aa2mass {bio3d}

Amino Acid Residues to Mass Converter

Description

Convert a sequence of amino acid residue names to mass.

Usage

aa2mass(pdb, inds=NULL, mass.custom=NULL, addter=TRUE, mmtk=FALSE)

Arguments

pdb

a character vector containing the atom names to convert to atomic masses. Alternatively, a object of type pdb can be provided.

inds

atom and xyz coordinate indices obtained from atom.select that selects the elements of pdb upon which the calculation should be based.

mass.custom

a list of amino acid residue names and their corresponding masses.

addter

logical, if TRUE terminal atoms are added to final masses.

mmtk

logical, if TRUE use the exact aminoacid residue masses as provided with the MMTK database (for testing purposes).

Details

This function converts amino acid residue names to their corresponding masses. In the case of a non-standard amino acid residue name mass.custom can be used to map the residue to the correct mass. User-defined amino acid masses (with argument mass.custom) will override mass entries obtained from the database.

See examples for more details.

Value

Returns a numeric vector of masses.

Note

When object of type pdb is provided, non-calpha atom records are omitted from the selection.

Author(s)

Lars Skjaerven

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

atom.index, atom2mass, aa.index

Examples

resi.names <- c("LYS", "ALA", "CYS", "HIS")
masses <- aa2mass(resi.names, addter=FALSE)

## Not run: 
## Fetch atomic masses in a PDB object
pdb <- read.pdb("3dnd")
masses <- aa2mass(pdb)

## or
masses <- aa2mass(pdb$atom[1:10,"resid"])

## Dealing with unconventional residues
#pdb <- read.pdb("1xj0")

#mass.cust <- list("CSX"=122.166)
#masses <- aa2mass(pdb, mass.custom=mass.cust)

## End(Not run)