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Encoding:	UTF-8
RoxygenNote:	7.3.2
VignetteBuilder:	knitr
URL:	https://github.com/selcukorkmaz/PubChemR
Depends:	R (≥ 3.6.0)
Imports:	dplyr, tibble, magrittr, stringr, tidyr, RJSONIO, httr, utils, RCurl, magick, rsvg, png, testthat
Suggests:	knitr, rmarkdown
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2025-03-07 12:12:05 UTC; selcukkorkmaz
Author:	Selcuk Korkmaz [aut, cre], Bilge Eren Yamasan [aut], Dincer Goksuluk [aut]
Maintainer:	Selcuk Korkmaz <selcukorkmaz@gmail.com>
Repository:	CRAN
Date/Publication:	2025-03-07 13:10:02 UTC

Assay, Compound, and Substance Identifiers

Description

These functions are used to retrieve identification information for assays, substances, and compounds from the PubChem database.

Usage

AIDs(object, ...)

CIDs(object, ...)

SIDs(object, ...)

## S3 method for class 'PubChemInstance_AIDs'
AIDs(object, .to.data.frame = TRUE, ...)

## S3 method for class 'PubChemInstance_CIDs'
CIDs(object, .to.data.frame = TRUE, ...)

## S3 method for class 'PubChemInstance_SIDs'
SIDs(object, .to.data.frame = TRUE, ...)

Arguments

Examples

# Retrieve Assay IDs
aids <- get_aids(identifier = c("aspirin", "caffeine"), namespace = "name")
AIDs(aids)

# Compound IDs
cids <- get_cids(identifier = c("aspirin", "caffein"), namespace = "name")
CIDs(cids)

# Substance IDs
sids <- get_sids(identifier = c("aspirin", "caffein"), namespace = "name")
SIDs(sids)

PubChemInstanceList and PubChemInstance Classes

Description

The PubChemInstanceList object is a superclass returned by a request for compound(s) from the PubChem Database, such as the output from get_compounds, get_assays, etc.

The PubChemInstance object is another superclass for a PubChem instance, such as an assay, compound, substance, etc. These instances are nested within the results slot of a PubChemInstanceList object. Similar to PubChemInstanceList, the PubChemInstance also contains the same slots as described below. For more details, see instance.

Slots

results:

A list containing elements of each of the requested compounds, assays, substances, etc.

request_args:

A list containing the input arguments of a PubChem request.

success:

A logical value indicating whether the request was successfully completed (TRUE) or not (FALSE).

error:

A list detailing any errors encountered during the request, if applicable.

Note

There is no constructor function for the PubChemInstanceList or PubChemInstance classes. These objects are constructed within related functions and returned as the output of PubChem requests.

There are several subclasses defined under the PubChemInstanceList and PubChemInstance superclasses. The PubChem API returns request results in a list; however, each request may have a different list structure and/or items within the returned list. Therefore, we have defined subclasses to make generic functions compatible with any PubChem request, such as assays, instances, substances, etc. These subclasses may include PC_Compounds, PC_Substance, PC_Properties, PubChemInstance_AIDs, PubChemInstance_SIDs, PubChemInstance_CIDs, PubChemInstance_Synonyms, and PubChemInstance_Substances.

Most of the defined subclasses have similar slots as described above. However, some classes may have additional slots not described here. Please refer to the contents of the returned object for more details.

Classes for Pug View Request

Description

The Pug View API of PubChem database returns more detailed information about a PubChem request, such as assays, compounds, substances, etc. A super-class PugViewInstance is defined, which is returned from get_pug_view function. This class has slots detailed below.

Slots

results:

A list containing elements of each of the requested compounds, assays, substances, etc.

request_args:

A list containing the input arguments of a PubChem request.

success:

A logical value indicating whether the request was successfully completed (TRUE) or not (FALSE).

error:

A list detailing any errors encountered during the request, if applicable.

Note

Pug View API returns many section about the requested instance, which includes detailed information from PubChem database. There may be many nested sections, where each contains details about different features of the instance requested. These sections can be listed via sectionList function.

Other classes, called PugViewSectionList and PugViewSection, are defined to control the outputs of available sections and sub-sections returned from get_pug_view. See related functions for details.

See Also

section, sectionList

Download Content from PubChem and Save to a File

Description

This function sends a request to PubChem to retrieve content in the specified format for a given identifier. It then writes the content to a specified file path.

