Commit 5f43174f authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

Add 7 enzymes

parent f26eec32
......@@ -26,10 +26,12 @@ Available enzymes
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:`gluc` 20: :ref:`lysc`
21: :ref:`lysn` 22: :ref:`ntcb` 23: :ref:`peps13`
24: :ref:`peps2` 25: :ref:`throm` 26: :ref:`thromsg`
27: :ref:`tryps`
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`
================== ================== ==================
.. _arg-c:
......@@ -420,6 +422,24 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
.. _form:
Formic acid
...........
Formic acid preferentially cleaves after D (`P1`).
**RPG definition:**
cleaving rule:
* ``(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH
.. _gluc:
Glu-C
......@@ -438,6 +458,78 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-
.. _glue:
Glutamyl endopeptidase
......................
Glutamyl endopeptidase preferentially cleaves after E (`P1`).
**RPG definition:**
cleaving rule:
* ``(E,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu
.. _gran:
Granzyme B
..........
Granzyme B preferentially cleaves after D (`P1`) preceded by IEP.
**RPG definition:**
cleaving rule:
* ``(I)(E)(P)(D,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB
.. _hydro:
Hydroxylamine
.............
Hydroxylamine (NH2OH) preferentially cleaves after N (`P1`) followed by G in `P1'`.
**RPG definition:**
cleaving rule:
* ``(N,)(G)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro
.. _iodo:
Iodosobenzoic acid
..................
Iodosobenzoic acid preferentially cleaves after W (`P1`).
**RPG definition:**
cleaving rule:
* ``(W,)``
More informations:
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo
.. _lysc:
Lys-C
......@@ -472,6 +564,23 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
.. _neut:
Neutrophil elastase
...................
Neutrophil elastase preferentially cleaves after A or V (`P1`).
**RPG definition:**
cleaving rule:
* ``(A or V,)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Elast
.. _ntcb:
NTCB
......@@ -543,6 +652,27 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
.. _prol:
Proline-endopeptidase
.....................
Proline-endopeptidase preferentially cleaves after P (`P1`) preceded by H, K or R in `P2` but will not cleaves if followed by P in `P1'`.
**RPG definition:**
cleaving rule:
* ``(H or K or R)(P,)``
exception rule:
* ``(H or K or R)(P,)(P)``
More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Pro
.. _throm:
Thrombin (PeptideCutter)
......
This diff is collapsed.
......@@ -48,35 +48,28 @@ 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: Casp"\
"ase-2\n5: Caspase-3\n6: Caspase-4\n7: Caspase-5\n8: Caspas"\
"e-6\n9: Caspase-7\n10: Caspase-8\n11: Caspase-9\n12: Caspa"\
"se-10\n13: Chymotrypsin-high\n14: Chymotrypsin-low\n15: Cl"\
"ostripain\n16: CNBr\n17: Enterokinase\n18: Factor-Xa\n19: "\
"Glu-C\n20: Lys-C\n21: Lys-N\n22: NTCB\n23: Pepsin-pH1.3\n2"\
"4: Pepsin-pH>=2\n25: Thrombin\n26: Thrombin-Sequencing-Gra"\
"de\n27: Trypsin\n"
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"
def test_create_enzymes_to_use(capsys):
"""Test function 'create_enzymes_to_use(enzymes, miscleavage)'"""
enzymes = [19, 22, 21]
enzymes = [20, 28, 26]
miscleavage = [1.1, 20]
res = RapidPeptidesGenerator.create_enzymes_to_use(enzymes, miscleavage)
assert res.__repr__() == "[Id: 19\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
assert res.__repr__() == "[Id: 20\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: 22"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 28"\
"\nName: NTCB\nRatio Miss Cleaveage: 20.00%\nRules"\
": [index=0\nletter=C\ncut=True\npos=0\n]\n, Id: "\
"21\nName: Lys-N\nRatio Miss Cleaveage: 0.00%\nRul"\
"26\nName: Lys-N\nRatio Miss Cleaveage: 0.00%\nRul"\
"es: [index=0\nletter=K\ncut=True\npos=0\n]\n]"
enzymes = [19, 22]
enzymes = [20, 28]
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: 19\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
assert res.__repr__() == "[Id: 20\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: 22"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 28"\
"\nName: NTCB\nRatio Miss Cleaveage: 20.00%\nRules"\
": [index=0\nletter=C\ncut=True\npos=0\n]\n]"
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