diff --git a/docs/enzymes.rst b/docs/enzymes.rst
index 51b9ffaf05b5ba82682d898583d924a058e5b18a..b498a789b86dd0d20a470388ca613d7d2d85b545 100644
--- a/docs/enzymes.rst
+++ b/docs/enzymes.rst
@@ -1,13 +1,13 @@
.. _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
diff --git a/docs/userguide.rst b/docs/userguide.rst
index 51391a1836934d862bca8bb3b896fb3baf2ea290..edf3aa08eafbf9ae3d458d703ea3aada7a7e3d3f 100644
--- a/docs/userguide.rst
+++ b/docs/userguide.rst
@@ -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
diff --git a/rpg/enzyme.py b/rpg/enzyme.py
index 3cf7a109b78a046b63d289bf5986791d636d05b3..b3ab07b53c68410edb7d6abf04042188e8db2d02 100644
--- a/rpg/enzyme.py
+++ b/rpg/enzyme.py
@@ -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")