Usage

download(
  filename = NULL,
  outformat,
  path,
  identifier,
  namespace = "cid",
  domain = "compound",
  operation = NULL,
  searchtype = NULL,
  overwrite = FALSE,
  options = NULL
)

Arguments

Value

No return value. The function writes the content to the specified file path and prints a message indicating the save location.

Examples

# Download JSON file for the compound "aspirin" into "Aspirin.JSON"
# A folder named "Compound" will be created under current directory"
download(
  filename = "Aspirin",
  outformat = "json",
  path = "./Compound",
  identifier = "aspirin",
  namespace = "name",
  domain = "compound",
  overwrite = TRUE
)

# Remove downloaded files and folders.
file.remove("./Compound/Aspirin.json")
file.remove("./Compound/")

Retrieve Assay IDs (AIDs) from PubChem

Description

This function queries the PubChem database to retrieve Assay IDs (AIDs) based on a given identifier.

Usage

get_aids(
  identifier,
  namespace = "cid",
  domain = "compound",
  searchtype = NULL,
  options = NULL
)

Arguments

Details

For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstance_AIDs', which is a list containing information retrieved from the PubChem database. Assay IDs can be extracted from the returned object using the getter function AIDs.

Note

To extract assay IDs from returned object, one may use AIDs function. See examples.

See Also

AIDs, get_pug_rest

Examples

# Request for multiple assays
# If assay identifier is unknown or incorrect, an error returns from PubChem Database
aids <- get_aids(
  identifier = c("aspirin", "ibuprofen", "rstudio"),
  namespace = "name"
)

print(aids)

# Return all Assay IDs.
AIDs(aids)

Retrieve All Sources from PubChem

Description

This function retrieves a list of all current depositors of substances or assays from PubChem.

Usage

get_all_sources(domain = "substance")

Arguments

Details

The PubChem PUG REST API provides a way to retrieve all current depositors (sources) for substances or assays. For more detailed information, please refer to the PubChem Data Sources documentation.

Value

A character vector containing the names of all sources for the specified domain.

Examples

get_all_sources(
  domain = 'substance'
)

Retrieve Assays from PubChem

Description

This function sends a request to PubChem to retrieve assay data based on the specified parameters.

Usage

get_assays(identifier, namespace = "aid", operation = NULL, options = NULL)

Arguments

Details

For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstanceList' containing the information retrieved from the PubChem database.

Note

To extract information about a specific assay from the returned list, use the instance function.

Each assay may include information on several properties. Specific information from the assay can be extracted using the retrieve function. See examples.

See Also

retrieve, instance

Examples

# Retrieve a list of assays from the PubChem database
assays <- get_assays(
  identifier = c(1234, 7815),
  namespace = 'aid'
)

# Return assay information for assay ID '1234'
assay1234 <- instance(assays, "1234")
print(assay1234)

# Retrieve specific elements from the assay output
retrieve(assay1234, "aid")

Retrieve Compound IDs (CIDs) from PubChem

Description

This function sends a request to PubChem to retrieve Compound IDs (CIDs) for given identifier(s).

Usage

get_cids(
  identifier,
  namespace = "name",
  domain = "compound",
  searchtype = NULL,
  options = NULL
)

Arguments

Details

For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstance_CIDs', which is a list containing information retrieved from the PubChem database. Compound IDs can be extracted from the returned object using the CIDs function.

Note

To extract compoud IDs from returned object, one may use CIDs function. See examples.

See Also

CIDs, get_pug_rest

Examples

compound <- get_cids(
  identifier = "aspirin",
  namespace = "name"
)

compound

# Extract compound IDs.
CIDs(compound)

Retrieve Compounds from PubChem

Description

This function sends a request to the PubChem database to retrieve compound data based on specified parameters.

Usage

get_compounds(
  identifier,
  namespace = "cid",
  operation = NULL,
  searchtype = NULL,
  options = NULL
)

Arguments

Details

For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstanceList' and 'PC_Compounds' containing compound information from the PubChem database.

See Also

retrieve, instance

Examples

compound <- get_compounds(
  identifier = c("aspirin", "ibuprofen", "rstudio"),
  namespace = "name"
)

print(compound)

# Return results for selected compound.
instance(compound, "aspirin")
instance(compound, "rstudio")
# instance(compound, "unknown"). # returns error.

