# 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 thorugh 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.

## 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 this file thorugh the Python method reacnetgenerator.tools.read_reactions. Note that $$\ce{A + B -> C + D}$$ information may be not accurate when HMM is enabled.

## 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.