3D_net.R

library("igraph")
rm(list = ls())
##########################################################################
# Read data
dataSet <- read.table("http://www.vesnam.com/Rblog/wp-content/uploads/2013/07/lesmis.txt",
                      header = FALSE, sep = "\t")

# Create a graph. Use simplify to ensure that there are no duplicated edges or self loops
gD <- simplify(graph.data.frame(dataSet, directed=FALSE))

# Calculate degree for all nodes
degAll <- degree(gD, v = V(gD), mode = "all")

coord3D <- layout.fruchterman.reingold(gD, dim = 3) 
nType <- 1

write2mol2 <- function(x, ...) write.table(x, sep="\t", row.names = FALSE, 
                                           col.names = FALSE, quote = FALSE, ...)

write2mol2("@<TRIPOS>MOLECULE", file="3D_lesmis.mol2")
write2mol2("Les Miserables", file="3D_lesmis.mol2", append = TRUE)
write2mol2(data.frame(vcount(gD), ecount(gD), nType), file="3D_lesmis.mol2", append=TRUE)
write2mol2("SMALL", file = "3D_lesmis.mol2", append = TRUE)
write2mol2("NO_CHARGES\n", file = "3D_lesmis.mol2", append = TRUE)
write2mol2("@<TRIPOS>ATOM", file = "3D_lesmis.mol2", append = TRUE)

isIn2 <- factor(cut(degAll, breaks = c(0, 1, 2, 5, 10, 15, Inf)),
                labels=c("He", "Na", "O", "Au", "P", "Cl"))

hlpL <- data.frame(i=1:vcount(gD),
                   name=V(gD)$name,
                   coord3D[, 1:3], 
                   isIn2,
                   isType=1,
                   0.0)

write2mol2(hlpL, file="3D_lesmis.mol2", append=TRUE)


write2mol2("@<TRIPOS>BOND", file = "3D_lesmis.mol2", append = TRUE)
isType <- 1


hlpL <- data.frame(i=1:ecount(gD),
                   get.edges(gD, 1:ecount(gD)),
                   isType=1)

write2mol2(hlpL, file = "3D_lesmis.mol2", append = TRUE)


################################
# Visualization adjustments using jmol scripts
#
# _He; spacefill 0.2; wireframe 10; color bonds blue; font label 10;
# select _Na; spacefill 0.4; wireframe 12; color bonds purple; font label 12;
# select _O; spacefill 0.6; wireframe 14; color bonds red; font label 14;
# select _Au; spacefill 0.8; wireframe 16; color bonds yellow; font label 16;
# select _P; spacefill 1.0; wireframe 18; color bonds orange; font label 18;
# select _Cl; spacefill 1.5; wireframe 20; color bonds green; font label 20;
#
# select _He; label hide;
# select _Na; label hide;
# select _O; label hide
################################