# Extract compound properties for the compound "aspirin".
# Use the 'retrieve()' function to extract specific slots from the compound list.
retrieve(instance(compound, "aspirin"), "props")

Retrieve Compound Properties from PubChem

Description

This function sends a request to PubChem to retrieve compound properties based on the specified parameters.

Usage

get_properties(
  properties = NULL,
  identifier,
  namespace = "cid",
  searchtype = NULL,
  options = NULL,
  propertyMatch = list(.ignore.case = FALSE, type = "contain")
)

property_map(
  x,
  type = c("match", "contain", "start", "end", "all"),
  .ignore.case = TRUE,
  ...
)

Arguments

Details

For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class "PubChemInstanceList" containing all the properties of the requested compounds.

Note

Property Map:

property_map() is not used to request properties directly from the PubChem database. This function is intended to list the available compound properties that can be requested from PubChem. It has flexible options to search properties from the available property list of the PubChem database. The output of property_map is used as the property input in the get_properties function. This function may be practically used to request specific properties across a range of compounds. See examples for usage.

Examples

# Isomeric SMILES of the compounds
props <- get_properties(
  properties = c("MolecularWeight", "MolecularFormula", "InChI"),
  identifier = c("aspirin", "ibuprofen", "caffeine"),
  namespace = "name"
)

# Properties for a selected compound
instance(props, "aspirin")
retrieve(props, .which = "aspirin", .slot = NULL)
retrieve(instance(props, "aspirin"), .slot = NULL)

# Combine properties of all compounds into a single data frame (or list)
retrieve(props, .combine.all = TRUE)

# Return selected properties
retrieve(props, .combine.all = TRUE,
  .slot = c("MolecularWeight", "MolecularFormula"))

# Return properties for the compounds in a range of CIDs
props <- get_properties(
  properties = c("mass", "molecular"),
  identifier = 2244:2255,
  namespace = "cid",
  propertyMatch = list(
    type = "contain"
  )
)

retrieve(props, .combine.all = TRUE, .to.data.frame = TRUE)

# Return all available properties of the requested compounds
props <- get_properties(
  properties = NULL,
  identifier = 2244:2245,
  namespace = "cid",
  propertyMatch = list(
    type = "all"
  )
)

retrieve(props, .combine.all = TRUE)



#### EXAMPLES FOR property_map() ####
# List all available properties:
property_map(type = "all")

# Exact match:
property_map("InChI", type = "match")
property_map("InChi", type = "match",
  .ignore.case = TRUE) # Returns no match. Ignores '.ignore.case'

# Match at the start/end:
property_map("molecular", type = "start", .ignore.case = TRUE)
property_map("mass", type = "end", .ignore.case = TRUE)

# Partial match with multiple search patterns:
property_map(c("molecular", "mass", "inchi"),
  type = "contain", .ignore.case = TRUE)

Retrieve Data from PubChem PUG REST API

Description

This function sends a request to the PubChem PUG REST API to retrieve various types of data for a given identifier. It supports fetching data in different formats and allows saving the output.

Usage

get_pug_rest(
  identifier = NULL,
  namespace = "cid",
  domain = "compound",
  operation = NULL,
  output = "JSON",
  searchtype = NULL,
  property = NULL,
  options = NULL,
  save = FALSE,
  dpi = 300,
  path = NULL,
  file_name = NULL,
  ...
)

Arguments

Details

For more information on the possible values for parameters such as namespace, domain, operation, output, searchtype, and property, please refer to the PUG REST API documentation.

Value

An object of class ''PugRestInstance'' containing:

'success'

Logical value indicating if the request was successful.

'error'

If 'success' is 'FALSE', a list containing error messages.

'result'

The content retrieved from the API; format depends on 'output'.

'request_args'

A list of the arguments used in the request.

'fileDetails'

If 'save' is 'TRUE', details about the saved file.

Examples

result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", output = "JSON")
pubChemData(result)

Retrieve PUG View Data from PubChem

Description

This function sends a request to the PubChem PUG View API to retrieve various types of data for a given identifier. It supports fetching annotations, QR codes, and more, with options for different output formats including JSON and SVG.

Usage

get_pug_view(
  annotation = NULL,
  identifier = NULL,
  domain = "compound",
  output = "JSON",
  heading = NULL,
  headingType = NULL,
  page = NULL,
  qrSize = "short",
  save = FALSE
)

Arguments

Details

The PubChem PUG View API allows users to retrieve detailed information about compounds, substances, and assays. This function constructs the appropriate API call based on the provided parameters. For more detailed information, please refer to the PubChem PUG View API documentation.

