File Formats

To simplify the creation of the reaction network rNets relies on the CSV format which is a tabular format that can be easily created using your preferred spreadsheet software or even a plain text editor. There are two types of files that are required, namely the "Compounds" file and the "Reactions" file. These files have multiple columns, where the column name may be repeated, and only a subset of all possible columns is required.

Warning

CSV stands for Comma Separated Values, and rNets assumes that convention. Some spreadsheet sofware may provide the option of using a different character for separating the values. Please note that providing a non-comma separated file as input for rNets may lead to errors or bad results.

Compounds File

The compounds file contains the individual entries of each species in the reaction network. Each entry must consist at least of a name, a text representation of the compound, and an energy. Below we have an example of how the compounds file may look like:

name,energy
reactant,0
intermediate,0
product,0

Here we have three species reactant, intermediate and product. In this case the energy of all of them is 0

Required columns

  • name Corresponds to the text label to uniquely identify the species. It is the text that will show in the generated graph to represent the compound.

  • energy Corresponds to the absolute or relative energy of the species. Typically the free energy.

Optional columns

  • fflags The format of the text for name, there are four possible options: b ( Bold ), i`( italics ), :code:`u ( underlined ) or if it is not specified it will be without any format.

  • visible This column allows to hide certain compounds to simplify the final graph, however these hidden compounds are still considered when the normalization is carried out. To hide a compound add f, to reduce its visibility but still show it grey and to show the node use v (although it is the default behavior so not specifying any other value will default to this option).

  • opts This allows to add more specific graphviz node attributes. these can be found in graphviz docs typically they are specified as "key=value" where key is the attribute, i.e. image, and the value is the value that the attribute will take for that node, i.e. path/to/my/beautiful.png.

Note

Hidden compounds (entries with an f value in the visibility column) are considered in for normalizing the color scale but are not shown in the graph.

Warning

Although opts allows a large degree of customization through graphviz please note that the default format of the nodes is specified with html, thus it is discouraged for beginner-level users to use this option.

Reactions File

The reactions file contains one reaction entry per row. The reaction may be unidirectional or bidirectional. The reactions are defined by the compounds that are involved, thus the same name values defined in the compounds file should be used. Below we have an example of how the reactions file may look like:

cleft,cright,direction,name,visible
reactant,,intermediate,,0.5,<->,R0,
intermediate,,product,,0.4,<->,R1,

Required columns

  • cleft Text label of the first reactant.

  • cright Text label of the first product.

At least 1 cleft and 1 cright must be specified. A second column cleft or cright is also accepted, which allows specifying bimolecular reactions, but this second column is optional. An example of a reactions file containing a bimolecular reaction is shown below:

cleft,cright,cright,direction,name,visible
reactant,,intermediate,,0.5,<->,R0,
intermediate,,product1,product2,0.4,<->,R1,

Optional columns

  • energy Absolute energy of the TS connecting reactants and products. Used to compute the energy barrier.

  • direction Direction of the reaction. <-> for reversible reactions and -> for irreversible reactions.

  • name Text identifier of the reaction, typically R0,R1,R2 ... It does not have any effect in the produced graph, but may be used as a guide by the user when preparing/editing the files for complex reaction networks.

  • visible This column allows to hide certain reactions with a similar effect as hiding compounds. To hide a reaction add f, to reduce its visibility but still show it grey and to show the node use v (although it is the default behavior so not specifying any other value will default to this option).

  • opts This allows to add more specific graphviz edge attributes. these can be found in graphviz docs typically they are specified as "key=value" where key is the attribute and the value is the value that the attribute will take for that edge.

Note

rNets does not allow the inclusion of tri-molecular reactions, as such the maximum number of reactants is 2 and the same for the number of products is 2.