# Chemical Thermodynamics and Activity Diagrams

## Documentation for package ‘CHNOSZ’ version 1.0.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P Q R S T U W Y Z

CHNOSZ-package | Chemical Thermodynamics and Activity Diagrams

## -- A --

A.ionization | Functions to Work With Chemical Affinities
aa2eos | Amino Acid Compositions of Proteins
aasum | Amino Acid Compositions of Proteins
add.obigt | Functions to Work with the Thermodynamic Database
add.protein | Amino Acid Compositions of Proteins
affinity | Chemical Affinities of Formation Reactions
allparents | Extract Data from NCBI Taxonomy Files
aminoacids | Functions to Work with Sequence Data
anim | Functions to Make Animations
anim.carboxylase | Functions to Make Animations
anim.plasma | Functions to Make Animations
anim.TCA | Functions to Make Animations
apc | Mass Transfer Calculations
as.chemical.formula | Functions to Work with Chemical Formulas
axis.label | Functions to Express Chemical Formulas and Properties

## -- B --

balance | Equilibrium Chemical Activities of Species
basis | Define Basis Species
basis.elements | Swap Basis Species
basis.logact | Swap Basis Species
browse.refs | Functions to Work with the Thermodynamic Database
buffer | Calculating Buffered Chemical Activities
buffers | Thermodynamic Database and System Definition

## -- C --

c2s | Functions to Manipulate Character Objects
caller.name | Functions for Various Programming Tasks
can.be.numeric | Functions to Manipulate Character Objects
cgl | Equations of State
check.obigt | Functions to Work with the Thermodynamic Database
checkEOS | Functions to Work with the Thermodynamic Database
checkGHS | Functions to Work with the Thermodynamic Database
convert | Functions to Convert Units
count.aa | Functions for Reading FASTA Files and Downloading from UniProt
count.charge | Parse Chemical Formulas
count.elements | Parse Chemical Formulas
count.formulas | Parse Chemical Formulas
CV | Objective Functions
CVRMSD | Objective Functions

## -- D --

DDGmix | Objective Functions
def2gi | Functions to Work with BLAST Output Files
demos | Run Examples from the Documentation
describe.basis | Functions to Express Chemical Formulas and Properties
describe.property | Functions to Express Chemical Formulas and Properties
describe.reaction | Functions to Express Chemical Formulas and Properties
DGinf | Objective Functions
DGmix | Objective Functions
DGtr | Objective Functions
diagram | Equilibrium Chemical Activity Diagrams
dimSums | Functions to Work with Multidimensional Arrays
dPdTtr | Functions for Miscellaneous Tasks
draw.transfer | Mass Transfer Calculations

## -- E --

E.units | Functions to Convert Units
element | Thermodynamic Database and System Definition
element.mu | Swap Basis Species
element.potentials | Gibbs Energy Minimization by Steepest Descent
energy | Functions to Work With Chemical Affinities
energy.args | Functions to Work With Chemical Affinities
entropy | Functions to Work with Chemical Formulas
envert | Functions to Convert Units
eos.args | Functions for Processing Argument Lists
EOScalc | Regress Equations-of-State Parameters for Aqueous Species
EOScoeffs | Regress Equations-of-State Parameters for Aqueous Species
EOSlab | Regress Equations-of-State Parameters for Aqueous Species
EOSplot | Regress Equations-of-State Parameters for Aqueous Species
EOSregress | Regress Equations-of-State Parameters for Aqueous Species
EOSvar | Regress Equations-of-State Parameters for Aqueous Species
eqdata | Read data from an EQ6 output file
equil.boltzmann | Equilibrium Chemical Activities of Species
equil.potentials | Gibbs Energy Minimization by Steepest Descent
equil.reaction | Equilibrium Chemical Activities of Species
equilibrate | Equilibrium Chemical Activities of Species
examples | Run Examples from the Documentation
expr.property | Functions to Express Chemical Formulas and Properties
expr.species | Functions to Express Chemical Formulas and Properties
expr.units | Functions to Express Chemical Formulas and Properties
extdata | Extra Data
extremes | Plots and Optima of Objective Functions

## -- F --

feldspar | Mass Transfer Calculations
find.tp | Equilibrium Chemical Activity Diagrams
findit | Gridded Search to Optimize Objective Functions

## -- G --

get.formula | Functions to Work with Chemical Formulas
get.objfun | Objective Functions
getnames | Extract Data from NCBI Taxonomy Files
getnodes | Extract Data from NCBI Taxonomy Files
getrank | Extract Data from NCBI Taxonomy Files
gfun | Equations of State
GHS | Functions to Work with Chemical Formulas
grep.file | Functions for Reading FASTA Files and Downloading from UniProt
group.formulas | Summaries of Thermodynamic Properties of Proteins
groups | Thermodynamic Database and System Definition
guess | Gibbs Energy Minimization by Steepest Descent

## -- H --

hkf | Equations of State

## -- I --

i2A | Functions to Work with Chemical Formulas
IAPWS95 | Properties of Water from IAPWS-95
IAPWS95.idealgas | Properties of Water from IAPWS-95
IAPWS95.residual | Properties of Water from IAPWS-95
ibasis | Swap Basis Species
id.blast | Functions to Work with BLAST Output Files
info | Search the Thermodynamic Database
info.approx | Search the Thermodynamic Database
info.character | Search the Thermodynamic Database
info.numeric | Search the Thermodynamic Database
info.text | Search the Thermodynamic Database
invertible.combs | Functions for Various Matrix Operations
ionize.aa | Properties of Ionization of Proteins
ip2aa | Amino Acid Compositions of Proteins
iprotein | Amino Acid Compositions of Proteins
is.near.equil | Gibbs Energy Minimization by Steepest Descent

