# Chemical Thermodynamics and Activity Diagrams

## Documentation for package ‘CHNOSZ’ version 0.9-7

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- 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 --

add.obigt | Functions to Work with the Thermodynamic Database
add.protein | Functions to Work with the Thermodynamic Database
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
axis.label | Functions to Create and Modify Plots

## -- B --

basis | Basis Species
basis.comp | Functions for Miscellaneous Tasks
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 Miscellaneous Tasks
can.be.numeric | Functions to Manipulate Character Objects
cgl | Equations of State
change | Functions to Work with the Thermodynamic Database
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
cvrmsd | Functions for Various Statistical Operations

## -- D --

def2gi | Functions to Work with BLAST Output Files
describe | Functions for Miscellaneous Tasks
diagram | Calculate and Plot Equilibrium Chemical Activities of Species
dimSums | Functions to Work with Multidimensional Arrays
dPdTtr | Functions for Miscellaneous Tasks
draw.transfer | Mass Transfer Calculations

## -- E --

element | Functions to Work with Chemical Formulas
energy | Chemical Affinities of Formation Reactions
energy.args | Chemical Affinities of Formation Reactions
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.boltz | Calculate Logarithms of Activity of Species
equil.react | Calculate Logarithms of Activity of Species
examples | Run examples from the documentation
expand.formula | Functions to Work with Chemical Formulas
extdata | Extra Data
extremes | Diversity Calculations for Chemical Species

## -- F --

feldspar | Mass Transfer Calculations
findit | Multidimensionally Optimize Chemical Activities

## -- G --

get.expr | Protein Expression Data
get.protein | Proteins from Model Organisms
getnames | Extract Data from NCBI Taxonomy Files
getnodes | Extract Data from NCBI Taxonomy Files
getrank | Extract Data from NCBI Taxonomy Files
GHS | Functions to Work with Chemical Formulas
grep.file | Functions for Accessing FASTA Files
groups | Thermodynamic Database and System Definition

## -- H --

hkf | Equations of State

## -- I --

id.blast | Functions to Work with BLAST Output Files
info | Search the Thermodynamic Database
ionize | Ionization Properties of Proteins
is.fasta | Functions for Accessing FASTA Files

## -- L --

label.plot | Functions to Create and Modify Plots
list2array | Functions to Work with Multidimensional Arrays
lograt | Functions for Various Statistical Operations
longex | Run examples from the documentation
lsub | Functions to Work with Lists
lsum | Functions to Work with Lists

## -- M --

makeup | Chemical Formulas and Compositions
mod.buffer | Calculating Buffered Chemical Activities
mod.obigt | Functions to Work with the Thermodynamic Database
MP90.cp | Functions for Miscellaneous Tasks
mtitle | Functions to Create and Modify Plots
mylapply | Functions to Work with Lists

## -- N --

nonideal | Functions for Miscellaneous Tasks
nucleicacids | Functions to Work with Sequence Data
nuts | Functions to Convert Units

## -- O --

OBIGT | Thermodynamic Database and System Definition
obigt2eos | Functions to Work with the Thermodynamic Database
opt | Thermodynamic Database and System Definition
outvert | Functions to Convert Units

## -- P --

parent | Extract Data from NCBI Taxonomy Files
plot.findit | Multidimensionally Optimize Chemical Activities
pprod | Functions to Work with Lists
protein | Properties of Proteins
protein.formula | Functions to Work with Chemical Formulas
protein.info | Properties of Proteins
protein.length | Functions for Miscellaneous Tasks
protein.residue | Properties of Proteins
psum | Functions to Work with Lists

## -- Q --

qqr | Functions for Various Statistical Operations

## -- R --

read.blast | Functions to Work with BLAST Output Files
read.fasta | Functions for Accessing FASTA Files
read.supcrt | Properties of Species and Reactions
refs | Thermodynamic Database and System Definition
residualsplot | Functions to Create and Modify Plots
residue.formula | Functions to Work with Chemical Formulas
residue.info | Properties of Proteins
revisit | Diversity Calculations for Chemical Species
richness | Diversity Calculations for Chemical Species
rmsd | Functions for Various Statistical Operations

## -- S --

s2c | Functions to Manipulate Character Objects
sciname | Extract Data from NCBI Taxonomy Files
slice | Functions to Work with Multidimensional Arrays
slice.affinity | Functions to Work with Multidimensional Arrays
spearman | Functions for Various Statistical Operations
species | Species of Interest
species.label | Functions to Create and Modify Plots
splitline | Functions for Accessing FASTA Files
state.args | Functions for Processing Argument Lists
stress | Thermodynamic Database and System Definition
strip | Calculate and Plot Equilibrium Chemical Activities of Species
subcrt | Properties of Species and Reactions
sum.refseq | Functions for Accessing FASTA Files

## -- T --

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
thermo.postscript | Functions to Create and Modify Plots
TP.args | Functions for Processing Argument Lists
transfer | Mass Transfer Calculations
trimfas | Functions for Accessing FASTA Files
Ttr | Functions for Miscellaneous Tasks

## -- U --

unitize | Functions for Miscellaneous Tasks
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.fasta | Functions for Accessing FASTA Files
util.formula | Functions to Work with Chemical Formulas
util.list | Functions to Work with Lists
util.misc | Functions for Miscellaneous Tasks
util.plot | Functions to Create and Modify Plots
util.seq | Functions to Work with Sequence Data
util.stat | Functions for Various Statistical Operations
util.units | Functions to Convert Units

## -- W --

water | Properties of Water
water.AW90 | Properties of Water
water.IAPWS95 | Properties of Water
water.lines | Functions to Create and Modify Plots
water.SUPCRT92 | Properties of Water
water.WP02 | Properties of Water
where.extreme | Diversity Calculations for Chemical Species
which.balance | Functions for Miscellaneous Tasks
which.pmax | Functions to Work with Lists
write.blast | Functions to Work with BLAST Output Files
write.supcrt | Properties of Species and Reactions

## -- Y --

yeastgfp | Proteins from Model Organisms

## -- Z --

ZC | Functions to Work with Chemical Formulas