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)
......
......@@ -71,29 +71,29 @@ CPT_ENZ += 1
# Caspase 1
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
# RULES: cut after D if prev1 is H, A or T and prev3 F, W, Y or L.
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after D if prev1 is H, A or T and prev3 F, W, Y or L.
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cut after D, preceded by H
EXECPT_AD = rule.Rule(-1, "A", False, -1) # Never cut after D, preceded by A
EXECPT_TD = rule.Rule(-1, "T", False, -1) # Never cut after D, preceded by T
EXECPT_HATD__F = rule.Rule(-3, "F", True, -1) # Always cut after D, preceded by H, A or T, preceded by F
EXECPT_HATD__L = rule.Rule(-3, "L", True, -1) # Always cut after D, preceded by H, A or T, preceded by L
EXECPT_HATD__W = rule.Rule(-3, "W", True, -1) # Always cut after D, preceded by H, A or T, preceded by W
EXECPT_HATD__Y = rule.Rule(-3, "Y", True, -1) # Always cut after D, preceded by H, A or T, preceded by Y
EXECPT_HATD__FLWY_P = rule.Rule(1, "P", False, -1) # Never cut after D, preceded by H, A or T, preceded by F, l, W, Y and followed by P
EXECPT_HATD__FLWY_E = rule.Rule(1, "E", False, -1) # Never cut after D, preceded by H, A or T, preceded by F, l, W, Y and followed by E
EXECPT_HATD__FLWY_D = rule.Rule(1, "D", False, -1) # Never cut after D, preceded by H, A or T, preceded by F, l, W, Y and followed by D
EXECPT_HATD__FLWY_Q = rule.Rule(1, "Q", False, -1) # Never cut after D, preceded by H, A or T, preceded by F, l, W, Y and followed by Q
EXECPT_HATD__FLWY_K = rule.Rule(1, "K", False, -1) # Never cut after D, preceded by H, A or T, preceded by F, l, W, Y and followed by K
EXECPT_HATD__FLWY_R = rule.Rule(1, "R", False, -1) # Never cut after D, preceded by H, A or T, preceded by F, l, W, Y and followed by R
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cleaves after D, preceded by H
EXECPT_AD = rule.Rule(-1, "A", False, -1) # Never cleaves after D, preceded by A
EXECPT_TD = rule.Rule(-1, "T", False, -1) # Never cleaves after D, preceded by T
EXECPT_HATD__F = rule.Rule(-3, "F", True, -1) # Always cleaves after D, preceded by H, A or T, preceded by F
EXECPT_HATD__L = rule.Rule(-3, "L", True, -1) # Always cleaves after D, preceded by H, A or T, preceded by L
EXECPT_HATD__W = rule.Rule(-3, "W", True, -1) # Always cleaves after D, preceded by H, A or T, preceded by W
EXECPT_HATD__Y = rule.Rule(-3, "Y", True, -1) # Always cleaves after D, preceded by H, A or T, preceded by Y
EXECPT_HATD__FLWY_P = rule.Rule(1, "P", False, -1) # Never cleaves after D, preceded by H, A or T, preceded by F, l, W, Y and followed by P
EXECPT_HATD__FLWY_E = rule.Rule(1, "E", False, -1) # Never cleaves after D, preceded by H, A or T, preceded by F, l, W, Y and followed by E
EXECPT_HATD__FLWY_D = rule.Rule(1, "D", False, -1) # Never cleaves after D, preceded by H, A or T, preceded by F, l, W, Y and followed by D
EXECPT_HATD__FLWY_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D, preceded by H, A or T, preceded by F, l, W, Y and followed by Q
EXECPT_HATD__FLWY_K = rule.Rule(1, "K", False, -1) # Never cleaves after D, preceded by H, A or T, preceded by F, l, W, Y and followed by K
EXECPT_HATD__FLWY_R = rule.Rule(1, "R", False, -1) # Never cleaves after D, preceded by H, A or T, preceded by F, l, W, Y and followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_HATD__F.rules.append(EXECPT_HATD__FLWY_P)
......@@ -160,28 +160,28 @@ CPT_ENZ += 1
# Caspase 2
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
# RULES: cut after DVAD, or DEHD,.
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after DVAD, or DEHD,.
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cut after D, preceded by H
EXECPT_AD = rule.Rule(-1, "A", False, -1) # Never cut after D, preceded by A
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cleaves after D, preceded by H
EXECPT_AD = rule.Rule(-1, "A", False, -1) # Never cleaves after D, preceded by A
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by H, preceded by E
EXECPT_VAD = rule.Rule(-2, "V", False, -1) # Never cut after D, preceded by A, preceded by V
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by H, preceded by E
EXECPT_VAD = rule.Rule(-2, "V", False, -1) # Never cleaves after D, preceded by A, preceded by V
EXECPT_DXXD = rule.Rule(-3, "D", True, -1) # Always cut after D, preceded by H (A), preceded by E (V), preceded by D
EXECPT_DXXD = rule.Rule(-3, "D", True, -1) # Always cleaves after D, preceded by H (A), preceded by E (V), preceded by D
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cut after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cut after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cut after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cut after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cut after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cut after D followed by R
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cleaves after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cleaves after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cleaves after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cleaves after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cleaves after D followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_DXXD.rules.append(EXECPT_P)
......@@ -215,28 +215,28 @@ CPT_ENZ += 1
# Caspase 3
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
# RULES: cut after DMQD, or DEVD,.
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after DMQD, or DEVD,.
