Commit 960fe817 authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

Correcting english

parent 312840d8
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in 14 minutes and 37 seconds
.. _enzymes:
===================
Enzymes definitions
===================
==================
Enzyme definitions
==================
All default available enzymes (`enzymes_definition.py`) are listed bellow.
For each of them, there is the equivalent in `RPG` grammar.
On the following, nomenclature of `Schechter and Berger <https://www.ncbi.nlm.nih.gov/pubmed/6035483>`_ is used. According to it, 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 '|':
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:: none
......@@ -45,7 +45,7 @@ Available enzymes
Arg-C
.....
Arg-C proteinase proteinase preferentially cleaves after R (`P1`)
Arg-C proteinase preferentially cleaves after R (`P1`)
**RPG definition:**
......@@ -53,7 +53,7 @@ cleaving rule:
* ``(R,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
......@@ -62,7 +62,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Asp-N
.....
Asp-N Sequencing Grade preferentially cleaves before C or D (`P1'`)
Asp-N Sequencing Grade preferentially cleaves before C or D (`P1'` )
**RPG definition:**
......@@ -70,7 +70,7 @@ cleaving rule:
* ``(,C or D)``
More informations: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
More information: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
......@@ -87,7 +87,7 @@ cleaving rule:
* ``(W,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
......@@ -104,7 +104,7 @@ cleaving rule:
* ``(K or A or Y,)``
More informations: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410479
More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410479
......@@ -125,7 +125,7 @@ exception rule:
* ``(F or W or Y or L)()(H or A or T)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
......@@ -148,7 +148,7 @@ exception rules:
* ``(D)(V)(A)(D,)(P or E or D or Q or K or R)``
* ``(D)(E)(H)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
......@@ -171,7 +171,7 @@ exception rules:
* ``(D)(M)(Q)(D,)(P or E or D or Q or K or R)``
* ``(D)(E)(V)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
......@@ -194,7 +194,7 @@ exception rules:
* ``(L)(E)(V)(D,)(P or E or D or Q or K or R)``
* ``(W or L)(E)(H)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
......@@ -211,7 +211,7 @@ cleaving rule:
* ``(W or L)(E)(H)(D,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
......@@ -232,7 +232,7 @@ exception rule:
* ``(V)(E)(I or H)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
......@@ -253,7 +253,7 @@ exception rule:
* ``(D)(E)(V)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
......@@ -274,7 +274,7 @@ exception rule:
* ``(I or L)(E)(T)(D,)(P or E or D or Q or K or R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
......@@ -291,7 +291,7 @@ cleaving rule:
* ``(L)(E)(H)(D,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
......@@ -308,7 +308,7 @@ cleaving rule:
* ``(I)(E)(A)(D,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
......@@ -330,7 +330,7 @@ exception rules:
* ``(F or Y or W,)(P)``
* ``(W,)(M)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
......@@ -354,7 +354,7 @@ exception rules:
* ``(M,)(Y)``
* ``(H,)(D or M or W)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
......@@ -371,7 +371,7 @@ cleaving rule:
* ``(R,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
......@@ -388,7 +388,7 @@ cleaving rule:
* ``(M,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
......@@ -405,7 +405,7 @@ cleaving rule:
* ``(D or E)(D or E)(D or E)(D or E)(K,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter
......@@ -422,7 +422,7 @@ cleaving rule:
* ``(A or F or I or L or V or W or G or T)(D or E)(G)(R,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
......@@ -439,7 +439,7 @@ cleaving rule:
* ``(A or V or I or L or F or Y or W)(G or S or E or Y,)``
More informations: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410578
More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410578
......@@ -456,7 +456,7 @@ cleaving rule:
* ``(D,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH
......@@ -473,7 +473,7 @@ cleaving rule:
* ``(D or E,)``
More informations: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
More information: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
......@@ -490,7 +490,7 @@ cleaving rule:
* ``(E,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu
......@@ -507,7 +507,7 @@ cleaving rule:
* ``(I)(E)(P)(D,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB
......@@ -524,7 +524,7 @@ cleaving rule:
* ``(N,)(G)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro
......@@ -541,7 +541,7 @@ cleaving rule:
* ``(W,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo
......@@ -558,7 +558,7 @@ cleaving rule:
* ``(K,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysC
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysC
......@@ -567,7 +567,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Lys-N
.....
LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (`P1'`).
LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (`P1'` ).
**RPG definition:**
......@@ -575,7 +575,7 @@ cleaving rule:
* ``(,K)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysN
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysN
......@@ -592,7 +592,7 @@ cleaving rule:
* ``(A or V,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Elast
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Elast
......@@ -601,7 +601,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
NTCB
....
