PubChemR (version 3.0.0)

pc_similarity_search: Similarity-Driven Identifier Search

Description

Performs similarity search requests and returns mapped identifiers in a typed result object.

Usage

pc_similarity_search(
  identifier,
  namespace = c("smiles", "cid", "inchi", "sdf"),
  domain = "compound",
  to = c("cids", "sids", "aids"),
  searchtype = c("similarity", "fastsimilarity_2d", "fastsimilarity_3d"),
  threshold = 95,
  max_records = NULL,
  options = NULL,
  ...
)

Value

A typed object inheriting from `PubChemIdMap`.

Arguments

identifier

Query identifier(s) for similarity search.

namespace

Namespace for query identifiers.

domain

PubChem domain.

to

Output mapping target (`"cids"`, `"sids"`, or `"aids"`).

searchtype

Similarity mode (`"similarity"`, `"fastsimilarity_2d"`, `"fastsimilarity_3d"`).

threshold

Similarity threshold.

max_records

Optional maximum number of records returned by PubChem.

options

Optional named list of additional query options.

...

Additional arguments passed to `pc_request()`.

Details

Similarity mode is controlled by `searchtype` and `threshold`. Optional `max_records` is translated to `list_return` and appended to query options.

Examples

sim <- pc_similarity_search("CC(=O)OC1=CC=CC=C1C(=O)O", namespace = "smiles", offline = TRUE)
inherits(sim, "PubChemIdMap")

if (FALSE) {
pc_similarity_search("CC(=O)OC1=CC=CC=C1C(=O)O", namespace = "smiles")
}