webchem

https://docs.ropensci.org/webchem/
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### Install webchem from GitHub

Source: https://docs.ropensci.org/webchem/index.html

Use these commands to install the development version of the package directly from the GitHub repository.

```R
install.packages("devtools")
library("devtools")
install_github("ropensci/webchem")
```

--------------------------------

### Download ChemSpider images example

Source: https://docs.ropensci.org/webchem/reference/cs_img.html

A basic example showing how to download images for specific CSIDs to a temporary directory.

```R
if (FALSE) { # \dontrun{
cs_img(c(582, 682), dir = tempdir())
} # }
```

--------------------------------

### Retrieve compound information examples

Source: https://docs.ropensci.org/webchem/reference/cs_compinfo.html

Examples demonstrating how to query specific fields for one or multiple ChemSpider IDs.

```R
if (FALSE) { # \dontrun{
cs_compinfo(171, c("SMILES", "CommonName"))
cs_compinfo(171:182, "SMILES")
} # }
```

--------------------------------

### Execute ChemSpider control examples

Source: https://docs.ropensci.org/webchem/reference/cs_control.html

Demonstrates default and modified control configurations.

```R
cs_control()
#> $datasources
#> logical(0)
#> 
#> $order_by
#> [1] "default"
#> 
#> $order_direction
#> [1] "default"
#> 
#> $include_all
#> [1] FALSE
#> 
#> $complexity
#> [1] "any"
#> 
#> $isotopic
#> [1] "any"
#> 
cs_control(order_direction = "descending")
#> $datasources
#> logical(0)
#> 
#> $order_by
#> [1] "default"
#> 
#> $order_direction
#> [1] "descending"
#> 
#> $include_all
#> [1] FALSE
#> 
#> $complexity
#> [1] "any"
#> 
#> $isotopic
#> [1] "any"
#> 
```

--------------------------------

### Example Usage of pc_synonyms

Source: https://docs.ropensci.org/webchem/reference/pc_synonyms.html

Demonstrates various ways to call the pc_synonyms function, including searching by name, CID, and handling multiple matches. These examples are for non-interactive use and may require manual execution.

```R
pc_synonyms("Aspirin")
```

```R
pc_synonyms(c("Aspirin", "Triclosan"))
```

```R
pc_synonyms(5564, from = "cid")
```

```R
pc_synonyms(c("Aspirin", "Triclosan"), match = "ask")
```

--------------------------------

### Retrieve ChEBI Entity Examples

Source: https://docs.ropensci.org/webchem/reference/chebi_comp_entity.html

Examples demonstrating how to retrieve data for a single ChEBI ID or multiple IDs.

```R
if (FALSE) { # \dontrun{
# might fail if API is not available
chebi_comp_entity('CHEBI:27744')

# multiple inputs
comp <- c('CHEBI:27744', 'CHEBI:27744')
chebi_comp_entity(comp)

} # }
```

--------------------------------

### Install webchem from CRAN

Source: https://docs.ropensci.org/webchem/index.html

Use this command to install the stable version of the package from the Comprehensive R Archive Network.

```R
install.packages("webchem")
```

--------------------------------

### Query compound_structural_alert resource with tidy=FALSE

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'compound_structural_alert' resource, setting tidy to FALSE to get raw results.

```R
chembl_query(
  "CHEMBL266429",
  resource = "compound_structural_alert",
  options = chembl_options(tidy = FALSE)
)
```

--------------------------------

### Examples of retrieving PubChem section data

Source: https://docs.ropensci.org/webchem/reference/pc_sect.html

Demonstrates usage of pc_sect across different domains and identifiers. Note that these examples are wrapped in a conditional block and may fail if the API is unavailable.

```R
# might fail if API is not available
if (FALSE) { # \dontrun{
pc_sect(176, "Dissociation Constants")
pc_sect(c(176, 311), "density")
pc_sect(2231, "depositor-supplied synonyms", "substance")
pc_sect(780286, "modify date", "assay")
pc_sect(9023, "Ensembl ID", "gene")
pc_sect("1ZHY_A", "Sequence", "protein")
} # }
```

--------------------------------

### Example of pinging the ChEMBL API

Source: https://docs.ropensci.org/webchem/reference/ping_service.html

Demonstrates how to call the ping_service function for the ChEMBL database.

```R
if (FALSE) { # \dontrun{
ping_service("chembl")
} # }
```

--------------------------------

### Query binding_site resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'binding_site' resource, which requires a site ID.

```R
chembl_query(2, resource = "binding_site")
```

--------------------------------

### Download ChEMBL database example

Source: https://docs.ropensci.org/webchem/reference/db_download_chembl.html

Demonstrates how to download a specific version of the ChEMBL database with verbose output enabled.

```R
if (FALSE) { # \dontrun{
db_download_chembl(version = "35", verbose = TRUE)
} # }
```

--------------------------------

### Example of using with_cts for identifier translation

Source: https://docs.ropensci.org/webchem/reference/with_cts.html

Demonstrates how to use the `with_cts` function to translate an InChIKey to an identifier that can be used with the `get_etoxid` function. This example is not run by default.

```R
if (FALSE) { # \dontrun{
with_cts("XDDAORKBJWWYJS-UHFFFAOYSA-N", from = "inchikey", .f = "get_etoxid")
} # }
```

