For character protein, pinfo returns the rownumber(s) of thermo()$protein that match the protein names.
The names can be supplied in the single protein argument (with an underscore, denoting protein_organism) or as pairs of proteins and organisms.
NA is returned for any unmatched proteins, including those for which no organism is given or that do not have an underscore in protein.
Alternatively, if regexp is TRUE, the protein argument is used as a pattern (regular expression); rownumbers of all matches of thermo()$protein$protein to this pattern are returned.
When using regexp, the organism can optionally be provided to return only those entries that also match thermo()$protein$organism.
For numeric protein, pinfo returns the corresponding row(s) of thermo()$protein.
Set residue to TRUE to return the per-residue composition (i.e. amino acid composition of the protein divided by total number of residues).
For dataframe protein, pinfo returns it unchanged, except for possibly the per-residue calculation.
The following functions accept any specification of protein(s) described above for pinfo:
protein.length returns the lengths (number of amino acids) of the proteins.
protein.formula returns a stoichiometrix matrix representing the chemical formulas of the proteins that can be pased to e.g. mass or ZC.
The amino acid compositions are multiplied by the output of group.formulas to generate the result.
protein.OBIGT calculates the thermodynamic properties and equations-of-state parameters for the completely nonionized proteins using group additivity with parameters taken from Dick et al., 2006 (aqueous proteins) and LaRowe and Dick, 2012 (crystalline proteins and revised aqueous methionine sidechain group).
The return value is a data frame in the same format as thermo()$OBIGT.
state indicates the physical state for the parameters used in the calculation (aq or cr).
The following functions also depend on an existing definition of the basis species:
protein.basis calculates the numbers of the basis species (i.e. opposite of the coefficients in the formation reactions) that can be combined to form the composition of each of the proteins.
The basis species must be present in thermo()$basis, and if H+ is among the basis species, the ionization states of the proteins are included.
The ionization state of the protein is calculated at the pH defined in thermo()$basis and at the temperature specified by the T argument.
If normalize is TRUE, the coefficients on the basis species are divided by the lengths of the proteins.
protein.equil produces a series of messages showing step-by-step a calculation of the chemical activities of proteins in metastable equilibrium. For the first protein, it shows the standard Gibbs energies of the reaction to form the nonionized protein from the basis species and of the ionization reaction of the protein (if H+ is in the basis), then the standard Gibbs energy/RT of the reaction to form the (possibly ionized) protein per residue. The per-residue values of logQstar and Astar/RT are also shown for the first protein. Equilibrium calculations are then performed, only if more than one protein is specified. This calculation applies the Boltzmann distribution to the calculation of the equilibrium degrees of formation of the residue equivalents of the proteins, then converts them to activities of proteins taking account of loga.protein and protein length. If the protein argument is numeric (indicating rownumbers in thermo()$protein), the values of Astar/RT are compared with the output of affinity, and those of the equilibrium degrees of formation of the residues and the chemical activities of the proteins with the output of diagram. If the values in any of these tests are are not all.equal an error is produced indicating a bug.