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docs/userguide.rst

@@ -156,9 +156,11 @@ Here are all available options in **RPG**:
 
 **-a, -\\-addenzyme**: Add a new user-defined enzyme. See :ref:`addenzyme` for more information.
 
+**-b, -\\-delenzyme**: Delete a user-define enzyme. See :ref:`delenzyme` for more information.
+
 **-d, -\\-digest**: Digestion mode. Either 's', 'sequential', 'c' or 'concurrent' (default: s). See :ref:`digestion` for more information.
 
-**-e, -\\-enzymes**: Enzyme(s) id number to use (*i.e.* -e 0 5 10 to use enzymes 0, 5 and 10). Use -l first to get enzyme ids. See :ref:`enzymes` for more information.
+**-e, -\\-enzymes**: Enzyme(s) id number or name to use (*e.g.* -e 1 Asp-N 10 to use enzymes 1, Asp-N and 10). Use -l first to get enzyme ids. See :ref:`enzymes` for more information.
 
 **-f, -\\-fmt**: Output file format. Either 'fasta', 'csv', or 'tsv' (default: fasta). See :ref:`formats` for more information.
 
@@ -168,14 +170,22 @@ Here are all available options in **RPG**:
 
 **-l, -\\-list**: Display the list of available enzymes.
 
-**-m, -\\-miscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*i.e.* -m 15 5.2 10). It works only for sequential digestion (default: 0). See :ref:`miscleavage` for more information.
+**-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.
 
 **-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.
+
+**-z, --exception**: Exception(s) when adding enzyme in non-interactive mode (*e.g.* -z "(D,)(W)" "(D,)(A)". See :ref:`addenzyme` for more information.
+
+**-y, --enzname**: Enzyme's name when adding enzyme in non-interactive mode. See :ref:`addenzyme` for more information.
+
 **-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt).
 
 **-p, -\\-pka**: Define pKa values. Either 'ipc2', 'stryer' or 'ipc' (default: ipc2). IPC2 values come from `IPC_peptide in Supplementary Table S1 <https://doi.org/10.1093/nar/gkab295>`_, Stryer values from Biochemistry Stryer, 7th edition and IPC values from `IPC_peptide <http://isoelectric.org/theory.html>`_.
 
+**-w, --mass**: Define atomic mass values. Either 'avg' for average mass or 'mono' for monoisotopic mass.
+
 **-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.
 
 **-c , -\\-processes**: Number of parallel processes to use (default: 1)
@@ -761,7 +771,13 @@ Example of enzymes
 
 All available enzymes are in :ref:`enzymes`, including their **RPG**'s definition.
 
+Non-interactive mode
+--------------------
+
+Using **-n, -\\-noninteractive** and **-a, -\\-addenzyme** options together is possible, but then requires to also use **-x, -\\-cleave** option to define cleaving site(s), **-y, --enzname** option to define the name of the enzyme and optionally **-z, --exception** option to define exceptions.
+
 
+.. _delenzyme:
 
 Deleting user-defined enzymes
 =============================
@@ -782,8 +798,8 @@ and finishes with:
 
 followed by 3 blank line.
 
-To remove an enzyme, be sure to backup the file **before** any modifications. Then just remove the whole Python code of the enzyme, including the above-mentioned lines. Do not do any other modifications, as this code is used in **RPG** and any wrong modifications will make the software unable to run.
+To remove an enzyme, use the option **-b, -\\-delenzyme** with the id or name of the user-defined enzyme to remove. It is not possible to remove predefined enzymes of **RPG**.
 
 To remove all user-defined enzymes, just delete ``~/rpg_user.py`` file. It will be created again (empty) at the next launch of **RPG**.
 
-Obviously, all deleted enzymes can not be recovered. If one wants to use them again they will need to be redefined in **RPG**, using -a option.
+Obviously, all deleted enzymes can not be recovered. If one wants to use them again they will need to be redefined in **RPG**, using **-a, -\\-addenzyme** option.
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