--------------------------------

### Query activity resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'activity' resource, which requires an activity ID.

```R
chembl_query("31863", resource = "activity")
```

--------------------------------

### Query CIR for CAS Number of Triclosan

Source: https://docs.ropensci.org/webchem/reference/cir_query.html

Example of querying the CIR service to get the CAS number for 'Triclosan'. This might fail if the API is unavailable.

```R
cir_query("Triclosan", "cas")
```

--------------------------------

### Example usage of etox_tests

Source: https://docs.ropensci.org/webchem/reference/etox_tests.html

Demonstrates retrieving test data for a chemical by name and querying multiple ETOX IDs directly.

```R
if (FALSE) { # \dontrun{
id <- get_etoxid('Triclosan', match = 'best')
out <- etox_tests(id$etoxid)
out[ , c('Organism', 'Effect', 'Duration', 'Time_Unit',
'Endpoint', 'Value', 'Unit')]
etox_tests( c("20179", "9051"))
} # }
```

--------------------------------

### Example usage of cts_from

Source: https://docs.ropensci.org/webchem/reference/cts_to.html

Demonstrates the syntax for calling the cts_from function, wrapped in a conditional block.

```R
if (FALSE) { # \dontrun{
cts_from()
} # }
```

--------------------------------

### Examples of get_chebiid

Source: https://docs.ropensci.org/webchem/reference/get_chebiid.html

Demonstrates how to perform searches for single compounds and multiple inputs using the get_chebiid function.

```R
if (FALSE) { # \dontrun{
# might fail if API is not available
get_chebiid('Glyphosate')
get_chebiid('BPGDAMSIGCZZLK-UHFFFAOYSA-N')

# multiple inputs
comp <- c('Iron', 'Aspirin', 'BPGDAMSIGCZZLK-UHFFFAOYSA-N')
get_chebiid(comp)

} # }
```

--------------------------------

### Exporting Chemical Structures to .mol Files

Source: https://docs.ropensci.org/webchem/reference/write_mol.html

Examples demonstrating how to export single and multiple chemical structures to .mol files using retrieved data.

```R
if (FALSE) { # \dontrun{
# export Mol file
csid <- get_csid("bergapten")
mol3d <- cs_compinfo(csid$csid, field = "Mol3D")
write_mol(mol3d$mol3D, file = mol3d$id)

# export multiple Mol files
csids <- get_csid(c("bergapten", "xanthotoxin"))
mol3ds <- cs_compinfo(csids$csid, field = "Mol3D")
mapply(function(x, y) write_mol(x, y), x = mol3ds$mol3D, y = mol3ds$id)
} # }
```

--------------------------------

### Example usage of etox_targets

Source: https://docs.ropensci.org/webchem/reference/etox_targets.html

Demonstrates retrieving quality targets for a specific substance using its ETOX ID and querying multiple IDs at once.

```R
if (FALSE) { # \dontrun{
id <- get_etoxid('Triclosan', match = 'best')
out <- etox_targets(id$etoxid)
out[ , c('Substance', 'CAS_NO', 'Country_or_Region', 'Designation',
'Value_Target_LR', 'Unit')]
etox_targets( c("20179", "9051"))

} # }
```

--------------------------------

### Example usage of atc_classes

Source: https://docs.ropensci.org/webchem/reference/chembl_atc_classes.html

Demonstrates how to call the function to retrieve ATC classes, noting that it may fail if the API is unavailable.

```R
if (FALSE) { # \dontrun{
# Might fail if API is not available

atc <- atc_classes()
} # }
```

--------------------------------

### Query compound_record resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'compound_record' resource, which requires a compound record ID.

```R
chembl_query("1", resource = "compound_record")
```

--------------------------------

### Query assay resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'assay' resource, which requires an assay ChEMBL ID.

```R
chembl_query("CHEMBL615117", resource = "assay")
```

--------------------------------

### Query molecule_form resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'molecule_form' resource, which requires a compound ChEMBL ID.

```R
chembl_query("CHEMBL6329", resource = "molecule_form")
```

--------------------------------

### Query atc_class resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'atc_class' resource, which requires an ATC class ID.

```R
chembl_query("A01AA01", resource = "atc_class")
```

--------------------------------

### GET chembl_resources

Source: https://docs.ropensci.org/webchem/reference/chembl_resources.html

Retrieves a list of available resources from the ChEMBL database.

```APIDOC
## GET chembl_resources

### Description
Lists available ChEMBL resources organized in the database.

### Method
GET

### Endpoint
chembl_resources()

### Response
#### Success Response (200)
- **resources** (list) - A list of available ChEMBL resources.
```

--------------------------------

### Check code style

Source: https://docs.ropensci.org/webchem/CONTRIBUTING.html

Use this command to check for nonconformances with the tidyverse style guide before committing.

```R
lintr::lint_file()
```

--------------------------------

### Query molecule resource with multiple IDs

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'molecule' resource with a vector of compound ChEMBL IDs.

```R
chembl_query(c("CHEMBL25", "CHEMBL1082"), resource = "molecule")
```

--------------------------------

### Query cell_line resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'cell_line' resource, which requires a ChEMBL ID.

```R
chembl_query("CHEMBL3307241", resource = "cell_line")
```

--------------------------------

### Query substructure resource with SMILES

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'substructure' resource using a compound SMILES string.

```R
chembl_query("CN(CCCN)c1cccc2ccccc12", resource = "substructure")
```

