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PubChem molecular structure

Source: R/pubchem_structure_chart_class.R
pubchem_structure.Rd

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 (2023). cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'. R package version 1.1.2, 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")