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_VD = rule.Rule(-1, "V", False, -1) # Never cut after D, preceded by V
EXECPT_QD = rule.Rule(-1, "Q", False, -1) # Never cut after D, preceded by Q
EXECPT_VD = rule.Rule(-1, "V", False, -1) # Never cleaves after D, preceded by V
EXECPT_QD = rule.Rule(-1, "Q", False, -1) # Never cleaves after D, preceded by Q
EXECPT_EVD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by V, preceded by E
EXECPT_MQD = rule.Rule(-2, "M", False, -1) # Never cut after D, preceded by Q, preceded by M
EXECPT_EVD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by V, preceded by E
EXECPT_MQD = rule.Rule(-2, "M", False, -1) # Never cleaves after D, preceded by Q, preceded by M
EXECPT_DXXD = rule.Rule(-3, "D", True, -1) # Always cut after D, preceded by H (A), preceded by E (V), preceded by D
EXECPT_DXXD = rule.Rule(-3, "D", True, -1) # Always cleaves after D, preceded by H (A), preceded by E (V), preceded by D
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cut after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cut after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cut after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cut after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cut after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cut after D followed by R
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cleaves after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cleaves after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cleaves after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cleaves after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cleaves after D followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_DXXD.rules.append(EXECPT_P)
......@@ -270,29 +270,29 @@ CPT_ENZ += 1
# Caspase 4
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
# RULES: cut after LEVD, or (W/L)EHD,.
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after LEVD, or (W/L)EHD,.
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_VD = rule.Rule(-1, "V", False, -1) # Never cut after D, preceded by V
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cut after D, preceded by H
EXECPT_VD = rule.Rule(-1, "V", False, -1) # Never cleaves after D, preceded by V
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cleaves after D, preceded by H
EXECPT_EVD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by V, preceded by E
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by H, preceded by E
EXECPT_EVD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by V, preceded by E
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by H, preceded by E
EXECPT_LEVD = rule.Rule(-3, "L", True, -1) # Always cut after D, preceded by V/H, preceded by E, preceded by L
EXECPT_WEHD = rule.Rule(-3, "W", True, -1) # Always cut after D, preceded by H, preceded by E, preceded by W
EXECPT_LEVD = rule.Rule(-3, "L", True, -1) # Always cleaves after D, preceded by V/H, preceded by E, preceded by L
EXECPT_WEHD = rule.Rule(-3, "W", True, -1) # Always cleaves after D, preceded by H, preceded by E, preceded by W
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cut after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cut after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cut after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cut after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cut after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cut after D followed by R
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cleaves after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cleaves after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cleaves after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cleaves after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cleaves after D followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_LEVD.rules.append(EXECPT_P)
......@@ -333,19 +333,19 @@ CPT_ENZ += 1
# Caspase 5
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
# RULES: cut after (W/L)EHD,
# RULES: cleaves after (W/L)EHD,
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cut after D, preceded by H
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cleaves after D, preceded by H
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by H, preceded by E
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by H, preceded by E
EXECPT_LEHD = rule.Rule(-3, "L", True, -1) # Always cut after D, preceded by H, preceded by E, preceded by L
EXECPT_WEHD = rule.Rule(-3, "W", True, -1) # Always cut after D, preceded by H, preceded by E, preceded by W
EXECPT_LEHD = rule.Rule(-3, "L", True, -1) # Always cleaves after D, preceded by H, preceded by E, preceded by L
EXECPT_WEHD = rule.Rule(-3, "W", True, -1) # Always cleaves after D, preceded by H, preceded by E, preceded by W
# Add exception to cutting rules: ...preceded by L/W
EXECPT_EHD.rules.append(EXECPT_LEHD)
......@@ -368,29 +368,29 @@ CPT_ENZ += 1
# Caspase 6
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
# RULES: cut after VEID, or VEHD,.
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after VEID, or VEHD,.