--------------------------------

### Full Parameter Usage for Image Generation - webchem

Source: https://docs.ropensci.org/webchem/reference/cir_img.html

Demonstrates the use of all available parameters for generating a chemical structure image, including detailed customization of size, colors, symbols, text, and frame. This example showcases the extensive configuration options.

```R
query  = "Triclosan"
cir_img(query,
        dir = tempdir(),
        format = "png",
        width = 600,
        height = 600,
        linewidth = 5,
        symbolfontsize = 30,
        bgcolor = "red",
        antialiasing = FALSE,
        atomcolor = "green",
        bondcolor = "yellow",
        csymbol = "all",
        hsymbol = "all",
        hcolor = "purple",
        header = "My funky chemical structure..",
        footer = "..is just so awesome!",
        frame = 1,
        verbose = getOption("verbose"))
```

--------------------------------

### GET etox_targets

Source: https://docs.ropensci.org/webchem/reference/etox_targets.html

Retrieves quality targets from the ETOX database for a given ETOX ID.

```APIDOC
## etox_targets

### Description
Query ETOX (Information System Ecotoxicology and Environmental Quality Targets) for quality targets associated with a specific chemical ID.

### Parameters
#### Arguments
- **id** (character) - Required - ETOX ID
- **verbose** (logical) - Optional - Print message during processing to console? (Default: getOption("verbose"))

### Value
A list of lists of two: `res` a data.frame with quality targets from the ETOX database, and source_url.

### Request Example
```r
etox_targets(c("20179", "9051"))
```

### Response
- **res** (data.frame) - Quality targets from the ETOX database
- **source_url** (string) - URL of the source data
```

--------------------------------

### Get citation information

Source: https://docs.ropensci.org/webchem/index.html

Retrieve the citation details for the webchem package within an R session.

```R
citation("webchem")
```

--------------------------------

### Query drug resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'drug' resource, which requires a compound ChEMBL ID.

```R
chembl_query("CHEMBL2", resource = "drug")
```

--------------------------------

### Query CIR for Molecular Weight

Source: https://docs.ropensci.org/webchem/reference/cir_query.html

Example of querying the CIR service to obtain the molecular weight ('mw') for 'Triclosan'.

```R
cir_query("Triclosan", "mw")
```

--------------------------------

### Query chembl_id_lookup resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'chembl_id_lookup' resource, which requires a ChEMBL ID to find its appropriate resource.

```R
chembl_query("CHEMBL1", resource = "chembl_id_lookup")
```

--------------------------------

### Query molecule resource with single ID

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'molecule' resource with a single compound ChEMBL ID.

```R
chembl_query("CHEMBL1082", resource = "molecule")
```

--------------------------------

### Query similarity resource with SMILES

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'similarity' resource using a compound SMILES string. The default similarity threshold is 70.

```R
chembl_query(
  "CC(=O)Oc1ccccc1C(=O)O", resource = "similarity",
  options = chembl_options(similarity = 70)
)
```

--------------------------------

### Basic SMILES to Image Conversion - webchem

Source: https://docs.ropensci.org/webchem/reference/cir_img.html

Converts a SMILES string to a chemical structure image and saves it to the specified directory. This is a basic usage example.

```R
cir_img("CCO", dir = tempdir()) # SMILES
```

--------------------------------

### Query CIR using Specific Resolver

Source: https://docs.ropensci.org/webchem/reference/cir_query.html

Example of querying the CIR service for the CAS number of '3380-34-5' and explicitly specifying the 'cas_number' resolver.

```R
cir_query("3380-34-5", "cas", resolver = "cas_number")
```

--------------------------------

### GET bcpc_query

Source: https://docs.ropensci.org/webchem/reference/bcpc_query.html

Queries the BCPC Compendium of Pesticide Common Names using either a chemical name or a CAS number.

```APIDOC
## GET bcpc_query

### Description
Query the BCPC Compendium of Pesticide Common Names to retrieve chemical details.

### Method
GET

### Parameters
#### Query Parameters
- **query** (character) - Required - The search string (name or CAS number).
- **from** (character) - Required - The type of input, either 'name' or 'cas'.
- **verbose** (logical) - Optional - Print message during processing to console.

### Response
#### Success Response (200)
- **common-name** (string) - Common name of the pesticide.
- **status** (string) - Status of the entry.
- **preferred IUPAC Name** (string) - Preferred IUPAC name.
- **IUPAC Name** (string) - IUPAC name.
- **cas** (string) - CAS registry number.
- **formula** (string) - Chemical formula.
- **activity** (string) - Primary activity.
- **subactivity** (string) - Sub-activity classification.
- **inchikey** (string) - InChIKey.
- **inchi** (string) - InChI string.
- **source url** (string) - URL to the source entry.
```

--------------------------------

### Query CIR with Multiple Identifiers

Source: https://docs.ropensci.org/webchem/reference/cir_query.html

Example demonstrating how to query the CIR service with a vector of chemical identifiers ('Triclosan', 'Aspirin') and retrieve the first CAS number match for each.

```R
comp <- c("Triclosan", "Aspirin")
cir_query(comp, "cas", match = "first")
```

--------------------------------

### Query CIR for CAS Number with 'first' Match

Source: https://docs.ropensci.org/webchem/reference/cir_query.html

Example of querying the CIR service for the CAS number of '3380-34-5' and retrieving only the first match.

```R
cir_query("3380-34-5", "cas", match = "first")
```

