util.seq

aminoacids

Return names or one- or three-letter abbreviations of amino acids.

An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ
also implements a group additivity algorithm for the standard thermodynamic
properties of proteins.

Jeffrey Dick

CHNOSZ

Thermodynamic Calculations and Diagrams for Geochemistry

util.seq function

<dl> <dt>nchar</dt>
<dd>numeric, \(1\) to return one-letter, \(3\) to return three-letter abbreviations for amino acids</dd> <dt>which</dt>
<dd>character, which amino acids to name</dd></dl>

Arguments

Functions to Work with Sequence Data — util.seq

<dl>

 <dt>nchar</dt>
<dd>numeric, \(1\) to return one-letter, \(3\) to return three-letter abbreviations for amino acids</dd>

 <dt>which</dt>
<dd>character, which amino acids to name</dd>

</dl>

util.seq: Functions to Work with Sequence Data

Description

Usage

Arguments

Details

See Also

Examples