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CHNOSZ (version 0.9-2)

Chemical Thermodynamics and Activity Diagrams

Description

Calculation of the standard molal thermodynamic properties and chemical affinities of reactions between and among minerals, inorganic, organic, and/or biomolecular aqueous and crystalline species. Incorporation of an extensive database of thermodynamic properties of species and algorithms for computing the standard thermodynamic properties of neutral and ionized proteins from amino acid group contributions. Generation of chemical speciation and predominance diagrams for stable and metastable equilibrium in open systems as a function of temperature, pressure, and chemical activities or fugacities of basis species.

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Version

Install

install.packages('CHNOSZ')

Monthly Downloads

838

Version

0.9-2

License

GPL (>= 2)

Maintainer

Jeffrey Dick

Last Published

August 26th, 2010

Functions in CHNOSZ (0.9-2)

thermo

Thermodynamic Properties and Compositional Data
util.data

Functions to Modify the Thermodynamic Database
util.misc

Miscellaneous Utility Functions
get.protein

Proteins from Model Organisms
revisit

Diversity Calculations for Chemical Species
util.formula

Functions to Work with Chemical Formulas
taxonomy

Extract Data from NCBI Taxonomy Files
util.array

Functions to Work with Multidimensional Arrays
CHNOSZ

Chemical Thermodynamics and Activity Diagrams
basis

Basis Species
diagram

Calculate and Plot Relative Abundances of Species
util.args

Functions for Processing Argument Lists
eos

Equations of State
subcrt

Properties of Species and Reactions
info

Search the Thermodynamic Database
util.plot

Functions to Create and Modify Plots
species

Species of Interest
ionize

Ionization Properties of Proteins
util.list

Functions to Work with Lists
eqdata

Read data from an EQ6 output file
affinity

Chemical Affinities of Formation Reactions
util.fasta

Functions for Accessing FASTA Files
util.seq

Functions to Work with Sequence Data
util.character

Functions to Manipulate Character Objects
water

Properties of Water
examples

Run examples from the documentation
buffer

Chemical Potential Buffers
protein

Properties of Proteins
util.blast

Functions to Work with BLAST Output Files
transfer

Mass Transfer Calculations
util.units

Functions to Convert Units
makeup

Chemical Formulas and Compositions