--------------------------------

### Load webchem and dependencies

Source: https://docs.ropensci.org/webchem/articles/webchem.html

Initialize the environment by loading the webchem and dplyr packages.

```R
library(webchem)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
```

--------------------------------

### Get PubChem Compound ID from Formula

Source: https://docs.ropensci.org/webchem/reference/get_cid.html

Retrieve CIDs by providing a chemical formula. The `from` argument must be set to "formula".

```R
get_cid("C26H52NO6P", from = "formula")
```

--------------------------------

### Get basic information from an ETOX ID

Source: https://docs.ropensci.org/webchem/reference/etox_basic.html

This function queries the ETOX: Information System Ecotoxicology and Environmental Quality Targets for basic information using an ETOX ID.

```APIDOC
## GET /etox/basic

### Description
Retrieves basic information from the ETOX database using a provided ETOX ID.

### Method
GET

### Endpoint
/etox/basic

### Parameters
#### Query Parameters
- **id** (character) - Required - The ETOX ID to query.
- **verbose** (logical) - Optional - If TRUE, prints processing messages to the console.

### Response
#### Success Response (200)
- **cas** (list) - A list of CAS numbers.
- **ec** (list) - A list of EC numbers.
- **gsbl** (list) - A list of GSBL numbers.
- **synonyms** (data.frame) - A data frame containing synonyms and the source URL.

### Request Example
```json
{
  "id": "20179",
  "verbose": true
}
```

### Response Example
```json
{
  "cas": ["123-45-6"],
  "ec": ["204-427-5"],
  "gsbl": ["GSBL00001"],
  "synonyms": {
    "synonym": ["Triclosan"],
    "url": ["https://webetox.uba.de/webETOX/disclaimer.do"]
  }
}
```
```

--------------------------------

### Get PubChem Compound ID from Depositor Name

Source: https://docs.ropensci.org/webchem/reference/get_cid.html

Retrieve CIDs by searching for substances associated with a depositor name. The `domain` must be set to "substance".

```R
get_cid("Optopharma Ltd", from = "sourceall", domain = "substance")
```

--------------------------------

### Retrieve ChemSpider Data Sources

Source: https://docs.ropensci.org/webchem/reference/cs_datasources.html

Use this function to get a list of available data sources from ChemSpider. This can help speed up queries by allowing you to specify which sources to search.

```R
cs_datasources(apikey = NULL, verbose = getOption("verbose"))
```

```R
cs_datasources()
```

--------------------------------

### Clone the repository

Source: https://docs.ropensci.org/webchem/CONTRIBUTING.html

Initial step to create a local copy of the repository from your GitHub account.

```bash
git clone https://github.com/<yourgithubusername>/webchem.git
```

--------------------------------

### GET chembl_query

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Retrieves data from a specified ChEMBL resource using a vector of identifiers.

```APIDOC
## GET chembl_query

### Description
Retrieve ChEMBL data using a vector of IDs. The function supports querying various resources such as molecules, drugs, and activities.

### Method
GET

### Parameters
#### Query Parameters
- **query** (character) - Required - A vector of IDs. The type of ID depends on the resource.
- **resource** (character) - Optional - The ChEMBL resource to query (default: "molecule").
- **mode** (character) - Optional - Either "ws" (webservice) or "offline" (local database) (default: "ws").
- **output** (character) - Optional - Either "raw" or "tidy" (default: "raw").
- **verbose** (logical) - Optional - Whether to print verbose output.
- **options** (list) - Optional - Resource- and mode-specific options including cache_file, similarity, and version.

### Response
#### Success Response (200)
- **result** (list) - A list of lists containing the query results.
```

--------------------------------

### Retrieve ETOX Basic Information

Source: https://docs.ropensci.org/webchem/reference/etox_basic.html

Demonstrates how to fetch basic chemical data for a single compound or multiple IDs using etox_basic.

```R
if (FALSE) { # \dontrun{
id <- get_etoxid('Triclosan', match = 'best')
etox_basic(id$etoxid)

# Retrieve data for multiple inputs
ids <- c("20179", "9051")
out <- etox_basic(ids)
out

# extract cas numbers
sapply(out, function(y) y$cas)
} # }
```

--------------------------------

### GET /wikidata/item-id

Source: https://docs.ropensci.org/webchem/reference/get_wdid.html

Retrieves Wikidata item identifiers for a given chemical search term.

```APIDOC
## GET /wikidata/item-id

### Description
Searches www.wikidata.org for wikidata item identifiers based on a provided query string. Note that this search is not limited to chemical substances.

### Method
GET

### Parameters
#### Query Parameters
- **query** (character) - Required - The search term to look up.
- **match** (character) - Optional - Strategy for handling multiple hits: 'best', 'first', 'all', 'ask', or 'na'.
- **verbose** (logical) - Optional - Whether to print processing messages to the console.
- **language** (character) - Optional - The language to perform the search in (default: 'en').

### Response
- **id** (string) - The Wikidata identifier.
- **matched text** (string) - The text that matched the query.
- **string distance** (numeric) - The distance between the match and the query.
- **queried string** (string) - The original input string.

### Request Example
get_wdid('Triclosan', language = 'de')

### Response Example
| id | matched text | string distance | queried string |
|----|--------------|-----------------|----------------|
| Q407616 | Triclosan | 0 | Triclosan |
```

