R: Atom Names/Types to Atomic Symbols Converter

atom2ele {bio3d} | R Documentation

## Atom Names/Types to Atomic Symbols Converter

### Description

Convert atom names/types into atomic symbols

### Usage

    atom2ele(...)

    ## Default S3 method:
    atom2ele(x, elety.custom=NULL, rescue=TRUE, ...)

    ## S3 method for class 'pdb'
    atom2ele(pdb, inds=NULL, ...)

### 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 converted based on matching with `bio3d::elements$symb`.
`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.

### Details

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.

### Value

Return a character vector of atomic symbols

### Author(s)

Julien Ide, Lars Skjaerven

### See Also

`atom.index`, `elements`, `read.pdb`, `atom2mass`, `formula2mass`

### Examples

    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)

[Package bio3d version 2.4-0 Index]