Convert a PDB Object to a Character String

Function to take a bio3d pdb structure object and convert it to a single element character vector that can then be used as input for the NGLVieweR and r3dmol packages.

Usage

pdb2string(pdb, ...)

Arguments

pdb

a bio3d pdb object as obtained from read.pdb().

...

Extra arguments that are passed to write.pdb().

Value

a single element character vector with return characters as required by NGLVieweR::NGLVieweR() function with format=pdb option. Note that no intermediate files are produced.

See also

view.pdb() which uses this function internally, NGLVieweR::NGLVieweR(), bio3d::read.pdb().

Author

Barry Grant, bjgrant@ucsd.edu

Examples

pdb <- bio3d::read.pdb("5p21")
#>   Note: Accessing on-line PDB file
#> Warning: /var/folders/jd/wjwf0lcj0kd0tch_70sd1l4w0000gn/T//RtmpEoJQ6k/5p21.pdb  exists. Skipping download

NGLVieweR::NGLVieweR(pdb2string(pdb), format="pdb") |>
  NGLVieweR::addRepresentation("cartoon")


# Or more simply
view.pdb(pdb)