## -- L --

label.figure | Functions to Create and Modify Plots
label.plot | Functions to Create and Modify Plots
list2array | Functions to Work with Multidimensional Arrays
logact | Objective Functions
lsub | Functions to Work with Lists
lsum | Functions to Work with Lists

## -- M --

makeup | Parse Chemical Formulas
mass | Functions to Work with Chemical Formulas
mod.basis | Define Basis Species
mod.buffer | Calculating Buffered Chemical Activities
mod.obigt | Functions to Work with the Thermodynamic Database
more.aa | Proteins from Model Organisms
mosaic | Chemical Affinities with Changing Basis Species
MP90.cp | Summaries of Thermodynamic Properties of Proteins
msgout | Functions for Various Programming Tasks
mtitle | Functions to Create and Modify Plots

## -- N --

nonideal | Activity coefficients of aqueous species
nucleic.complement | Functions to Work with Sequence Data
nucleic.formula | Functions to Work with Sequence Data

## -- O --

OBIGT | Thermodynamic Database and System Definition
obigt2eos | Functions to Work with the Thermodynamic Database
objective | Objective Functions
opt | Thermodynamic Database and System Definition
optimal.index | Plots and Optima of Objective Functions
outvert | Functions to Convert Units

## -- P --

P.units | Functions to Convert Units
palply | Functions for Various Programming Tasks
parent | Extract Data from NCBI Taxonomy Files
pearson | Objective Functions
plot_findit | Gridded Search to Optimize Objective Functions
pprod | Functions to Work with Lists
preset.basis | Define Basis Species
preset.logact | Define Basis Species
protein | Examples of Calculations for Proteins
protein.basis | Summaries of Thermodynamic Properties of Proteins
protein.equil | Summaries of Thermodynamic Properties of Proteins
protein.formula | Summaries of Thermodynamic Properties of Proteins
protein.info | Summaries of Thermodynamic Properties of Proteins
protein.length | Summaries of Thermodynamic Properties of Proteins
put.basis | Define Basis Species

## -- Q --

qqr | Objective Functions

## -- R --

read.aa | Amino Acid Compositions of Proteins
read.blast | Functions to Work with BLAST Output Files
read.expr | Experimental Data for Protein Abundances and Localizations
read.fasta | Functions for Reading FASTA Files and Downloading from UniProt
refs | Thermodynamic Database and System Definition
residualsplot | Functions to Create and Modify Plots
revisit | Plots and Optima of Objective Functions
RH2obigt | Functions to Work with the Thermodynamic Database
rho.IAPWS95 | Functions for Properties of Water and Steam
richness | Plots and Optima of Objective Functions
RMSD | Objective Functions
run.guess | Gibbs Energy Minimization by Steepest Descent
run.wjd | Gibbs Energy Minimization by Steepest Descent

## -- S --

s2c | Functions to Manipulate Character Objects
sciname | Extract Data from NCBI Taxonomy Files
SD | Objective Functions
seq2aa | Amino Acid Compositions of Proteins
shannon | Objective Functions
sideeffects | Side effects of functions in CHNOSZ
slice | Functions to Work with Multidimensional Arrays
slice.affinity | Functions to Work with Multidimensional Arrays
spearman | Objective Functions
species | Species of Interest
species.basis | Species of Interest
state.args | Functions for Processing Argument Lists
stress | Experimental Data for Protein Abundances and Localizations
strip | Equilibrium Chemical Activity Diagrams
subcrt | Properties of Species and Reactions
swap.basis | Swap Basis Species

## -- T --

T.units | Functions to Convert Units
taxonomy | Extract Data from NCBI Taxonomy Files
thermo | Thermodynamic Database and System Definition
thermo.axis | Functions to Create and Modify Plots
thermo.plot.new | Functions to Create and Modify Plots
today | Functions to Work with the Thermodynamic Database
TP.args | Functions for Processing Argument Lists
transfer | Mass Transfer Calculations
Ttr | Functions for Miscellaneous Tasks

## -- U --

uniprot.aa | Functions for Reading FASTA Files and Downloading from UniProt
unitize | Functions for Miscellaneous Tasks
usrfig | Functions to Create and Modify Plots
util.affinity | Functions to Work With Chemical Affinities
util.args | Functions for Processing Argument Lists
util.array | Functions to Work with Multidimensional Arrays
util.blast | Functions to Work with BLAST Output Files
util.character | Functions to Manipulate Character Objects
util.data | Functions to Work with the Thermodynamic Database
util.expression | Functions to Express Chemical Formulas and Properties
util.fasta | Functions for Reading FASTA Files and Downloading from UniProt
util.formula | Functions to Work with Chemical Formulas
util.list | Functions to Work with Lists
util.matrix | Functions for Various Matrix Operations
util.misc | Functions for Miscellaneous Tasks
util.plot | Functions to Create and Modify Plots
util.program | Functions for Various Programming Tasks
util.seq | Functions to Work with Sequence Data
util.units | Functions to Convert Units
util.water | Functions for Properties of Water and Steam

## -- W --

water | Properties of Water
water.AW90 | Functions for Properties of Water and Steam
water.IAPWS95 | Properties of Water
water.lines | Functions to Create and Modify Plots
water.props | Properties of Water
water.SUPCRT92 | Properties of Water
which.balance | Functions for Miscellaneous Tasks
which.pmax | Functions to Work with Lists
wjd | Gibbs Energy Minimization by Steepest Descent
WP02.auxiliary | Functions for Properties of Water and Steam
write.blast | Functions to Work with BLAST Output Files

## -- Y --

yeastgfp | Experimental Data for Protein Abundances and Localizations

## -- Z --

ZC | Functions to Work with Chemical Formulas