Package: rbcmodel 1.0.1

Overview | 1. plot_slice_3D() arguments | 2. Changing labels | 3. Creating a custom color palette | 4. Adding elements to the graph | 5. permute_4D_grid()

Abstract | 1. Introduction | 2. Creating an enzyme | 2.1 search_enzyme(): Searching Rubisco Kinetics | 2.2 Creating an enzyme from the database: Enzyme() and check_enzyme() | 3. Calculating Rates | 3.1 Creating a temperature dependence scale: search_DHScale(),DHScale(), and modify_DHScale() | 3.2 CO2_dependence(): Calculating rates of net carboxylation | 4 Plotting rates | 4.1 make_4D_grid(): Extrapolating a CO2_dependence object over many values | 4.2 slice_4D_grid(): Slicing the grid for visualization | 4.3 plot_slice_3D(): Plotting a 3D slice | 4.4 transpose_3D_slice(): Swapping the x- & y-axes | 5. Comparing enzymes | 6. The included database | 6.1 Abridged table: the curated kinetics data | 6.2 Comprehensive table | 6.3 Temperature dependence tables | 7. References & Acknowledgements | 7.1 Acknowledgements: | 7.2 References

Overview | 1. Searching for my enzyme | 1.1 Recommendations for searching | 1.2 Taxonomic classifications | 1.3 Forms of Rubisco | 2. Kinetics | 2.1 I have measured the kinetics for my enzyme (or there's a study not in the database) | 2.1.1 new_enzyme() Arguments | 2.2 There are multiple complete studies for my enzyme | 2.2.1 merge_entries() arguments | 2.3 All kinetics for my enzyme have been measured, but not in the same study | 2.4 Some of the kinetics for my enzyme have been measured | 2.4.1 Other members of the genus have been measured | 2.4.2 Other members of the taxonomic group or Rubisco form have been measured | 2.5 None of the kinetics for my enzyme have been measured | 2.6 Some of the kinetics for my Rubisco form are not measured | 3. Temperature Dependences | 3.1 I have measured the temperature dependences for my enzyme | 3.1.1 new_DHScale() Arguments | 3.2 All temperature dependences for my enzyme have been measured, but not in the same study | 3.3 Some of the temperature dependences for my enzyme have been measured | 3.3.1 Other members of the genus have been measured | 3.3.2 Other members of the taxonomic group or Rubisco form have been measured | 3.4 None of the temperature dependences for my enzyme/taxonomic group/form have been measured | 3.4.1 Some of the temperature dependences for my form of Rubisco have never been measured | 3.4.2 None of the temperature dependences have been measured for my form of Rubisco | 4. Adding an appropriate PGS pathway | 5. How we constructed the averages and composites | 5.1 Composite kinetics entries for model enzymes | 5.2 Average kinetics for Rubisco forms and taxonomic groups | 5.3 Average temperature dependence scales for Rubisco forms and taxonomic groups