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.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 |
| 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 |
| 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 |
| 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.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 |
| feldspar | Mass Transfer Calculations |
| find.tp | Equilibrium Chemical Activity Diagrams |
| findit | Gridded Search to Optimize Objective Functions |
| 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 |
| hkf | Equations of State |
| 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 |
| 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 |
| 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 |
| nonideal | Activity coefficients of aqueous species |
| nucleic.complement | Functions to Work with Sequence Data |
| nucleic.formula | Functions to Work with Sequence Data |
| 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.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 |
| qqr | Objective Functions |
| 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 |
| 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.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 |
| 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 |
| 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 |
| yeastgfp | Experimental Data for Protein Abundances and Localizations |
| ZC | Functions to Work with Chemical Formulas |