Input file

This manual explains the configuration parameters of the config.yaml file. A key decision is whether to connect to the MongoDB database, where Chemoton’s exploration data is stored. By default, VizChemoton renders the final .html file without requiring a MongoDB connection (db.active: False), as the reactions and compounds data are stored in the resources folder. However, if you wish to adapt VizChemoton to your own system, you need to configure the MongoDB connection (db) and specify the computational methodology (method) that was used.

db:
  active: False
  name: "ozone_tme_lcpbe"
  ip: "localhost"
  port: "8889"

method:
  method_family: "dft"
  method: "lc-pbe"
  basis_set: "def2-svp"
  program: "orca"

files:
  pathfinder:
    path: "./vizchemoton/resources/crn_pathfinder.json"
    mode: "read"
  reactions:
    path: "./vizchemoton/resources/reactions.csv"
    mode: "read"
  compounds:
    path: "./vizchemoton/resources/compounds.json"
    mode: "read"

output:
  file: "network.html"
  title: "Chemoton graph"
  verbose: True

graph:
  dist_adduct: 3.0
  size: [1400, 800]
  layout: "kamada_kawai"
  map_field: "degree"

Here we break down all the parameters that can be defined in the input file:

1. Database

  • active (bool): Enables (True) or disables (False) the use of the MongoDB. If it is disabled, then this section is omitted.

  • name (str): Name of the MongoDB.

  • ip (str): IP address of the MongoDB server.

  • port (str): Port number for MongoDB communication.

2. Method

  • method_family (str): Specifies the family of the computational method (e.g., dft).

  • method (str): Name of the computational method (e.g., lc-pbe).

  • basis_set (str): Basis set used in the calculation (e.g., def2-svp).

  • program (str): Quantum chemistry program used (e.g., orca).

3. Files

pathfinder

  • path (str): Path to the json file containing CRN data.

  • mode (str): Either read a preexisting file (read), or write a new file (write). Even if it is set to read, it will be necessary to have an active connection to the MongoDB.

reactions

  • path (str): Path to the csv file containing reaction data.

  • mode (str): Either read a preexisting file (read) or write a new file (write). If one sets it to read, because there is a preexisting file, it is not necessary to have an active connection to the MongoDB.

compounds

  • path (str): Path to the json file containing compound data.

  • mode (str): Either read a preexisting file (read) or write a new file (write). If one sets it to read, because there is a preexisting file, it is not necessary to have an active connection to the MongoDB.

4. Settings

  • dist_adduct (float): Distance threshold for adduct detection.

  • size (list[int, int]): Graph size in pixels ([width, height]).

  • layout (str): Graph layout algorithm (e.g., kamada_kawai).

  • map_field (str): Property used for node mapping (e.g., degree).

5. Output

  • file (str): Output file name for the generated network visualization.

  • title (str): Title of the network visualization.

  • verbose (bool): Enables (True) or disables (False) the call to the print statements during runtime of the code.