Generated files

The following files are reported:

Web page

suffix: .html

The web page including analysis. Here is an example. You can open it using a modern browser. Note that \(\ce{A + B -> C + D}\) information may be not accurate when HMM is enabled.

Data file

suffix: .json

The JSON file storing necessary data for the web page. You can load it through the web page loader.

Species file

suffix: .species

This text file stores the number of each species in each time step. One can read this file through the Python method reacnetgenerator.tools.read_species. Note that when HMM is enabled, information in this file may not be accurate.

Molecule file

suffix: .moname

This file contains information of each molecule. In each line, the first column is its SMILES. The second column is the atomic index (starts from 0) of atoms. The last column shows all the bonds in the molecule. This file always keeps the historical three-column format.

Molecule timeline file

suffix: .molecules.csv

This optional CSV file is written when --show-molecule-time, --molecule-frame, or --molecule-timestep is enabled. It contains one row per molecule occurrence in an analyzed frame, with the following columns:

Timestep,Species,AtomIDs,BondIDs

Rows are sorted by Timestep. Timestep is the original timestep value from the input trajectory. AtomIDs and BondIDs are semicolon-separated lists. Bond IDs use atom1-atom2-order labels. The --molecule-frame and --molecule-timestep filters limit the CSV rows to selected frames or timesteps.

Route file

suffix: .route

This file contains the route of each atom. It shows which species an atom is inside thorugh the whole trajectory in the following format:

Atom {idx}: {time} {SMILES} -> {time} {SMILES} -> ...

Reaction files

suffix: .reaction, .reactionabcd

.reaction shows the frequency of the reaction \(\ce{A -> B}\) while .reactionabcd shows the frequency of the reaction \(\ce{A + B -> C + D}\). One can read these files through the Python method reacnetgenerator.tools.read_reactions. Note that \(\ce{A + B -> C + D}\) information may be not accurate when HMM is enabled.

Reaction event file

suffix: .reactionevent.csv

This optional CSV file is written when --reaction-event is enabled. It contains one row per reaction event detected between two adjacent analyzed frames:

Timestep_Index,Reactant,Product

Timestep_Index is the analyzed transition index. A value of 0 means the reaction was detected between analyzed frames 0 and 1. Reactant and Product use the same species names as the reaction summary files.

Reaction matrix file

suffix: .table

This file shows the reaction matrix. To save space, only first top 100 species are printed. You can process reaction files manually for other information.

Reaction network

suffix: .svg

A SVG file to show reaction networks.