NTCB +Ni (2-nitro-5-thiocyanobenzoic acid) preferentially cleaves before C (`P1'`).
NTCB +Ni (2-nitro-5-thiocyanobenzoic acid) preferentially cleaves before C (`P1'` ).
**RPG definition:**
......@@ -609,7 +609,7 @@ cleaving rule:
* ``(,C)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#NTCB
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#NTCB
......@@ -630,7 +630,7 @@ exception rule:
* ``(A or V or I or L or F or Y or W)(R or K,)(V)``
More informations: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606
More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606
......@@ -639,7 +639,7 @@ More informations: https://www.sigmaaldrich.com/life-science/biochemicals/bioche
Pepsin pH 1.3
.............
This pepsin preferentially cleaves around F or L (`P1` or `P1'`). It will not cleave before F or L in `P1'` followed by P in `P2'`. It will not cleave before F or L in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F or L in `P1` followed by P in `P2'`. It will not cleave after F or L in `P1` preceded by P in `P2` or H/K/R in `P3`.
This pepsin preferentially cleaves around F or L (`P1` or `P1'` ). It will not cleave before F or L in `P1'` followed by P in `P2'`. It will not cleave before F or L in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F or L in `P1` followed by P in `P2'`. It will not cleave after F or L in `P1` preceded by P in `P2` or H/K/R in `P3`.
**RPG definition:**
......@@ -657,7 +657,7 @@ exception rules:
* ``(P)(F or L,)``
* ``(H or K or R)()(F or L,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps
......@@ -666,7 +666,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Pepsin pH >=2
.............
This pepsin preferentially cleaves around F, L, W or Y (`P1` or `P1'`). It will not cleave before F, L, W or Y in `P1'` followed by P in `P2'`. It will not cleave before F, L, W or Y in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F, L, W or Y IN `P1` followed by P in `P2'`. It will not cleave after F, L, W or Y in `P1` preceded by P in `P2` or H/K/R in `P3`.
This pepsin preferentially cleaves around F, L, W or Y (`P1` or `P1'` ). It will not cleave before F, L, W or Y in `P1'` followed by P in `P2'`. It will not cleave before F, L, W or Y in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F, L, W or Y IN `P1` followed by P in `P2'`. It will not cleave after F, L, W or Y in `P1` preceded by P in `P2` or H/K/R in `P3`.
**RPG definition:**
......@@ -684,7 +684,7 @@ exception rules:
* ``(P)(F or L or W or Y,)``
* ``(H or K or R)()(F or L or W or Y,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps
......@@ -705,7 +705,7 @@ exception rule:
* ``(H or K or R)(P,)(P)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Pro
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Pro
......@@ -722,7 +722,7 @@ cleaving rule:
* ``(F or W or Y or T or E or A or V or L or I,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ProtK
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ProtK
......@@ -743,7 +743,7 @@ exception rule:
* ``(E)(E,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Staph
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Staph
......@@ -760,7 +760,7 @@ cleaving rule:
* ``(E)()()(Y)()(Q,)(G or S)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#TEV
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#TEV
......@@ -769,7 +769,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Thermolysin
...........
Thermolysin preferentially cleaves before A,F,I,L,M or V (`P1'`) when not followed by P in `P2'` nor preceded by D or E in `P1`.
Thermolysin preferentially cleaves before A,F,I,L,M or V (`P1'` ) when not followed by P in `P2'` nor preceded by D or E in `P1`.
**RPG definition:**
......@@ -782,7 +782,7 @@ exception rules:
* ``(,A or F or I or L or M or V)(P)``
* ``(D or E)(,A or F or I or L or M or V)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Therm
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Therm
......@@ -791,9 +791,9 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Thrombin (PeptideCutter)
........................
This thrombin preferentially cleaves after R (`P1`). Optimum cleavage is when R is preceded and followed by G (`P2` and `P1'`). Cleavage also occurs when R is preceded by P in `P2` and A/F/I/L/V/W/G/T in `P3` and `P4`. It will not cleave after R followed by D/E in `P1'` or `P2'`.
This thrombin preferentially cleaves after R (`P1`). Optimum cleavage is when R is preceded and followed by G (`P2` and `P1'` ). Cleavage also occurs when R is preceded by P in `P2` and A, F, I, L, V, W, G or T in `P3` and `P4`. It will not cleave after R followed by D/E in `P1'` or `P2'`.
It not strictly coherent with the definition as differences exist in PeptideCutter between definition, summary and behavior of this enzyme.
It is not strictly coherent with the definition in PeptideCutter, as in this software there are differences between definition, summary and behavior of this enzyme.
