Commit 6d52637c authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

Add the 7 last enzymes

parent 8e0b76ce
......@@ -7,11 +7,15 @@ 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 '|'::
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 '|':
.. code-block:: none
...P3-P2-P1-|-P1'-P2'-P3'...
In **RPG**, this nomenclature is represented as::
In **RPG**, this nomenclature is represented as:
.. code-block:: none
...(P3)(P2)(P1)(,)(P1')(P2')(P3')...
......@@ -20,18 +24,20 @@ Available enzymes
-----------------
================== ================== ==================
0: :ref:`arg-c` 1: :ref:`asp-n` 2: :ref:`bnps`
3: :ref:`casp1` 4: :ref:`casp2` 5: :ref:`casp3`
6: :ref:`casp4` 7: :ref:`casp5` 8: :ref:`casp6`
9: :ref:`casp7` 10: :ref:`casp8` 11: :ref:`casp9`
12: :ref:`casp10` 13: :ref:`chymh` 14: :ref:`chyml`
15: :ref:`clost` 16: :ref:`cnbr` 17: :ref:`enter`
18: :ref:`fxa` 19: :ref:`form` 20: :ref:`gluc`
21: :ref:`glue` 22: :ref:`gran` 23: :ref:`hydro`
24: :ref:`iodo` 25: :ref:`lysc` 26: :ref:`lysn`
27: :ref:`neut` 28: :ref:`ntcb` 29: :ref:`peps13`
30: :ref:`peps2` 31: :ref:`prol` 32: :ref:`throm`
33: :ref:`thromsg` 34: :ref:`tryps`
1: :ref:`arg-c` 2: :ref:`asp-n` 3: :ref:`bnps`
4: :ref:`brom` 5: :ref:`casp1` 6: :ref:`casp2`
7: :ref:`casp3` 8: :ref:`casp4` 9: :ref:`casp5`
10: :ref:`casp6` 11: :ref:`casp7` 12: :ref:`casp8`
13: :ref:`casp9` 14: :ref:`casp10` 15: :ref:`chymh`
16: :ref:`chyml` 17: :ref:`clost` 18: :ref:`cnbr`
19: :ref:`enter` 20: :ref:`fxa` 21: :ref:`ficin`
22: :ref:`form` 23: :ref:`gluc` 24: :ref:`glue`
25: :ref:`gran` 26: :ref:`hydro` 27: :ref:`iodo`
28: :ref:`lysc` 29: :ref:`lysn` 30: :ref:`neut`
31: :ref:`ntcb` 32: :ref:`pap` 33: :ref:`peps13`
34: :ref:`peps2` 35: :ref:`prol` 36: :ref:`protk`
37: :ref:`staphI` 38: :ref:`tev` 39: :ref:`throm`
40: :ref:`therm` 41: :ref:`thromsg` 42: :ref:`tryps`
================== ================== ==================
.. _arg-c:
......@@ -47,8 +53,7 @@ cleaving rule:
* ``(R,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
......@@ -65,8 +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 informations: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
......@@ -83,8 +87,24 @@ cleaving rule:
* ``(W,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
.. _brom:
Bromelain
.........
Bromelain preferentially cleaves after K, A or Y (`P1`)
**RPG definition:**
cleaving rule:
* ``(K or A or Y,)``
More informations: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410479
......@@ -105,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
......@@ -129,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
......@@ -153,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
......@@ -177,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
......@@ -195,8 +211,7 @@ cleaving rule:
* ``(W or L)(E)(H)(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
......@@ -217,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
......@@ -239,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
......@@ -261,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
......@@ -279,8 +291,7 @@ cleaving rule:
* ``(L)(E)(H)(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
......@@ -297,8 +308,7 @@ cleaving rule:
* ``(I)(E)(A)(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
......@@ -320,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
......@@ -345,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
......@@ -363,8 +371,7 @@ cleaving rule:
* ``(R,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
......@@ -381,8 +388,7 @@ cleaving rule:
* ``(M,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
......@@ -399,8 +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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter
......@@ -417,8 +422,24 @@ 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 informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
.. _ficin:
Ficin
.....
Ficin preferentially cleaves after G, S, E or Y (`P1`) preceded by A, V, I, L ,F, Y or W in `P2`.
**RPG definition:**
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
......@@ -435,8 +456,7 @@ cleaving rule:
* ``(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH
......@@ -453,8 +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 informations: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
......@@ -471,8 +490,7 @@ cleaving rule:
* ``(E,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu
......@@ -489,8 +507,7 @@ cleaving rule:
* ``(I)(E)(P)(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB
......@@ -507,8 +524,7 @@ cleaving rule:
* ``(N,)(G)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro
......@@ -525,8 +541,7 @@ cleaving rule:
* ``(W,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo
......@@ -598,6 +613,27 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
.. _pap:
Papain
......
Papain preferentially cleaves after R or K (`P1`) preceded by A, V, I, L ,F, Y or W in `P2`. It will not cleave if followed by V in `P1'`.
**RPG definition:**
cleaving rule:
* ``(A or V or I or L or F or Y or W)(R or K,)``
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
.. _peps13:
Pepsin pH 1.3
......@@ -673,6 +709,83 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
.. _protk:
Proteinase K
.....................
Proteinase K preferentially cleaves after F, W, Y, T, E, A, V, L or I (`P1`). The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids.