Value

Depending on the output format, this function returns different types of content: JSON or JSONP format returns parsed JSON content. SVG format returns an image object. For QR codes, it returns an image object or saves a PNG file.

Examples

result <- get_pug_view(identifier = "2244", annotation = "linkout", domain = "compound")
retrieve(result, .slot = "ObjUrl", .to.data.frame = FALSE)

Retrieve/Save SDF Data from PubChem

Description

This function sends a request to PubChem to retrieve data in SDF format based on the specified parameters. It then saves the retrieved data as an SDF file in the current working directory (or into the system-specific temporary folder).

Usage

get_sdf(
  identifier,
  namespace = "cid",
  domain = "compound",
  operation = NULL,
  searchtype = NULL,
  path = NULL,
  file_name = NULL,
  options = NULL
)

Arguments

Details

The PubChem PUG REST API allows users to retrieve compound data in various formats, including SDF. This function constructs the appropriate API call and saves the SDF data to a file. For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

The function saves the retrieved data as an SDF file in the current working directory and prints a message indicating the file's location.

Examples

get_sdf(
  identifier = "aspirin",
  namespace = "name",
  path = NULL
)

Retrieve Substance IDs (SIDs) from PubChem

Description

This function sends a request to PubChem to retrieve Substance IDs (SIDs) for a given identifier.

Usage

get_sids(
  identifier,
  namespace = "cid",
  domain = "compound",
  searchtype = NULL,
  options = NULL
)

Arguments

Details

#' For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstance_SIDs', which is a list containing information retrieved from the PubChem database. Substance IDs can be extracted from the returned object using the SIDs function.

Examples

result <- get_sids(
  identifier = c("aspirin", "ibuprofen"),
  namespace = "name"
)

# Extract substance IDs of all compounds
SIDs(result)

Retrieve Substances from PubChem

Description

This function sends a request to PubChem to retrieve substance data based on the specified parameters.

Usage

get_substances(identifier, namespace = "sid", operation = NULL, options = NULL)

Arguments

Details

For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstanceList' containing all the substance information of requested compounds.

Examples

subs <- get_substances(
  identifier = c("aspirin", "ibuprofen"),
  namespace = "name"
)

instance(subs, "aspirin")
retrieve(instance(subs, "aspirin"), "source")

Retrieve Synonyms from PubChem

Description

This function sends a request to PubChem to retrieve synonyms for a given identifier. It returns a list of synonyms corresponding to the provided identifier.

Usage

get_synonyms(
  identifier,
  namespace = "cid",
  domain = "compound",
  searchtype = NULL,
  options = NULL
)

Arguments

Details

The PubChem PUG REST API allows for retrieving synonyms related to various domains. The table below summarizes valid combinations for retrieving synonyms: For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstance_Synonyms', which is a list containing information retrieved from the PubChem database. Synonyms data can be extracted from the returned object using the synonyms function.

Examples

syns <- get_synonyms(
  identifier = "aspirin",
  namespace = "name"
)

syns

synonyms(syns)

Retrieve Information for Requested Instances

Description

This function extracts the results of a PubChem instance from an object. It is designed to retrieve information about a compound from a comprehensive list where multiple elements (such as assay, compound, etc.) are requested.

Usage

instance(object, ...)

## S3 method for class 'PubChemInstanceList'
instance(object, .which = NULL, ...)

Arguments

Examples

compounds <- get_compounds(
  identifier = c("aspirin", "ibuprofen"),
  namespace = "name"
)

instance(compounds)  # Returns the results for "aspirin"
instance(compounds, "ibuprofen")

Retrieve Raw Data from PUG REST Object

Description

A short description...

Usage

pubChemData(object, ...)

## S3 method for class 'PugRestInstance'
pubChemData(object, ...)

Arguments

Value

a vector, list, or data.frame containing the raw data retrieved from Pub Chem database through PUG REST API.

See Also

get_pug_rest

Examples

result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", output = "JSON")
pubChemData(result)

Retrieve Function Inputs

Description

This function retrieves the input arguments from a specified PubChem database request object.

Usage

request_args(object, .which = NULL, ...)

