atom2mass: Atom Names/Types to Mass Converter

In bio3d: Biological Structure Analysis

Atom Names/Types to Mass Converter

Description

Convert atom names/types into atomic masses.

Usage

atom2mass(...)
## Default S3 method:
atom2mass(x, mass.custom=NULL, elety.custom=NULL,
                            grpby=NULL, rescue=TRUE, ...) 
## S3 method for class '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(s)

Julien Ide, Lars Skjaerven

See Also

elements, atom.index, atom2ele, read.pdb

Examples

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


# PDB server connection required - testing excluded
try({

## Get atomic symbols from a PDB object with a customized data set
pdb <- read.pdb("3RE0", verbose=FALSE)
inds <- atom.select(pdb, resno=201, verbose=FALSE)

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

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

## 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)

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

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.