Nothing
as.pdb.mol2 <- function(mol, ...) {
cl <- match.call()
natoms <- nrow(mol$atom)
pdbn <- list()
allset <- FALSE
resid <- strtrim(mol$atom$resid, 3)
chain <- NULL
if(!is.null(mol$substructure)) {
if(all(c("root_atom", "subst_type", "chain") %in% colnames(mol$substructure))) {
key1 <- paste(mol$atom$resno, mol$atom$resid, sep="-")
rownames(mol$substructure) <- key1[ mol$subs$root_atom ]
resid <- mol$substructure[key1, "sub_type"]
chain <- mol$substructure[key1, "chain"]
allset <- TRUE
}
}
if(!allset & length(unique(mol$resid)) > 1) {
warning("insuffient data in SUBSTRUCTURE to set residue and chain identifiers in PDB")
}
pdb <- as.pdb.default(pdb = NULL,
xyz = mol$xyz,
type = rep("ATOM", natoms),
resno = mol$atom$resno,
resid = resid,
eleno = mol$eleno,
elety = mol$atom$elena,
chain = chain,
insert = NULL,
alt = NULL,
o=NULL, b=NULL, segid=NULL,
elesy=unlist(lapply(strsplit(mol$atom$elety, split="[.]"),
function(x) x[1])),
charge=mol$atom$charge)
pdb$call <- cl
return(pdb)
}
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