Imine condensation

Thermodynamic representations

The files required for the generation of the reaction networks of the imine condensation example of the rNets' article can be found in the examples/example_imine_thermo folder. This folder contains the following files:

example_imine_thermo
  -README.txt
  assets
    -comps_paper.csv
    -reactions_paper.csv
    -comps_paper_simple.csv
    -reactions_paper_simple.csv
    -comps_32.csv
    -reactions_32.csv
    -comps_32_simple.csv
    -reactions_32_simple.csv
  -dotfile.py
  -run.py

In the assets folder we have 4 different compound-reaction file pairs:

comps_paper_simple.csv and reactions_paper_simple.csv

comps_32_simple.csv and reactions_32_simple.csv

comps_paper.csv and reactions_paper.csv

comps_32.csv and reactions_32.csv

The files with the termination simple.csv include the ones required to generate the figures as presented in the manuscript. The files without the termination simple.csv correspond to the full reaction network. All the numerical values included in these files come from the original publication (DOI: 10.1021/acs.orglett.0c00367). Specifically, the files in a are used to generate a simplified reaction network with the uncorrected DFT energies, hiding some compounds and species. The files in b are used to generate the same representation of the network but with a corrected set of energies. The files in c are the uncorrected full reaction network and the files in d are used for the corrected full reaction network.

Preliminary steps

For the present example the only required software is rNets and graphviz. Please follow the installation instructions of rNets.

Quickstart

For convenience we created the run.py script which facilitates the generation of all the figures in one go. To execute the code the user will have to type in the following command:

python run.py

Upon execution two new folders will appear: temp and res. The temp folder contains the .dot files, which serve as input to graphviz for the actual image generation. The res folder will contain the automatically rendered .png files.

Manual Generation of the network graphs

The procedure for the generation of all images is the same one, only needing to change the compounds and reactions files. We will use the files in a) ( uncorrected and simplified reaction network ) to illustrate the procedure.

Warning

The following step by step examples assume a UNIX-like OS. In the case of Windows OS please adapt accordingly the paths to the files or use the run.py script.

First we will generate the .dot file containing the reaction network from the compounds and reactions files. To do so we will execute the following line:

$ python dotfile.py assets/comps_paper_simple.csv assets/reactions_paper_simple.csv figure_3a.dot

This will generate a file named figure_3a.dot in the current directory. Next we will render the figure with graphviz as a .png file, (other formats such as svg are also possible). To do so, we will execute the following command:

$ dot -Tpng figure_3a.dot -o figure_3a.png

With this we have generated the image of the reaction network.

Note

Please note that within dotfile.py, a custom treatment for the simple.csv files is included. This is not necessary to generate a reaction network graph, but it was used to add some control over the final layout to guarantee that the resulting figure would fit in the manuscript. It has also been added to the examples to ensure the reproducibility of the figures in the article.

Kinetic representations

The files required for the generation of the reaction networks of the imine condensation example of the rNets' article can be found in the examples/example_imine_kinetic folder. This folder contains the following files:

example_imine_kinetic
 -README.txt
 assets
   -comps_draco_42.csv
   -reactions_draco_42.csv
   -comps_draco_42_simple.csv
   -reactions_draco_42_simple.csv
 -kinetic_model.py
 -kinetic_model.index
 -kinetic_snapshots.py
 -kinetic_gif.py
 -run.py

Here we have 4 different types of files:

assets/comps_draco_42_simple.csv , assets/reactions_draco_42_simple.csv, assets/comps_draco_42.csv, assets/reactions_draco_42.csv

kinetic_model.py , assets/kinetic_model.index

kinetic_snapshots.py

kinetic_gif.py

run.py

Files in a are used to create the reaction network and provide the energetics needed to compute the kinetic constants and thus the net rates of the reactions. Files in b are files generated using the pykinetic software, the .index file contains similar information to the rNets compounds and reaction files, to simplify re-creating the input needed for pykinetic. The kinetic_model.py contains how to carry out the actual microkinetic simulation, and will generate a .data file containing the concentrations at each time of all species. The file in c is a script to generate the .dot files at different times, which are used in the generation the static graph figures which are the focus of the present section. The file in d is a script to generate all the .dot files required to generate the .gif file which is the focus of the following section. The file in e integrates all the workflow within a single script.