Arguments

Value

A list or string vector containing the options used in the function call.

Examples

request <- get_cids("aspirin", namespace = "name")

request_args(request, "identifier")
request_args(request)

Retrieve Information from PubChem Instances

Description

This generic function extracts a specific slot from a PubChem instance.

Usage

retrieve(object, ...)

## S3 method for class 'PubChemInstance'
retrieve(object, .slot = NULL, .to.data.frame = TRUE, .verbose = FALSE, ...)

## S3 method for class 'PubChemInstanceList'
retrieve(
  object,
  .which = NULL,
  .slot = NULL,
  .to.data.frame = TRUE,
  .combine.all = FALSE,
  ...
)

## S3 method for class 'PC_Substance'
retrieve(
  object,
  .slot = NULL,
  .idx = 1,
  .to.data.frame = TRUE,
  .verbose = FALSE,
  ...
)

## S3 method for class 'PugViewInstance'
retrieve(object, .slot = NULL, .to.data.frame = TRUE, ...)

## S3 method for class 'PugViewSection'
retrieve(object, .slot = NULL, .to.data.frame = FALSE, ...)

Arguments

Details on 'PugViewInstance' and 'PugViewSection'

The PugView API returns a detailed list related to PubChem requests. The 'Section' slot in this list is structured into a sub-class called 'PugViewSection'. This object contains information organized through several sections (or sub-sections), which can be retrieved using section-specific functions such as section and sectionList.

The function argument .to.data.frame is ignored if the "Section" slot is being extracted from the complete list. For other slots, .to.data.frame is considered as usual. See examples for usage.

Note

If the object is from the 'PC_Properties' class, the .slot can be defined as NULL. If .slot = NULL, retrieve() will return all available properties. If 'object' is of class other than 'PC_Properties', .slot should be length of 1.

Extracting multiple slots.

In some cases, it may be practical to extract multiple slots from 'object'. For example, one may wish to extract properties from the output of get_properties by running the functions in a loop. See codes below for a practical example:

  library(dplyr)

  props <- get_properties(
    properties = c("MolecularWeight", "MolecularFormula", "HBondDonorCount",
                   "HBondAcceptorCount", "InChIKey", "InChI"),
    identifier = 2244,
    namespace = "cid",
    propertyMatch = list(
      .ignore.case = TRUE,
      type = "contain"
    )
  )

  bind_columns <- function(x, ...){
    part1 <- x[[1]][ ,"Identifier"]
    part2 <- lapply(x, "[", 2) 
      bind_cols()

    bind_cols(part1, part2)
  }

  propsToExtract <- c("MolecularWeight", "MolecularFormula", "HBondDonorCount")
  tmp <- lapply(propsToExtract, retrieve, object = props, .which = "2244")
  bind_columns(tmp)

Use of the '.verbose' argument

retrieve returns output silently (invisibly) when .verbose = TRUE. However, the function behaves differently under the following scenarios:

• .verbose is ignored if .combine.all = TRUE. The output is returned silently.

• .verbose is ignored if the requested slot is not printable to the R console because it is too complicated to print.

Examples

compounds <- get_compounds(
  identifier = c("aspirin", "ibuprofen", "rstudio"),
  namespace = "name"
 )

# Extract information for "aspirin"
aspirin <- instance(compounds, "aspirin")
# print(aspirin)

# Extract a specific slot from the "aspirin" compound.
retrieve(aspirin, "props", .to.data.frame = TRUE)

# Examples (PubChemInstanceList)
retrieve(compounds, "aspirin", "props", .to.data.frame = TRUE)

# Verbose Assay References to R Console
assays <- get_assays(identifier = c(1234, 7815), namespace = "aid")

instance(assays, "7815")
retrieve(assays, "7815", "xref", .verbose = TRUE)

# Print assay protocol to R console (if available)
# Note that it may be too long to print for some assays.
# retrieve(assays, "1234", "protocol", .verbose = TRUE)

# No protocol is available for assay "1234".
# retrieve(assays, "7815", "protocol", .verbose = TRUE)

# Ignores ".verbose" and ".which" if ".combine.all = TRUE".
retrieve(assays, .slot = "xref", .verbose = TRUE, .combine.all = TRUE)

### PUG VIEW EXAMPLES ###
pview <- get_pug_view(identifier = "2244", annotation = "data", domain = "compound")

# PugViewSectionList object.
# This object contains all the section information related to the PubChem request.
sect <- retrieve(pview, .slot = "Section")
print(sect)

retrieve(pview, .slot = "RecordType", .to.data.frame = TRUE)

Extract Sections from Pug View Request

Description

section returns section details from a Pug View request.

