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")