Note

The kinetic_model.py obtained from pykinetic (v0.1.0) has been slighly modified to facilitate the re-generation of all figures under the run.py script (see the Quickstart subsection)

The files with the termination simple.csv are used to draw a simplified version of the reaction network. The files without the termination simple.csv correspond to the full reaction network. The 42 makes reference to the systematic bias included into the DFT computed energies, specifically 4.2 kcal/mol which in kJ is 17.56 kJ/mol.

Preliminary steps

The first step is to run the microkinetic simulation. For this task we only require to have installed the python libraries numpy and scipy, (one of the main design features of pykinetic is the generation of standalone scripts that do not require the pykinetic to run).

After ensuring that we have numpy and scipy installed, we now proceed to run the simulation:

$ python kinetic_model.py

This will generate a kinetic_model.data file in the assets 2-6 mins depending on the CPU performance of the computer.

Quickstart

For convenience we created the run.py script which facilitates the generation of all the figures and gifs in one go. To execute the code the user will have to type in the following command:

python run.py

Upon execution two new folders will appear: temp and res. The temp folder contains the .dot files, which serve as input to graphviz for the actual image generation. The res folder will contain the automatically rendered .png files as well as the .gif file.

Manual Generation of the network graphs

Warning

The following step by step examples assume a UNIX-like OS. In the case of Windows OS please adapt accordingly the paths to the files or use the run.py script.

Next, we proceed to generate the reaction network, colored by concentration of the different species at different times during the simulation. For the example the simple.csv files will be used but the files for the full network can also be used.

$ python kinetic_snapshots.py assets/comps_draco_42_simple.csv assets/reactions_draco_42_simple.csv kinetic_model.data

This will generate 2 .dot files, snapshot_00600.dot and snapshot_02400.dot. The following step is to use graphviz to render the images:

$ dot -Tpng snapshot_00600.dot -o figure_7a.png
$ dot -Tpng snapshot_02400.dot -o figure_7b.png

An animation of the kinetic evolution

The files required for the generation of the reaction networks of the imine condensation example of the rNets' article can be found in the examples/example_imine_kinetic folder. This folder contains the following files:

example_imine_kinetic
 -README.txt
 assets
   -comps_draco_42.csv
   -reactions_draco_42.csv
   -comps_draco_42_simple.csv
   -reactions_draco_42_simple.csv
 -kinetic_model.py
 -kinetic_model.index
 -kinetic_snapshots.py
 -kinetic_gif.py
 -run.py

For a detailed explanation of the purpose of each of this files please look at the previous section. The focus of this section is to generate a gif changing the color of the species as the kinetic simulation progresses.

Warning

The following step by step examples assume a UNIX-like OS. In the case of Windows OS please adapt accordingly the paths to the files or use the run.py script.

Preliminary steps

The first step is to run the microkinetic simulation. For this task we only require to have installed the python libraries numpy and scipy, (one of the main design features of pykinetic is the generation of standalone scripts that do not require the pykinetic to run). Finally to generate the final .gif we will require a software to merge together all the frames, for this example GIMP or imagemagick are recommended.

After ensuring that we have numpy and scipy installed, we now proceed to run the simulation:

$ python kinetic_model.py

This will generate a kinetic_model.data file in 2-6 mins depending on the CPU performance of the computer.

GIF generation

To generate a GIF file showing the evolution of the species over time we will start by generating a .dot file for every 10s of simulation into a folder named gif_folder. To preform this task the python script kinetic_gif.py is included.

To use it we need to provide the compounds and reactions files and the data from the kinetic simulation:

$ python kinetic_gif.py assets/comps_draco_42.csv assets/reactions_draco_42.csv kinetic_model.data

Our next step is to transform all the generated dot files into png format. We can do that manually or we can use some bash scripting. The following command will work in a bash shell:

$ for dotfile in gif_folder/*.dot; do dot -Tpng $dotfile -o ${dotfile%.*}.png; done

Finally we need to convert all the .png files into an animated gif. Specifically for the manuscript, the GIMP <https://www.gimp.org/> software was used for this task. An alternative through command line is imagemagick which can provide a decent-quality gif using the following command:

$ convert -delay 0 -loop 1 gif_folder/*.png imine_graph_animation.gif

Upon successfull completion of the '.png' to '.gif' the imine_graph_animation.gif will contain the desired gif file.