Functions to get amino acid compositions and add them to protein list for use by other functions.
1 2 3
data frame, amino acid composition in the format of
character, name of protein; numeric, indices of proteins (rownumbers of
character, protein sequence
numeric, abundances of proteins
logical, return the weighted average of amino acid counts?
character, name of organism
A protein in CHNOSZ is defined by its identifying information and the amino acid composition, stored in
The names of proteins in CHNOSZ are distinguished from those of other chemical species by having an underscore character ("_") that separates two identifiers, referred to as the
An example is LYSC_CHICK.
The purpose of the functions described here is to identify proteins and work with their amino acid compositions.
From the amino acid compositions, the thermodynamic properties of the proteins can be estimated by group additivity.
seq2aa returns a data frame of amino acid composition, in the format of
thermo()$protein, corresponding to the provided
protein argument indicates the name of the protein with an underscore (e.g. LYSC_CHICK).
aasum returns a data frame representing the sum of amino acid compositions in the rows of the input
aa data frame.
The amino acid compositions are multiplied by the indicated
abundance; that argument is recycled to match the number of rows of
average is TRUE the final sum is divided by the number of input compositions.
The name used in the output is taken from the first row of
aa or from
organism if they are specified.
Given amino acid compositions returned by the
*aa functions described above,
add.protein adds them to
thermo()$protein for use by other functions in CHNOSZ.
The amino acid compositions of proteins in
aa with the same name as one in
thermo()$protein are replaced.
The value returned by this function is the rownumbers of
thermo()$protein that are added and/or replaced.
pinfo for protein-level functions (length, chemical formulas, reaction coefficients of basis species).
protein for examples of affinity calculations and diagrams.
1 2 3 4 5 6 7 8 9 10
# manually adding a new protein # Human Gastric juice peptide 1 aa <- seq2aa("GAJU_HUMAN", "LAAGKVEDSD") ip <- add.protein(aa) stopifnot(protein.length(ip)==10) # the chemical formula of this peptide as.chemical.formula(protein.formula(ip)) # "C41H69N11O18" # we can also calculate a formula without using add.protein aa <- seq2aa("pentapeptide_test", "ANLSG") as.chemical.formula(protein.formula(aa))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.