utilities

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These commands are useful utilities that aren't necessary used in the main polymerization and interactions scripts.

-ABN : none
Prints out acidic/basic/neutral breakdown of amino acids for reference.

-print_feats : none
Prints out a list of all FMs with their costs in (eur/mMol) and (eur/Mol).

-print_feats : none
Writes out a csv and images of RDkit pharmacophore features for all FMs and amino acids.

-print_fms : none
Prints out a list of all FMs and their encoded names.

-print_smiles : none
Prints out a list of all FMs and their smiles codes.

-regen : string string, default None None
Regenerates forcefields from PDB files and combined template and complex if both are specified.

-write_pdb : string, default None
Writes out a pdb from the FM list. This is useful if you need to create inputs that adhere to MIPkit molecule orders.

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These commands are global, but not particularly important unless you need them for any specific reason.

-basedir : string, default None
Creates and uses this directory as the base directory. This probably should be done in bash instead.

-noclean : none, default False
Prevents cleaning. This helps with trouble shooting.

-timer : none, default False
Times the run.

-verbose : none, default False
Makes the runs verbose. Theres a lot of console prints, so probably keep this one off.