aa2mass. bio3d 2.3-0

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).

Description

Convert a sequence of amino acid residue names to mass.

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.

Note

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

Value

Returns a numeric vector of masses.

References

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

Examples

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

## Fetch atomic masses in a PDB object
pdb <- read.pdb("3dnd")

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE

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)

Author

Lars Skjaerven

Amino Acid Residues to Mass Converter