**RPG definition:**
......@@ -807,9 +807,9 @@ exception rules:
* ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)``
* ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)()(D or E)``
.. warning:: do not use ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)(D or E)`` instead, it will cleave on [...](R,)(D or E) otherwise.
.. warning:: the following combined exception ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)(D or E)`` cannot be used instead, as it will cleave on [...](R,)(D or E).
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Throm https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288055/
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Throm https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288055/
......@@ -820,7 +820,7 @@ Thrombin SG
This thrombin (Sequencing Grade) preferentially cleaves after R (`P1`) preceded by P in `P2`, V in `P3` and L in `P4` and followed by G in `P1'` and S `P2'`.
This thrombin is defined in several kit (see below).
This thrombin is defined in several kits (see below).
**RPG definition:**
......@@ -828,7 +828,7 @@ cleaving rule:
* ``(L)(V)(P)(R,)(G)(S)``
More informations: see thrombin cleavage kit of
More information: see thrombin cleavage kits of
`Abcam <http://www.abcam.com/thrombin-cleavage-kit-ab207000.html>`_,
`BioVision <https://www.biovision.com/documentation/datasheets/K377.pdf>`_,
`Merck <http://www.merckmillipore.com/FR/fr/life-science-research/protein-sample-preparation/protein-purification/cleavage-enzymes/0Uqb.qB.V5gAAAFBOFJlvyyv,nav#thrombin>`_ or
......@@ -862,4 +862,4 @@ exception rules:
* ``(R)(R,)(H)``
* ``(R)(R,)(R)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Tryps
More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Tryps
......@@ -389,7 +389,7 @@ Creating a new enzyme
Option **-a, -\\-addenzyme** allows the user to define new enzymes. An enzyme contains one or several rules and exceptions.
On 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 '|':
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:: none
......@@ -438,7 +438,7 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
(C)()(B)(,A)(D)
Create a cleaving rule (c) or an exception (e)? (q) to quit:
q
Add an other enzyme? (y/n)
Add another enzyme? (y/n)
n
$ rpg -i CWBADE -e 43
......@@ -452,14 +452,14 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
FAD
In order for this enzyme to also cleave before AD (before A `(P1')` followed by D in `P2'` ), on top of the previous rule, one has to define one more rule in **RPG**:
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:: none
(,A)(D)
(C)()(B)(,A)(D)
It is important to note that for each enzyme, it is enough that one of the rule is broken for the cleavage to not occur. In this example, the defined enzyme will **not** cleave BAD, as it is specified that it will cleave before A preceded by B in `P1` **if there is C in `P3`**. Identically, it will **not** cleave C*BA*, as D is required in `P2'` for the second rule.
It is important to note that for each enzyme, it is enough that one of the rule is broken for the cleavage to not occur. In this example, the defined enzyme will **not** cleave BAD, as it is specified that it will cleave before A preceded by B in `P1` **if there is C in `P3`**. Identically, it will **not** cleave C*BA*, as D is required in `P2'` for both rules.
.. code-block:: none
......@@ -477,7 +477,7 @@ It is important to note that for each enzyme, it is enough that one of the rule
(C)()(B)(,A)(D)
Create a cleaving rule (c) or an exception (e)? (q) to quit:
q
Add an other enzyme? (y/n)
Add another enzyme? (y/n)
n
$ rpg -i CWBADE -e 43
......@@ -496,7 +496,7 @@ It is important to note that for each enzyme, it is enough that one of the rule
>Input_0_rpg_example_userguide_0_3_204.18268_3.6
BAD
The order of inputted rules is not relevant. This enzyme:
The order of inputted rules is not relevant. In other words, this enzyme:
.. code-block:: none
......@@ -512,16 +512,16 @@ and this second one:
are identical.
It is possible to define none related cleavage rules for the same enzyme, for example:
It is possible to define none-related cleavage rules for the same enzyme, for example:
.. code-block:: none
(P)(W,)(E)(T)
(G,)(G)
(P)(W,)(E)(T)
This enzyme will cleave after G (position `P1`) followed by G in `P1'` and also after W (`P1`) preceded by P in `P2` and followed by E in `P1'` and T in `P2'`.
Note that each rule must concerned only **one** cleavage site. It is not possible to input rule like:
Note that each rule must concern only **one** cleavage site. It is not possible to input rule like:
.. code-block:: none
......@@ -534,21 +534,21 @@ This would define an enzyme cleaving after A in `P1` followed by B in `P1'` but
(A,)(B)
(A)(B,)
However, it is possible to wrote rules in a more efficient way as explain in :ref:`easy`.
However, it is possible to write rules in a more efficient way as explained in :ref:`easy`.
