Atom Names/Types to Atomic Symbols Converter
Convert atom names/types into atomic symbols
atom2ele(...) ## Default S3 method: atom2ele(x, elety.custom=NULL, rescue=TRUE, ...) ## S3 method for class 'pdb' atom2ele(pdb, inds=NULL, ...)
x |
a character vector containing atom names/types to be converted. |
elety.custom |
a customized data.frame containing atom names/types and corresponding atomic symbols. |
rescue |
logical, if TRUE the atomic symbols will be converted
based on matching with |
pdb |
an object of class ‘pdb’ for which |
inds |
an object of class ‘select’ indicating a subset of
the |
... |
further arguments passed to or from other methods. |
The default method searchs for the atom names/types in the
atom.index data set and returns their corresponding atomic
symbols. If elety.custom is specified it is combined with
atom.index (using rbind) before
searching. Therefore, elety.custom must contains columns named
name and symb.
The S3 method for object of class ‘pdb’, pass
pdb$atom[,"elety"] to the default method.
Return a character vector of atomic symbols
Julien Ide, Lars Skjaerven
atom.names <- c("CA", "O", "N", "OXT")
atom2ele(atom.names)
# PDB server connection required - testing excluded
## Get atomic symbols from a PDB object with a customized data set
pdb <- read.pdb("3RE0",verbose=FALSE)
lig <- trim(pdb, "ligand")
## maps PT1 to Pt, CL2 to Cl, C4A to C
atom2ele(lig)
## map atom name to element manually
myelety <- data.frame(name = "CL2", symb = "Cl")
atom2ele(lig, elety.custom = myelety)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.