diff --git a/docs/userguide.rst b/docs/userguide.rst index 52556ecdbad87df044d2e73e7bed86c75461600d..466f952d3b90c282d1bacec3a00a2feee4c10249 100644 --- a/docs/userguide.rst +++ b/docs/userguide.rst @@ -174,7 +174,7 @@ Here are all available options in **RPG**: **-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt). -**-p, -\\-pka**: Define pKa values. Either 'ipc' or 'stryer' (default: ipc). IPC values come from `IPC_peptide <http://isoelectric.org/theory.html>`_ and Stryer values from Biochemistry Stryer, 7th edition. +**-p, -\\-pka**: Define pKa values. Either 'ipc2', 'stryer' or 'ipc' (default: ipc2, ipc is deprecated). 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>`_. **-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information. @@ -399,13 +399,13 @@ Option **-a, -\\-addenzyme** allows the user to define new enzymes. An enzyme co In the following, nomenclature of `Schechter and Berger <https://www.ncbi.nlm.nih.gov/pubmed/6035483>`_ is used. Amino acids before the cleavage site are designated as `P1`, `P2`, `P3`, etc in the N-terminal direction, and as `P1'`, `P2'`, `P3'`, etc in the C-terminal direction. For example, with cleavage site represented as '|': -.. code-block:: shell +.. code-block:: none ...P3-P2-P1-|-P1'-P2'-P3'... In **RPG**, this nomenclature is represented as: -.. code-block:: shell +.. code-block:: none ...(P3)(P2)(P1)(,)(P1')(P2')(P3')... @@ -417,25 +417,25 @@ A rule specifies which amino acid is targeted by the enzyme, the cleavage positi For example, to define a cleavage occurring **before** A, one must input: -.. code-block:: shell +.. code-block:: none (,A) To define a cleavage occurring **after** B, one must input: -.. code-block:: shell +.. code-block:: none (B,) The surrounding context is specified by adding other amino acids, before or after the targeted one. For example, to define a cleavage occurring **before** A, position `P1'`, preceded by B in position `P1`, C in position `P3` and followed by D in position `P2'`, one must input: -.. code-block:: shell +.. code-block:: none (C)()(B)(,A)(D) Note that this enzyme will only cleave if it finds the motif C*BAD, where * could be **any** amino acid. It will **not** cleave BAD, nor C*BA, BA, etc. For example, creating and using enzyme `rpg_example_userguide` (enzyme id 43): -.. code-block:: shell +.. code-block:: none $ rpg -a Name of the new enzyme? @@ -462,7 +462,7 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul In order for this enzyme to also cleave before AD (before A in `P1'` followed by D in `P2'` ), on top of the previous rule, one has to define one more rule in **RPG**: -.. code-block:: shell +.. code-block:: none (,A)(D) (C)()(B)(,A)(D) @@ -506,14 +506,14 @@ It is important to note that for each enzyme, it is enough that one of the rule The order of inputted rules is not relevant. In other words, this enzyme: -.. code-block:: shell +.. code-block:: none (,A)(D) (C)()(B)(,A)(D) and this second one: -.. code-block:: shell +.. code-block:: none (C)()(B)(,A)(D) (,A)(D) @@ -522,7 +522,7 @@ are identical. It is possible to define none-related cleavage rules for the same enzyme, for example: -.. code-block:: shell +.. code-block:: none (G,)(G) (P)(W,)(E)(T) @@ -531,13 +531,13 @@ This enzyme will cleave after G (position `P1`) followed by G in `P1'` and also Note that each rule must concern only **one** cleavage site. It is not possible to input rule like: -.. code-block:: shell +.. code-block:: none (A,)(B,) This would define an enzyme cleaving after A in `P1` followed by B in `P1'` but also cleaving after B in `P1` preceded by A in `P2`. The proper way to input this is by using two separate rules: -.. code-block:: shell +.. code-block:: none (A,)(B) (A)(B,) @@ -552,13 +552,13 @@ An exception specifies when a cleavage should **not** occur. **Exceptions must a For example, to define a cleavage occurring **before** A (`P1'` ), one must input: -.. code-block:: shell +.. code-block:: none (,A) Exceptions can then be inputted. For example, to define "a cleavage occurs before A, except when P is in `P2'` ", the following exception needs to be added: -.. code-block:: shell +.. code-block:: none (,A)(P) @@ -594,7 +594,7 @@ This enzyme will always cleave before A when not followed by P: It is possible to input complex exceptions. For the previous enzyme, we can add the following exception: -.. code-block:: shell +.. code-block:: none (G)(T)()(,A)()(F) @@ -648,13 +648,13 @@ This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` ) It is important to understand that an exception should always be linked to a rule. If one inputs this rule: -.. code-block:: shell +.. code-block:: none (A,) followed by this exception: -.. code-block:: shell +.. code-block:: none (B,)(C) @@ -671,26 +671,26 @@ To make enzyme creation easier to use, two tricks are available. The first one simplifies the definition of enzymes cleaving **before** and **after** a given amino acid. Defining an enzyme cleaving, for example, before **and** after A, can be done with two rules: -.. code-block:: shell +.. code-block:: none (,A) (A,) or simply using: -.. code-block:: shell +.. code-block:: none (,A,) The second trick is the use of the keyword `or`. This allows multiple possibilities for on position. For example: -.. code-block:: shell +.. code-block:: none (,A or B) is equivalent to: -.. code-block:: shell +.. code-block:: none (,A) (,B) @@ -701,7 +701,7 @@ Those two tricks help on complex enzymes. For example, :ref:`peps13` preferentia It can be defined either by: -.. code-block:: shell +.. code-block:: none cleaving rules: @@ -737,7 +737,7 @@ It can be defined either by: or, in a condensed way: -.. code-block:: shell +.. code-block:: none cleaving rule: