Atom Names/Types to Mass Converter

Usage

atom2mass(...)
"atom2mass"(x, mass.custom=NULL, elety.custom=NULL, grpby=NULL, rescue=TRUE, ...) 
"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).
...
.

Atom Names/Types to Mass Converter

Description

Convert atom names/types into atomic masses.

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

Examples

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



[1] 12.0107 15.9994 14.0067 15.9994





# 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)

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



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




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


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] 30.97376 14.00670 14.00670 12.01070




## 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

See also

elements, atom.index, atom2ele, read.pdb

Author

Julien Ide, Lars Skjaerven