Definition of exceptions
------------------------
An exception specify when a cleavage should **not** occurs. **Exceptions must always be linked to a rule**.
An exception specifies when a cleavage should **not** occur. **Exceptions must always be linked to a rule**.
For example, to define a cleavage occurring **before** A `(P1')`, one must input:
For example, to define a cleavage occurring **before** A (`P1'` ), one must input:
.. code-block:: none
(,A)
Exceptions can then be inputted, for example a cleavage occurs before A in `P1'`, except when P is in `P2'` is defined by adding this exception:
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:: none
......@@ -571,7 +571,7 @@ This enzyme will always cleave before A when not followed by P:
(,A)(P)
Create a cleaving rule (c) or an exception (e)? (q) to quit:
q
Add an other enzyme? (y/n)
Add another enzyme? (y/n)
n
rpg -i CWBADE -e 43
......@@ -590,7 +590,7 @@ It is possible to input complex exceptions. For the previous enzyme, we can add
(G)(T)()(,A)()(F)
This enzyme will always cleave before A when not followed by P or preceded by G in `P3`, T in `P2` and F in `P3'` **at the same time**:
This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` ) or preceded by G in `P3`, T in `P2`, by any amino acid in `P1` and `P2'`, and F in `P3'` **at the same time**:
.. code-block:: none
......@@ -611,7 +611,7 @@ This enzyme will always cleave before A when not followed by P or preceded by G
(G)(T)()(,A)()(F)
Create a cleaving rule (c) or an exception (e)? (q) to quit:
q
Add an other enzyme? (y/n)
Add another enzyme? (y/n)
n
rpg -i CWBADE -e 43
......@@ -624,15 +624,15 @@ This enzyme will always cleave before A when not followed by P or preceded by G
>Input_0_rpg_example_userguide_0_6_604.67828_3.6
CWBAPE
rpg -i GTBAPF -e 43
rpg -i GTBAMF -e 43
>Input_0_rpg_example_userguide_0_6_491.54438_5.54
GTBAPF
GTBAMF
rpg -i GTBAPE -e 43
rpg -i GTBAME -e 43
>Input_0_rpg_example_userguide_3_3_176.17228_5.54
GTB
>Input_1_rpg_example_userguide_6_3_315.32628_3.6
APE
AME
It is important to understand that an exception should always be linked to a rule. If one inputs this rule:
......@@ -657,7 +657,7 @@ Easily writing complex enzymes
To make enzyme creation easier to use, two tricks are available.
The first one simplify 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:
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:: none
......@@ -670,7 +670,7 @@ or simply using:
(,A,)
The second tricks is the use of the keyword `or`. This allows multiple possibilities for on position. For example:
The second trick is the use of the keyword `or`. This allows multiple possibilities for on position. For example:
.. code-block:: none
......@@ -685,7 +685,7 @@ is equivalent to:
.. warning:: do not input ``(,A or ,B)``, as a comma must always directly preceding or following a parenthesis.
Those two tricks help one complex enzymes. For example, :ref:`peps13` preferentially cleaves around F or L, sometimes before, sometimes after, depending on the context. More specifically, it will not cleave before F or L in `P1'` followed by P in `P2'`. It will not cleave before F or L in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F or L in `P1` followed by P in `P2'`. And it will not cleave after F or L in `P1` preceded by P in `P2` or H/K/R in `P3`.
Those two tricks help on complex enzymes. For example, :ref:`peps13` preferentially cleaves around F or L, sometimes before, sometimes after, depending on the context. More specifically, it will not cleave before F or L in `P1'` followed by P in `P2'`. It will not cleave before F or L in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F or L in `P1` followed by P in `P2'`. And it will not cleave after F or L in `P1` preceded by P in `P2` or H/K/R in `P3`.
It can be defined either by:
......@@ -754,7 +754,7 @@ All available enzymes are in :ref:`enzymes`, including their **RPG**'s definitio
Deleting user-defined enzymes
=============================
All user-defined enzymes are stored in ``~/rpg_user.py``. This file is automatically generated by **RPG** en written in **Python**.
All user-defined enzymes are stored in ``~/rpg_user.py``. This file is automatically generated by **RPG** and written in **Python**.
Each enzyme definition starts with:
......@@ -770,8 +770,8 @@ 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 mentioned lines above. 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, 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 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 and will need to be defined again in **RPG**, using -a option, if one wants to use them again.
\ No newline at end of file
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.
\ No newline at end of file
......@@ -323,4 +323,4 @@ def user_creation_enzyme(all_enzymes):
all_name_enz.add(new_enz.name)
# End of this new enzyme
add_enzyme = input("Add an other enzyme? (y/n)\n")
add_enzyme = input("Add another enzyme? (y/n)\n")
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