@@ -172,6 +172,11 @@ Here are all available options in **RPG**:
**-m, -\\-miscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*e.g.* -m 15 5.2 10). It works only for sequential digestion (default: 0). See :ref:`miscleavage` for more information.
**-t, -\\-theoretical**: Maximum number of miscleavages, by enzyme(s). RPG will produce all theoretical peptides allowing at most -t miscleavages. It should be in the same order than -\\-enzymes options (*e.g.* -t 1 3 2). Only for sequential digestion (default: 0). See :ref:`theoretical` for more information.
**-n, -\\-noninteractive**: Non-interactive mode. No standard output, only error(s) (-\\-quiet enable, overwrite -v). If output filename already exists, output file will be overwritten. See :ref:`nointer` for more information.
**-x, -\\-cleave**: Cleavage site(s) when adding enzyme in non-interactive mode (*e.g.* -x "(D or E,)", similar to -x "(D,)" "(E,)". See :ref:`addenzyme` for more information.
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@@ -269,6 +274,38 @@ For example, using:
will assign a miscleavage probability of `1.4%` to enzyme `1`, a miscleavage probability of `2.6%` to enzyme `2` and a miscleavage probability of `0%` to enzyme `3` (default behavior). For enzyme `1`, each cleavage will then have a probability of 0.014 to **not** occur.
.. _theoretical:
All theoretical miscleavage
===========================
You can compute all theoretical peptides with at most **n** miscleavages. **RPG** will then produce all peptides without any miscleavage, with 1 miscleavage, with 2 miscleavage, etc, up to **n**.
