2. Command line interfaceΒΆ

The command line interface provides five functions to easily manipulate BcForms-encoded descriptions of complexes.

  • Get help with the `BcForms` command line interface. The following commands return inline help information about the command line interface:

    bcforms
    bcforms -h
    bcforms --help
    
  • Validate a `BcForms`-encoded description of a form of a complex. The following command can be used to verify if description of a complex is syntactically and semantically valid. The command line interface will print any errors to the standard error:

    bcforms validate <bcform>
    
    bcforms validate '2 * a + 3 * b'
    # Form is valid
    
  • Calculate the formula of a complex. The following command can be used to calculate the formula of a complex:

    bcforms get-formula --help
    
    bcforms get-formula <bcform> <dictionary of formulae of subunits>
    
    # Calculate the formula of a complex
    bcforms get-formula '2 * a + 3 * b' '{a: CHO, b: C2H2O2}'
    # C8H8O8
    
  • Calculate the charge of a complex. The following command can be used to calculate the charge of a complex:

    bcforms get-charge --help
    
    bcforms get-charge <bcform> <dictionary of charges of subunits>
    
    # Calculate the charge of a complex
    bcforms get-charge '2 * a + 3 * b' '{a: 1, b: 2}'
    # 8
    
  • Calculate the molecular weight of a complex. The following command can be used to calculate the molecular weight of a complex:

    bcforms get-molwt --help
    bcforms get-molwt <bcform> <dictionary of molecular weights of subunits>
    
    # Calculate the molecular weight of a complex
    bcforms get-molwt '2 * a + 3 * b' '{a: 1, b: 2}'
    # 8