2.4. Command line interfaceΒΆ

The command line interface provides four functions to easily manipulate BpForms.

  • Help. The following commands return inline help information about the command line interface:

    bpforms
    bpforms -h
    bpforms --help
    
  • BpForms validation. The following command can be used to verify if a monomer sequence is syntactically valid. The command line interface will print any syntax errors to the standard error:

    bpforms validate <alphabet_name> <bpform_sequence>
    
  • Protonation of biopolymer forms. The following command can be used to calculate the major protonation and tautomerization state of each monomer in a biopolymer form. This command will print the sequence of the major protonation/tautomerization states. Note, this function requires a structure for each monomer:

    bpforms get-major-micro-species <alphabet_name> <bpform_sequence> <ph_value>
    
  • Calculation of the physical properties of biopolymer forms. The following command can be used to calculate the length, formula, mass, and charge of a bipolymer form. The optional ph argument can be used to calculate the major protonation and tautomerization state of the biopolymer at a specific pH. Note, this function requires a structure for each monomer:

    bpforms get-properties <alphabet_name> <bpform_sequence> [--ph ph]