Read, Write, Visualize and Manipulate PDB Files

Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.

Rpdb: Read, Write, Visualize and Manipulate PDB Files

• Reanimated the Rpdb package from the CRAN archive;
• Original author: Julien Idé;

Changes

• see [News.md] for all changes;

Usage

library(Rpdb)
# or: devtools::load_all(_path_)

# Download some legacy PDB files:
x = read.pdb(file.choose())
visualize(x, type="l")

Example:

# Download legacy PDB files from:
# https://www.rcsb.org/
x = read.pdb("7K3G.pdb")

# NMR Structure:
# Name of function drop.h: not yet stable;
x0H = drop.h(x)
con = connect(x0H) # Brute-force connectivity;
# Visualisation:
visualize(atoms(x0H), connect = con, type="l", pbc = F); addBBox(x)

# Labels:
res = residues(x0H, "A")
cols = rep("#84A232", nrow(res))
cols[res$resname %in% c("SER", "THR", "ASN")] = "red"
mark.pdb(x0H, ch = "A", col = cols, lwd = 2)

Note:

• Visualisation is incomplete;
• Started redesigning the Bounding box vs PBC box;
• Some functions are not yet visible in Rpdb, but can be accessed using: Rpdb:::function(...);