Add structure

Add a structure to the NGLVieweR object, either from a PDB entry code, a file, or directly from the R environment.

addStructure(NGLVieweR, data, format = NULL)

Arguments

NGLVieweR

A NGLVieweR object.

data

Structure data to be added, in the same forms as in NGLVieweR(): a PDB entry code (e.g. "7CID"), a file path (also compressed with gzip, bzip2 or xz), or the file contents as a single string or a vector of lines.

format

Format of the structure, as in NGLVieweR() (e.g. "pdb", "cif"). Needed for file contents and when the format cannot be inferred from the file name. For a PDB entry code it picks the file downloaded from RCSB, as in NGLVieweR().

Value

An updated NGLVieweR object with the added structure.

Details

This function allows you to add a structure to the NGLVieweR widget. You can add the structure using a PDB entry code, by specifying a local file, or by providing the structure data directly. If the format is not clear from the input, you may need to specify it using the format parameter.

Examples

NGLVieweR("1CRN") %>%
  addRepresentation("cartoon", param = list(color = "blue")) %>%
  addStructure("1CRN") %>%
  addRepresentation("cartoon", param = list(color = "orange")) %>%
  setPosition(x = 20, y = 0, z = 0) %>%
  setRotation(x = 2, y = 0, z = 0, degrees = FALSE) %>% 
  setScale(0.5)


# Note: The first "1CRN" structure is represented in blue, while the second 
# "1CRN" structure is represented in orange. Transformations such as 
# setPosition, setRotation, and setScale apply to the second 
# (most recently added) structure.