**RPG definition:**
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
.. _staphI:
Staphylococcal peptidase I
..........................
Staphylococcal peptidase I preferentially cleaves after E (`P1`). It will not cleave after E in `P1` preceded by E in `P2`, but cleaves after E in `P1` followed by E in `P1'`.
**RPG definition:**
cleaving rule:
* ``(E,)``
exception rule:
* ``(E)(E,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Staph
.. _tev:
Tobacco etch virus protease
...........................
Tobacco etch virus protease (TEV) preferentially cleaves after Q (`P1`) when followed by G or S in `P1'` and preceded by Y in `P3` and E in `P6`.
**RPG definition:**
cleaving rule:
* ``(E)()()(Y)()(Q,)(G or S)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#TEV
.. _therm:
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`.
**RPG definition:**
cleaving rule:
* ``(,A or F or I or L or M or V)``
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
.. _throm:
Thrombin (PeptideCutter)
......@@ -702,10 +815,10 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
.. _thromsg:
Thrombin Sequencing Grade
Thrombin SG
.........................
This thrombin 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 (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).
......
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......@@ -48,28 +48,39 @@ def test_list_enzyme(capsys):
"""
RapidPeptidesGenerator.list_enzyme()
out, _ = capsys.readouterr()
assert out == "0: Arg-C\n1: Asp-N\n2: BNPS-Skatole\n3: Caspase-1\n4: Caspase-2\n5: Caspase-3\n6: Caspase-4\n7: Caspase-5\n8: Caspase-6\n9: Caspase-7\n10: Caspase-8\n11: Caspase-9\n12: Caspase-10\n13: Chymotrypsin-high\n14: Chymotrypsin-low\n15: Clostripain\n16: CNBr\n17: Enterokinase\n18: Factor-Xa\n19: Formic-acid\n20: Glu-C\n21: Glutamyl-endopeptidase\n22: Granzyme-B\n23: Hydroxylamine\n24: Iodosobenzoic-acid\n25: Lys-C\n26: Lys-N\n27: Neutrophil-elastase\n28: NTCB\n29: Pepsin-pH1.3\n30: Pepsin-pH>=2\n31: Proline-endopeptidase\n32: Thrombin\n33: Thrombin-Sequencing-Grade\n34: Trypsin\n"
assert out == "1: Arg-C\n2: Asp-N\n3: BNPS-Skatole\n4: Bromelain\n5: Casp"\
"ase-1\n6: Caspase-2\n7: Caspase-3\n8: Caspase-4\n9: Caspas"\
"e-5\n10: Caspase-6\n11: Caspase-7\n12: Caspase-8\n13: Casp"\
"ase-9\n14: Caspase-10\n15: Chymotrypsin-high\n16: Chymotry"\
"psin-low\n17: Clostripain\n18: CNBr\n19: Enterokinase\n20:"\
" Factor-Xa\n21: Papain\n22: Formic-acid\n23: Glu-C\n24: Gl"\
"utamyl-endopeptidase\n25: Granzyme-B\n26: Hydroxylamine\n2"\
"7: Iodosobenzoic-acid\n28: Lys-C\n29: Lys-N\n30: Neutrophi"\
"l-elastase\n31: NTCB\n32: Papain\n33: Pepsin-pH1.3\n34: Pe"\
"psin-pH>=2\n35: Proline-endopeptidase\n36: Proteinase-K\n3"\
"7: Staphylococcal-peptidase-I\n38: Tobacco-Etch-Virus\n39:"\
" Thermolysin\n40: Thrombin\n41: Thrombin-SG\n42: Trypsin\n"
def test_create_enzymes_to_use(capsys):
"""Test function 'create_enzymes_to_use(enzymes, miscleavage)'"""
enzymes = [20, 28, 26]
enzymes = [23, 31, 29]
miscleavage = [1.1, 20]
res = RapidPeptidesGenerator.create_enzymes_to_use(enzymes, miscleavage)
assert res.__repr__() == "[Id: 20\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
assert res.__repr__() == "[Id: 23\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
"0%\nRules: [index=0\nletter=D\ncut=True\npos=1\n,"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 28"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 31"\
"\nName: NTCB\nRatio Miss Cleaveage: 20.00%\nRules"\
": [index=0\nletter=C\ncut=True\npos=0\n]\n, Id: "\
"26\nName: Lys-N\nRatio Miss Cleaveage: 0.00%\nRul"\
"29\nName: Lys-N\nRatio Miss Cleaveage: 0.00%\nRul"\
"es: [index=0\nletter=K\ncut=True\npos=0\n]\n]"
enzymes = [20, 28]
enzymes = [23, 31]
miscleavage = [1.1, 20, 40]
res = RapidPeptidesGenerator.create_enzymes_to_use(enzymes, miscleavage)
_, err = capsys.readouterr()
assert err == "Warning: Too much miscleavage values. Last values will "\
"be ignored.\n"
assert res.__repr__() == "[Id: 20\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
assert res.__repr__() == "[Id: 23\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
"0%\nRules: [index=0\nletter=D\ncut=True\npos=1\n,"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 28"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 31"\
"\nName: NTCB\nRatio Miss Cleaveage: 20.00%\nRules"\
": [index=0\nletter=C\ncut=True\npos=0\n]\n]"
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