--------------------------------

### GET fn_percept

Source: https://docs.ropensci.org/webchem/reference/fn_percept.html

Retrieves flavor percepts for a given CAS number from the Flavornet database.

```APIDOC
## GET fn_percept

### Description
Retrieve flavor percepts from http://www.flavornet.org. Flavornet is a database of 738 compounds with odors perceptible to humans detected using gas chromatography olfactometry (GCO).

### Method
GET

### Parameters
#### Query Parameters
- **query** (character) - Required - CAS number to search by.
- **from** (character) - Optional - Currently only CAS numbers are accepted.
- **verbose** (logical) - Optional - Should a verbose output be printed on the console?

### Request Example
fn_percept("123-32-0")

### Response
- **Value** (named character vector) - A named character vector containing flavor percepts or NA's in the case of CAS numbers that are not found.
```

--------------------------------

### Update package documentation

Source: https://docs.ropensci.org/webchem/CONTRIBUTING.html

Run this command to update documentation after making changes to roxygen2 tags.

```R
devtools::document()
```

--------------------------------

### Retrieve chemical information using cts_compinfo

Source: https://docs.ropensci.org/webchem/reference/cts_compinfo.html

Demonstrates how to fetch chemical details for a single InChIKey and how to process multiple inputs using the cts_compinfo function.

```R
cts_compinfo(
  query,
  from = "inchikey",
  verbose = getOption("verbose"),
  inchikey
)
```

```R
if (FALSE) { # \dontrun{
# might fail if API is not available
out <- cts_compinfo("XEFQLINVKFYRCS-UHFFFAOYSA-N")
# = Triclosan
str(out)
out[[1]][1:5]

### multiple inputs
inchikeys <- c("XEFQLINVKFYRCS-UHFFFAOYSA-N","BSYNRYMUTXBXSQ-UHFFFAOYSA-N" )
out2 <- cts_compinfo(inchikeys)
str(out2)
# a list of two
# extract molecular weight
sapply(out2, function(y) y$molweight)
} # }
```

--------------------------------

### Sync with upstream

Source: https://docs.ropensci.org/webchem/CONTRIBUTING.html

Commands to fetch and merge changes from the upstream repository to keep the local copy up to date.

```bash
git fetch upstream
```

```bash
git pull upstream
```

--------------------------------

### Query ChEMBL GO Slim Resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Use this to query GO slim annotations. Requires a GO ID.

```R
chembl_query("GO:0000003", resource = "go_slim")
```

--------------------------------

### Query biotherapeutic resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Example of querying the 'biotherapeutic' resource, which requires a compound ChEMBL ID.

```R
chembl_query("CHEMBL448105", resource = "biotherapeutic")
```

--------------------------------

### GET cts_from

Source: https://docs.ropensci.org/webchem/reference/cts_from.html

Retrieves a character vector of all valid identifiers supported by the CTS 'from' argument.

```APIDOC
## GET cts_from

### Description
Returns a list of all possible chemical identifiers that can be used in the 'from' argument for CTS conversion services.

### Method
GET

### Endpoint
cts_from()

### Parameters
#### Arguments
- **verbose** (logical) - Optional - Should a verbose output be printed on the console?

### Response
- **Returns** (character vector) - A list of valid identifier strings.

### Request Example
cts_from(verbose = TRUE)

### Response Example
["Chemical Name", "InChIKey", "PubChem CID", "CAS"]
```

--------------------------------

### Track upstream repository

Source: https://docs.ropensci.org/webchem/CONTRIBUTING.html

Configure the local repository to track changes from the main ropensci/webchem repository.

```bash
git remote add upstream https://github.com/ropensci/webchem.git
```

--------------------------------

### Usage of etox_basic

Source: https://docs.ropensci.org/webchem/reference/etox_basic.html

The function signature for querying the ETOX database.

```R
etox_basic(id, verbose = getOption("verbose"))
```

--------------------------------

### Multiple Queries and Formats - webchem

Source: https://docs.ropensci.org/webchem/reference/cir_img.html

Generates chemical structure images for multiple identifiers and specifies a transparent background with antialiasing disabled. This demonstrates handling multiple queries and customizing background/antialiasing.

```R
query = c("Glyphosate", "Isoproturon", "BSYNRYMUTXBXSQ-UHFFFAOYSA-N")
cir_img(query, dir = tempdir(), bgcolor = "transparent", antialising = 0)
```

--------------------------------

### Usage syntax for fn_percept

Source: https://docs.ropensci.org/webchem/reference/fn_percept.html

Displays the function signature for querying flavor percepts.

```R
fn_percept(query, from = "cas", verbose = getOption("verbose"), CAS, ...)
```

--------------------------------

### Query CIR for SMILES Representation

Source: https://docs.ropensci.org/webchem/reference/cir_query.html

Example of querying the CIR service to retrieve the SMILES string for '3380-34-5'.

```R
cir_query("3380-34-5", "smiles")
```

--------------------------------

### GET pc_sect

Source: https://docs.ropensci.org/webchem/reference/pc_sect.html

Retrieves the lowest level information from PubChem content pages for a given identifier and section.

```APIDOC
## GET pc_sect

### Description
Retrieves the lowest level information from PubChem content pages. Chemical information is organized into sections and subsections, and this function targets the lowest level of these sections.

### Method
GET

### Parameters
#### Request Body
- **id** (numeric or character) - Required - A vector of PubChem identifiers to search for.
- **section** (character) - Required - The section of the content page to be imported (not case sensitive, requires full name).
- **domain** (character) - Optional - The query domain. Can be one of "compound", "substance", "assay", "gene", "protein" or "patent". Defaults to "compound".
- **verbose** (logical) - Optional - Should a verbose output be printed on the console?

### Response
#### Success Response (200)
- **tibble** (object) - Returns a tibble of query results containing SourceName and SourceID.
```

--------------------------------

### GET get_etoxid

Source: https://docs.ropensci.org/webchem/reference/get_etoxid.html

Retrieves ETOX substance IDs based on a provided query string and identifier type.

```APIDOC
## GET get_etoxid

### Description
Queries the ETOX database to retrieve a substance ID based on a chemical name or identifier.

### Method
GET

### Parameters
#### Query Parameters
- **query** (character) - Required - The search term (chemical name or ID).
- **from** (character) - Optional - Type of input: "name", "cas", "ec", "gsbl", or "rtecs".
- **match** (character) - Optional - Handling of multiple hits: "all", "best", "first", "ask", or "na".
- **verbose** (logical) - Optional - Whether to print messages during processing.

### Response
#### Success Response (200)
- **tibble** (object) - A tibble containing 3 columns: query, match, and etoxID.
```

--------------------------------

### Retrieve PubChem Properties and Join Data

Source: https://docs.ropensci.org/webchem/articles/webchem.html

Fetches IUPAC Name and XLogP from PubChem for a list of compound IDs and joins the results with existing data. Ensure PubChem IDs are correctly formatted.

```r
y <- pc_prop(lc50_sub2$cid, properties = c("IUPACName", "XLogP"))
y$CID <- as.character(y$CID)
lc50_sub3 <- full_join(lc50_sub2, y, by = c("cid" = "CID"))
head(lc50_sub3)
```

--------------------------------

### GET etox_tests

Source: https://docs.ropensci.org/webchem/reference/etox_tests.html

Retrieves ecotoxicological test results from the ETOX database using a provided ETOX ID.

```APIDOC
## GET etox_tests

### Description
Queries the ETOX database for ecotoxicological test results associated with a specific ETOX ID.

### Method
GET

### Parameters
#### Arguments
- **id** (character) - Required - ETOX ID to query.
- **verbose** (logical) - Optional - Print message during processing to console. Defaults to getOption("verbose").

### Value
A list of lists containing a data.frame with test results and the source_url.

### Request Example
etox_tests(id = "20179")

### Response
- **data.frame** (object) - Contains columns: Organism, Effect, Duration, Time_Unit, Endpoint, Value, Unit.
- **source_url** (string) - The URL source of the data.
```

--------------------------------

### Access the Jagst dataset

Source: https://docs.ropensci.org/webchem/reference/jagst.html

Load the preprocessed environmental monitoring data for use in R.

```R
jagst
```

--------------------------------

### GET cs_compinfo

Source: https://docs.ropensci.org/webchem/reference/cs_compinfo.html

Retrieves record details for a given ChemSpider ID (CSID) based on specified fields.

```APIDOC
## GET cs_compinfo

### Description
Submit a ChemSpider ID (CSID) and the fields you are interested in to retrieve record details.

### Parameters
#### Arguments
- **csid** (numeric) - Required - The ChemSpider ID, can be obtained using get_csid.
- **fields** (character) - Required - Fields to retrieve. Valid values: "SMILES", "Formula", "InChI", "InChIKey", "StdInChI", "StdInChIKey", "AverageMass", "MolecularWeight", "MonoisotopicMass", "NominalMass", "CommonName", "ReferenceCount", "DataSourceCount", "PubMedCount", "RSCCount", "Mol2D", "Mol3D".
- **verbose** (logical) - Optional - Should a verbose output be printed on the console? Default: getOption("verbose").
- **apikey** (character) - Required - Your ChemSpider API key.

### Response
- **Value** (data frame) - Returns a data frame containing the requested chemical information.
```

--------------------------------

### Access the lc50 dataset

Source: https://docs.ropensci.org/webchem/reference/lc50.html

Use this command to load or reference the preprocessed acute toxicity data frame.

```R
lc50
```

--------------------------------

### GO Slim Resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Retrieves Gene Ontology (GO) slim information using a GO ID.

```APIDOC
## GET /resource/go_slim

### Description
Retrieves Gene Ontology (GO) slim information.

### Method
GET

### Endpoint
/resource/go_slim

### Parameters
#### Query Parameters
- **go_id** (string) - Required - The GO ID.

### Request Example
```json
{
  "go_id": "GO:0000003"
}
```

### Response
#### Success Response (200)
- **go_slim_data** (object) - GO slim information.

#### Response Example
```json
{
  "go_slim_data": {
    "term": "Cellular Component",
    "description": "Part of a cell."
  }
}
```
```

