Generated files#
The following files are reported: suffix: 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. suffix: The JSON file storing necessary data for the web page. You can load it through the web page loader. suffix: This text file stores the number of each species in each time step. One can read this file thorugh the Python method suffix: 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. suffix: This file contains the route of each atom. It shows which species an atom is inside thorugh the whole trajectory in the following format: suffix: suffix: 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. suffix: A SVG file to show reaction networks.Web page#
.html
Data file#
.json
Species file#
.species
reacnetgenerator.tools.read_species
. Note that when HMM is enabled, information in this file may not be accurate.Molecule file#
.moname
Route file#
.route
Atom {idx}: {time} {SMILES} -> {time} {SMILES} -> ...
Reaction files#
.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#
.table
Reaction network#
.svg