Atom Names/Types to Mass Converter

Convert atom names/types into atomic masses.

atom2mass(...)
# S3 method for default
atom2mass(x, mass.custom=NULL, elety.custom=NULL,
                            grpby=NULL, rescue=TRUE, ...) 
# S3 method for pdb
atom2mass(pdb, inds=NULL, mass.custom=NULL,
                        elety.custom=NULL, grpby=NULL, rescue=TRUE, ...)

Arguments

x

a character vector containing atom names/types to be converted.
mass.custom

a customized data.frame containing atomic symbols and corresponding masses.
elety.custom

a customized data.frame containing atom names/types and corresponding atomic symbols.
grpby

a ‘factor’, as returned by as.factor, used to group the atoms.
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).
...

.

Details

The default method first convert atom names/types into atomic symbols using the atom2ele function. Then, atomic symbols are searched in the elements data set and their corresponding masses are returned. If mass.custom is specified it is combined with elements (using rbind) before searching. Therefore, mass.custom must have columns named symb and mass (see examples). If grpby is specified masses are splitted (using split) to compute the mass of groups of atoms defined by grpby.

The S3 method for object of class ‘pdb’, pass pdb$atom$elety to the default method.

Value

Return a numeric vector of masses.

Author

Julien Ide, Lars Skjaerven

See also

elements, atom.index, atom2ele, read.pdb

Examples

atom.names <- c("CA", "O", "N", "OXT")
atom2mass(atom.names)

#> [1] 12.0107 15.9994 14.0067 15.9994

# \donttest{
# 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
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/3RE0.pdb  exists. Skipping download
#>    PDB has ALT records, taking A only, rm.alt=TRUE
inds <- atom.select(pdb, resno=201, verbose=FALSE)

## selected atoms
print(pdb$atom$elety[inds$atom])

#> [1] "PT1" "N1"  "N2"  "CL2"

## default will map CL2 to C
atom2mass(pdb, inds)

#> Warning: 
#> 	mapped element PT1 to Pt
#> 	mapped element N1 to N
#> 	mapped element N2 to N
#> 	mapped element CL2 to Cl
#> [1] 195.0780  14.0067  14.0067  35.4530

## map element CL2 correctly to Cl
myelety  <- data.frame(name = c("CL2","PT1","N1","N2"), symb = c("Cl","Pt","N","N"))
atom2mass(pdb, inds, elety.custom = myelety)

#> [1] 195.0780  14.0067  14.0067  35.4530

## custom masses
mymasses <- data.frame(symb = c("Cl","Pt"), mass = c(35.45, 195.08))
atom2mass(pdb, inds, elety.custom = myelety, mass.custom = mymasses)

#> [1] 195.0800  14.0067  14.0067  35.4500

# }