Atom Names/Types to Atomic Symbols Converter

Usage

atom2ele(...)
"atom2ele"(x, elety.custom=NULL, rescue=TRUE, ...)
"atom2ele"(pdb, inds, elety.custom=NULL, rescue=TRUE, ...)

Arguments

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 mapped to the first character of the atom names/types.

pdb

an object of class ‘pdb’ for which elety will be converted.

inds

an object of class ‘select’ indicating a subset of the pdb object to be used (see atom.select and trim.pdb).

...

further arguments passed to or from other methods.

Examples

atom.names <- c("CA", "O", "N", "OXT")
atom2ele(atom.names)

[1] "C" "O" "N" "O"



# PDB server connection required - testing excluded

## Get atomic symbols from a PDB object with a customized data set
pdb <- read.pdb("3RE0",verbose=FALSE)

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE

inds <- atom.select(pdb, resno=201, verbose=FALSE)

## maps CL2 to C
atom2ele(pdb, inds, elety.custom = NULL)

Warning message:

	unknown element: mapped PT1 to P
	unknown element: mapped N1 to N
	unknown element: mapped N2 to N
	unknown element: mapped CL2 to C
[1] "P" "N" "N" "C"


## map CL2 to Cl manually
myelety <- data.frame(name = "CL2", symb = "Cl")
atom2ele(pdb, inds, elety.custom = myelety)

Warning message:

	unknown element: mapped PT1 to P
	unknown element: mapped N1 to N
	unknown element: mapped N2 to N
[1] "P"  "N"  "N"  "Cl"

See also

Author