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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(…);

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.