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Nicolas MAILLET
rpg
Commits
5f43174f
Commit
5f43174f
authored
May 04, 2018
by
Nicolas MAILLET
Browse files
Add 7 enzymes
parent
f26eec32
Changes
3
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docs/enzymes.rst
View file @
5f43174f
...
...
@@ -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)
...
...
rpg/enzymes_definition.py
View file @
5f43174f
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tests/test_RapidPeptidesGenerator.py
View file @
5f43174f
...
...
@@ -48,35 +48,28 @@ def test_list_enzyme(capsys):
"""
RapidPeptidesGenerator
.
list_enzyme
()
out
,
_
=
capsys
.
readouterr
()
assert
out
==
"0: Arg-C
\n
1: Asp-N
\n
2: BNPS-Skatole
\n
3: Caspase-1
\n
4: Casp"
\
"ase-2
\n
5: Caspase-3
\n
6: Caspase-4
\n
7: Caspase-5
\n
8: Caspas"
\
"e-6
\n
9: Caspase-7
\n
10: Caspase-8
\n
11: Caspase-9
\n
12: Caspa"
\
"se-10
\n
13: Chymotrypsin-high
\n
14: Chymotrypsin-low
\n
15: Cl"
\
"ostripain
\n
16: CNBr
\n
17: Enterokinase
\n
18: Factor-Xa
\n
19: "
\
"Glu-C
\n
20: Lys-C
\n
21: Lys-N
\n
22: NTCB
\n
23: Pepsin-pH1.3
\n
2"
\
"4: Pepsin-pH>=2
\n
25: Thrombin
\n
26: Thrombin-Sequencing-Gra"
\
"de
\n
27: Trypsin
\n
"
assert
out
==
"0: Arg-C
\n
1: Asp-N
\n
2: BNPS-Skatole
\n
3: Caspase-1
\n
4: Caspase-2
\n
5: Caspase-3
\n
6: Caspase-4
\n
7: Caspase-5
\n
8: Caspase-6
\n
9: Caspase-7
\n
10: Caspase-8
\n
11: Caspase-9
\n
12: Caspase-10
\n
13: Chymotrypsin-high
\n
14: Chymotrypsin-low
\n
15: Clostripain
\n
16: CNBr
\n
17: Enterokinase
\n
18: Factor-Xa
\n
19: Formic-acid
\n
20: Glu-C
\n
21: Glutamyl-endopeptidase
\n
22: Granzyme-B
\n
23: Hydroxylamine
\n
24: Iodosobenzoic-acid
\n
25: Lys-C
\n
26: Lys-N
\n
27: Neutrophil-elastase
\n
28: NTCB
\n
29: Pepsin-pH1.3
\n
30: Pepsin-pH>=2
\n
31: Proline-endopeptidase
\n
32: Thrombin
\n
33: Thrombin-Sequencing-Grade
\n
34: Trypsin
\n
"
def
test_create_enzymes_to_use
(
capsys
):
"""Test function 'create_enzymes_to_use(enzymes, miscleavage)'"""
enzymes
=
[
19
,
2
2
,
2
1
]
enzymes
=
[
20
,
2
8
,
2
6
]
miscleavage
=
[
1.1
,
20
]
res
=
RapidPeptidesGenerator
.
create_enzymes_to_use
(
enzymes
,
miscleavage
)
assert
res
.
__repr__
()
==
"[Id:
19
\n
Name: Glu-C
\n
Ratio Miss Cleaveage: 1.1"
\
assert
res
.
__repr__
()
==
"[Id:
20
\n
Name: Glu-C
\n
Ratio Miss Cleaveage: 1.1"
\
"0%
\n
Rules: [index=0
\n
letter=D
\n
cut=True
\n
pos=1
\n
,"
\
" index=0
\n
letter=E
\n
cut=True
\n
pos=1
\n
]
\n
, Id: 2
2
"
\
" index=0
\n
letter=E
\n
cut=True
\n
pos=1
\n
]
\n
, Id: 2
8
"
\
"
\n
Name: NTCB
\n
Ratio Miss Cleaveage: 20.00%
\n
Rules"
\
": [index=0
\n
letter=C
\n
cut=True
\n
pos=0
\n
]
\n
, Id: "
\
"2
1
\n
Name: Lys-N
\n
Ratio Miss Cleaveage: 0.00%
\n
Rul"
\
"2
6
\n
Name: Lys-N
\n
Ratio Miss Cleaveage: 0.00%
\n
Rul"
\
"es: [index=0
\n
letter=K
\n
cut=True
\n
pos=0
\n
]
\n
]"
enzymes
=
[
19
,
2
2
]
enzymes
=
[
20
,
2
8
]
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
\n
Name: Glu-C
\n
Ratio Miss Cleaveage: 1.1"
\
assert
res
.
__repr__
()
==
"[Id:
20
\n
Name: Glu-C
\n
Ratio Miss Cleaveage: 1.1"
\
"0%
\n
Rules: [index=0
\n
letter=D
\n
cut=True
\n
pos=1
\n
,"
\
" index=0
\n
letter=E
\n
cut=True
\n
pos=1
\n
]
\n
, Id: 2
2
"
\
" index=0
\n
letter=E
\n
cut=True
\n
pos=1
\n
]
\n
, Id: 2
8
"
\
"
\n
Name: NTCB
\n
Ratio Miss Cleaveage: 20.00%
\n
Rules"
\
": [index=0
\n
letter=C
\n
cut=True
\n
pos=0
\n
]
\n
]"
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