Usage

section(object, ...)

## S3 method for class 'PugViewInstance'
section(object, .id = "S1", .verbose = FALSE, ...)

## S3 method for class 'PugViewSectionList'
section(object, .id = "S1", .verbose = FALSE, ...)

## S3 method for class 'PugViewSection'
section(object, .id = "S1", .verbose = FALSE, ...)

Arguments

Note

Sections in a Pug View Request

A Pug View Request returns a detailed list from the PubChem database. This list may include data under many nested sections, each corresponding to a different property structured within further nested sections. The complicated structure of the returned object makes it impossible to print all information to the R console at once. Therefore, it is recommended to print sections selectively. Furthermore, one may navigate through the nested sections using the section function. See Examples.

Use the sectionList function to list available sections (or subsections of a section) of a Pug View request and related section IDs.

Use of '.verbose' to Print Section Details

It is possible to print section details to the R console. If .verbose = TRUE, the resulting object is returned invisibly and a summary of section details is printed to the R console. This might be useful to navigate through nested sections and sequentially print multiple sections to the R console. For example, consider following command:

> section(section(request, "S1", .verbose = TRUE), "S3", .verbose = TRUE)

This command will print section "S1" and the subsection "S3" located under "S1" to the R console. One may navigate through sections under other sections, similar to exploring dreams within dreams as depicted in the exceptional movie Inception. (SPOILER WARNING!!) However, be careful not to get lost or stuck in the dreams!! Also, note that this strategy works only if .verbose = TRUE for all sections and/or subsections.

See Also

sectionList

Examples

# Pug View request for the compound "aspirin (CID = 2244)".
pview <- get_pug_view(identifier = "2244", annotation = "data", domain = "compound")

section(pview, "S1")
section(pview, "S1", .verbose = TRUE)

# List all available sections
sectionList(pview)

# Subsections under the section "S1"
sectionList(section(pview, "S1"))

# Print multiple sections
# section(section(pview, "S1", .verbose = TRUE), "S3", .verbose = TRUE)

List Available Section/Subsections

Description

This function may be used to list available sections (or subsections) of a PubChem request returned from get_pug_view. It is useful when one wants to extract a specific section (or subsection) from PubChem request. It supports patteern-specific searches within sections. See Detail/Note below for more information.

Usage

sectionList(object, ...)

## S3 method for class 'PugViewInstance'
sectionList(object, ...)

## S3 method for class 'PugViewSectionList'
sectionList(
  object,
  .pattern = NULL,
  .match_type = c("contain", "match", "start", "end"),
  ...
)

## S3 method for class 'PugViewSection'
sectionList(
  object,
  .pattern = NULL,
  .match_type = c("contain", "match", "start", "end"),
  ...
)

Arguments

Details

Pattern matching is used to filter sections that match user-defined patterns. It is useful when there are more sections than allowed to print R console. In such situations, it may be reasonable to print a subset of all section list to R console that meets search criteria. There are several pattern matching methods as described below

• Partial Matching ("contain", "start", "end"): Returns the section names that contains or starts/ends by given text patterns.

• Exact Matching ("match"): Returns the section names that exactly matches given text patterns.

See Also

section

Examples

pview <- get_pug_view(identifier = "2244", annotation = "data", domain = "compound")

# List all section names
sectionList(pview)

# Pattern-matched section names
sectionList(pview, .pattern = c("safety", "chemical"), .match_type = "contain")
sectionList(pview, .pattern = "safety", .match_type = "match")
sectionList(pview, .pattern = "properties", .match_type = "end")

# Use section IDs to extract section data from Pug View request
section(pview, "S12") # Safety and Hazards

Getter function for 'Synonyms'

Description

Extracts synonym data from a PubChem request using the function get_synonyms.

Usage

synonyms(object, ...)

## S3 method for class 'PubChemInstance_Synonyms'
synonyms(object, .to.data.frame = TRUE, ...)

Arguments

Value

A data.frame (or list) object containing the synonym data.

Examples

syns <- get_synonyms(identifier = c("aspirin", "caffeine"), namespace = "name")
synonyms(syns)