--------------------------------

### GET get_cid

Source: https://docs.ropensci.org/webchem/reference/get_cid.html

Retrieves compound IDs (CIDs) from PubChem based on a search query, input type, and domain.

```APIDOC
## get_cid

### Description
Retrieve compound IDs (CIDs) from PubChem using various search terms and domains.

### Parameters
#### Arguments
- **query** (character) - Required - Search term, one or more compounds.
- **from** (character) - Optional - Type of input (e.g., "name", "smiles", "inchi", "inchikey", "formula", "cas", "sid", "aid").
- **domain** (character) - Optional - Query domain, can be one of "compound", "substance", "assay".
- **match** (character) - Optional - How to handle multiple hits: "all", "first", "ask", or "na".
- **verbose** (logical) - Optional - Should a verbose output be printed on the console?
- **arg** (character) - Optional - Optional arguments like "name_type=word".

### Value
A tibble containing the retrieved CIDs.

### Request Example
get_cid("Triclosan")
get_cid("CCCC", from = "smiles")
get_cid("56-40-6", from = "xref/rn")
```

--------------------------------

### Define pc_synonyms Function

Source: https://docs.ropensci.org/webchem/reference/pc_synonyms.html

This is the function definition for searching synonyms in PubChem. It outlines the available parameters and their types.

```R
pc_synonyms(
  query,
  from = c("name", "cid", "sid", "aid", "smiles", "inchi", "inchikey"),
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  arg = NULL,
  choices = NULL,
  ...
)
```

--------------------------------

### GET cts_to

Source: https://docs.ropensci.org/webchem/reference/cts_to.html

Retrieves a character vector of all possible identifiers that can be used in the 'to' argument of chemical conversion functions.

```APIDOC
## GET cts_to

### Description
Returns a list of all possible identifiers that can be used in the 'to' argument for chemical translation services.

### Method
GET

### Endpoint
cts_to()

### Parameters
#### Arguments
- **verbose** (logical) - Optional - Should a verbose output be printed on the console?

### Response
- **Returns** (character vector) - A list of valid identifiers.

### Request Example
```r
cts_to(verbose = TRUE)
```
```

--------------------------------

### Query ChEMBL Xref Source Resource

Source: https://docs.ropensci.org/webchem/reference/chembl_query.html

Use this to query cross-reference sources. Requires the name of the resource.

```R
chembl_query("AlphaFoldDB", resource = "xref_source")
```

--------------------------------

### GET cts_compinfo

Source: https://docs.ropensci.org/webchem/reference/cts_compinfo.html

Retrieves chemical record details from the Chemical Translation Service (CTS) based on a provided InChIkey.

```APIDOC
## GET cts_compinfo

### Description
Retrieves record details from the Chemical Translation Service (CTS) for a given InChIkey.

### Parameters
#### Arguments
- **query** (character) - Required - The InChIkey to search for.
- **from** (character) - Optional - The source format, currently only accepts "inchikey".
- **verbose** (logical) - Optional - Whether to print verbose output to the console.

### Value
A list of lists containing: inchikey, inchicode, molweight, exactmass, formula, synonyms, and externalIds.

### Request Example
cts_compinfo("XEFQLINVKFYRCS-UHFFFAOYSA-N")

### Response Example
list(
  inchikey = "XEFQLINVKFYRCS-UHFFFAOYSA-N",
  inchicode = "...",
  molweight = 289.54,
  exactmass = 287.97,
  formula = "C12H7Cl3O2",
  synonyms = c("Triclosan", ...),
  externalIds = list(...)
)
```

--------------------------------

### Query BCPC Compendium with Multiple Names

Source: https://docs.ropensci.org/webchem/reference/bcpc_query.html

Pass a vector of names to query multiple pesticides simultaneously. The results can be processed using functions like `sapply`.

```R
out <- bcpc_query(c('Fluazinam', 'Diclofop'), from = 'name')
out
# extract subactivity from object
sapply(out, function(y) y$subactivity[1])
```

--------------------------------

### GET /cir_img

Source: https://docs.ropensci.org/webchem/reference/cir_img.html

Retrieves a chemical structure image from the Chemical Identifier Resolver (CIR) service and saves it to a local directory.

```APIDOC
## GET /cir_img

### Description
Interface to the Chemical Identifier Resolver (CIR) to generate and download chemical structure images based on chemical identifiers like CAS, InChI, or SMILES.

### Method
GET

### Parameters
#### Query Parameters
- **query** (character) - Required - Search term (e.g., CAS, INCHI(KEY), SMILES).
- **dir** (character) - Required - Directory to save the image.
- **format** (character) - Optional - Output format: "png" or "gif".
- **width** (integer) - Optional - Width of the image.
- **height** (integer) - Optional - Height of the image.
- **linewidth** (integer) - Optional - Width of lines.
- **symbolfontsize** (integer) - Optional - Fontsize of atoms.
- **bgcolor** (character) - Optional - Background color.
- **antialiasing** (logical) - Optional - Whether to use antialiasing.
- **atomcolor** (character) - Optional - Color of the atoms.
- **bondcolor** (character) - Optional - Color of the bond lines.
- **csymbol** (character) - Optional - Carbon symbol display: "special" or "all".
- **hsymbol** (character) - Optional - Hydrogen symbol display: "special" or "all".
- **hcolor** (character) - Optional - Color of hydrogen atoms.
- **header** (character) - Optional - Header text for the image.
- **footer** (character) - Optional - Footer text for the image.
- **frame** (integer) - Optional - Whether to plot a frame.
- **verbose** (logical) - Optional - Whether to print verbose output.

### Response
#### Success Response (200)
- **file** (file) - Image written to disk.
```

