PubChem molecular structure — pubchem

Query the PubChem api and retrieve a display an image of the matching molecular structure.

Usage

pubchem_structure(
  query_column,
  search_by,
  row_index,
  record_type = "2d",
  image_size = "large",
  ...
)

Arguments

query_column: (character) The name of the annotation_source column with compound identifiers of the type specified in the search_by param.
search_by: (character) The PubChem domain to search for matches to the annotation_column.
row_index: (integer, numeric) The row index of the annotation_source to request an image of the molecular structure of.
record_type: (character) The record type to return from the PubChem query. Can be one of "2d" or "3d". The default is "2d".
image_size: (character) The size of the image to return from the PubChem query. Can be one of "large" or "small". For record_type = "2d" an arbitrary image size can be specified e.g. 123x123. The default is "large".
...: Additional slots and values passed to struct_class.

Value

A pubchem_structure object. This object has no output slots. See chart_plot in the struct package to plot this chart object.

Details

This object makes use of functionality from the following packages:

cowplot

This object queries the PubChem API for matches to your query without caching the results. It is therefore intended for limited use. If you wish to obtain images for a large number of moelucules you should seek an alternative solution.

Inheritance

A pubchem_structure object inherits the following struct classes:

[pubchem_structure] -> [chart] -> [struct_class]

References

Wilke C (2024). cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'. R package version 1.1.3, https://CRAN.R-project.org/package=cowplot.

Examples

M <- pubchem_structure(
        query_column = "V1",
        search_by = "cid",
        row_index = 1,
        record_type = "2d",
        image_size = "large")