--------------------------------

### Retrieve flavor percepts using fn_percept

Source: https://docs.ropensci.org/webchem/reference/fn_percept.html

Demonstrates how to query the Flavornet database for specific chemical compounds using CAS numbers.

```R
if (FALSE) { # \dontrun{
# might fail if website is not available
fn_percept("123-32-0")

CASs <- c("75-07-0",  "64-17-5",  "109-66-0", "78-94-4",  "78-93-3")
fn_percept(CASs)
} # }
```

--------------------------------

### Download Images from ChemSpider

Source: https://docs.ropensci.org/webchem/reference/cs_img.html

Retrieves images of substances from ChemSpider and exports them in PNG format.

```APIDOC
## POST /chemspider/images

### Description
Retrieve images of substances from ChemSpider and export them in PNG format.

### Method
POST

### Endpoint
/chemspider/images

### Parameters
#### Request Body
- **csid** (numeric) - Required - The ChemSpider ID (CSID) of the substance. This will also be the name of the image file.
- **dir** (character) - Required - The download directory. Accepts both absolute and relative paths.
- **overwrite** (logical) - Optional - Should existing files in the directory with the same name be overwritten? Defaults to TRUE.
- **apikey** (character) - Optional - Your API key. If NULL, `cs_check_key()` will look for it in .Renviron or .Rprofile.
- **verbose** (logical) - Optional - Should a verbose output be printed on the console? Defaults to the value of getOption("verbose").

### Request Example
```json
{
  "csid": [582, 682],
  "dir": "/path/to/download/directory",
  "overwrite": true,
  "apikey": "YOUR_API_KEY",
  "verbose": true
}
```

### Response
#### Success Response (200)
- **status** (string) - Indicates the success of the operation.
- **message** (string) - A message detailing the outcome, including paths to downloaded files or errors encountered.

#### Response Example
```json
{
  "status": "success",
  "message": "Images downloaded successfully to /path/to/download/directory. Files: image_582.png, image_682.png"
}
```

### Note
An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & Conditions found at https://developer.rsc.org/terms.

### References
https://developer.rsc.org/docs/compounds-v1-trial/1/overview

### See also
`get_csid`, `cs_check_key`
```

--------------------------------

### GET /cs_datasources

Source: https://docs.ropensci.org/webchem/reference/cs_datasources.html

Retrieves a vector of available data sources used by ChemSpider to allow for query restriction and improved performance.

```APIDOC
## GET cs_datasources

### Description
Returns a character vector of available data sources used by ChemSpider. Restricting sources in subsequent queries can improve performance.

### Method
GET

### Parameters
#### Query Parameters
- **apikey** (character) - Optional - Your ChemSpider API key. If NULL, the function checks .Renviron or .Rprofile.
- **verbose** (logical) - Optional - Whether to print verbose output to the console.

### Request Example
cs_datasources(apikey = "your_api_key_here")

### Response
#### Success Response (200)
- **vector** (character) - A character vector containing the names of available data sources.

#### Response Example
["ChemSpider", "PubChem", "Wikipedia"]
```

--------------------------------

### GET chembl_atc_classes

Source: https://docs.ropensci.org/webchem/reference/chembl_atc_classes.html

Retrieve all available classes within the Anatomical Therapeutic Chemical (ATC) classification system from the ChEMBL database.

```APIDOC
## GET chembl_atc_classes

### Description
Retrieve all available classes within the Anatomical Therapeutic Chemical (ATC) classification system.

### Method
GET

### Endpoint
chembl_atc_classes()

### Parameters
#### Arguments
- **verbose** (logical) - Optional - Should a verbose output be printed on the console?
- **...** (dots) - Optional - Additional arguments, only used for internal testing.

### Request Example
chembl_atc_classes(verbose = TRUE)

### Response
#### Success Response (200)
- **data** (data.frame) - A data frame containing the ATC classification system classes.
```

--------------------------------

### Retrieve PubChem CIDs and merge data

Source: https://docs.ropensci.org/webchem/articles/webchem.html

Fetch PubChem Compound IDs using InChIKeys and join the results with the existing dataset.

```R
x <- get_cid(lc50_sub$inchikey, from = "inchikey", match = "first", verbose = FALSE)
library(dplyr)
lc50_sub2 <- full_join(lc50_sub, x, by = c("inchikey" = "query"))
head(lc50_sub2)
#>       cas        value                    inchikey  cid
#> 1 50-29-3    12.415277 YVGGHNCTFXOJCH-UHFFFAOYSA-N 3036
#> 2 52-68-6     1.282980 NFACJZMKEDPNKN-UHFFFAOYSA-N 5853
#> 3 55-38-9    12.168138 PNVJTZOFSHSLTO-UHFFFAOYSA-N 3346
#> 4 56-23-5 35000.000000 VZGDMQKNWNREIO-UHFFFAOYSA-N 5943
#> 5 56-38-2     1.539119 LCCNCVORNKJIRZ-UHFFFAOYSA-N  991
#> 6 57-74-9    98.400000 BIWJNBZANLAXMG-UHFFFAOYSA-N 5993
```

--------------------------------

### Get Multiple PubChem Compound IDs

Source: https://docs.ropensci.org/webchem/reference/get_cid.html

Retrieve CIDs for multiple search terms by passing a character vector to the `query` argument.

```R
get_cid(c("Triclosan", "Aspirin"))
```
Tokens:
Raw