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_ID = rule.Rule(-1, "I", False, -1) # Never cut after D, preceded by I
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cut after D, preceded by H
EXECPT_ID = rule.Rule(-1, "I", False, -1) # Never cleaves after D, preceded by I
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cleaves after D, preceded by H
EXECPT_EID = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by I, preceded by E
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by H, preceded by E
EXECPT_EID = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by I, preceded by E
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by H, preceded by E
EXECPT_VEID = rule.Rule(-3, "V", True, -1) # Always cut after D, preceded by I, preceded by E, preceded by V
EXECPT_VEHD = rule.Rule(-3, "V", True, -1) # Always cut after D, preceded by H, preceded by E, preceded by V
EXECPT_VEID = rule.Rule(-3, "V", True, -1) # Always cleaves after D, preceded by I, preceded by E, preceded by V
EXECPT_VEHD = rule.Rule(-3, "V", True, -1) # Always cleaves after D, preceded by H, preceded by E, preceded by V
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cut after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cut after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cut after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cut after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cut after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cut after D followed by R
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cleaves after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cleaves after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cleaves after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cleaves after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cleaves after D followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_VEID.rules.append(EXECPT_P)
......@@ -430,26 +430,26 @@ CPT_ENZ += 1
# Caspase 7
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
# RULES: cut after DEVD,.
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after DEVD,.
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_VD = rule.Rule(-1, "V", False, -1) # Never cut after D, preceded by V
EXECPT_VD = rule.Rule(-1, "V", False, -1) # Never cleaves after D, preceded by V
EXECPT_EVD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by V, preceded by E
EXECPT_EVD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by V, preceded by E
EXECPT_DEVD = rule.Rule(-3, "D", True, -1) # Always cut after D, preceded by V, preceded by E, preceded by D
EXECPT_DEVD = rule.Rule(-3, "D", True, -1) # Always cleaves after D, preceded by V, preceded by E, preceded by D
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cut after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cut after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cut after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cut after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cut after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cut after D followed by R
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cleaves after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cleaves after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cleaves after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cleaves after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cleaves after D followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_DEVD.rules.append(EXECPT_P)
......@@ -479,27 +479,27 @@ CPT_ENZ += 1
# Caspase 8
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
# RULES: cut after (I/L)ETD,
# Do not cut if followed by P, E, D, Q, K or R
# RULES: cleaves after (I/L)ETD,
# Do not cleaves if followed by P, E, D, Q, K or R
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_TD = rule.Rule(-1, "T", False, -1) # Never cut after D, preceded by T
EXECPT_TD = rule.Rule(-1, "T", False, -1) # Never cleaves after D, preceded by T
EXECPT_ETD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by T, preceded by E
EXECPT_ETD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by T, preceded by E
EXECPT_IETD = rule.Rule(-3, "I", True, -1) # Always cut after D, preceded by T, preceded by E, preceded by I
EXECPT_LETD = rule.Rule(-3, "L", True, -1) # Always cut after D, preceded by T, preceded by E, preceded by L
EXECPT_IETD = rule.Rule(-3, "I", True, -1) # Always cleaves after D, preceded by T, preceded by E, preceded by I
EXECPT_LETD = rule.Rule(-3, "L", True, -1) # Always cleaves after D, preceded by T, preceded by E, preceded by L
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cut after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cut after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cut after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cut after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cut after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cut after D followed by R
EXECPT_P = rule.Rule(1, "P", False, -1) # Never cleaves after D followed by P
EXECPT_E = rule.Rule(1, "E", False, -1) # Never cleaves after D followed by E
EXECPT_D = rule.Rule(1, "D", False, -1) # Never cleaves after D followed by D
EXECPT_Q = rule.Rule(1, "Q", False, -1) # Never cleaves after D followed by Q
EXECPT_K = rule.Rule(1, "K", False, -1) # Never cleaves after D followed by K
EXECPT_R = rule.Rule(1, "R", False, -1) # Never cleaves after D followed by R
# Add exception to cutting rules: ...followed by PEDQKR
EXECPT_IETD.rules.append(EXECPT_P)
......@@ -537,18 +537,18 @@ CPT_ENZ += 1
# Caspase 9
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
# RULES: cut after LEHD,
# RULES: cleaves after LEHD,
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cut after D, preceded by H
EXECPT_HD = rule.Rule(-1, "H", False, -1) # Never cleaves after D, preceded by H
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by H, preceded by E
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by H, preceded by E
EXECPT_LEHD = rule.Rule(-3, "L", True, -1) # Always cut after D, preceded by H, preceded by E, preceded by L
EXECPT_LEHD = rule.Rule(-3, "L", True, -1) # Always cleaves after D, preceded by H, preceded by E, preceded by L
# Add exception to cutting rules: ...preceded by L/W
EXECPT_EHD.rules.append(EXECPT_LEHD)
......@@ -570,23 +570,23 @@ CPT_ENZ += 1
# Caspase 10
# https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
# RULES: cut after IEAD,
# RULES: cleaves after IEAD,
ENZ = []
# Cutting rule
AFTER_D = rule.Rule(0, "D", False, 1) # Never cut after D, except...
AFTER_D = rule.Rule(0, "D", False, 1) # Never cleaves after D, except...
# Exceptions
EXECPT_AD = rule.Rule(-1, "A", False, -1) # Never cut after D, preceded by A
EXECPT_AD = rule.Rule(-1, "A", False, -1) # Never cleaves after D, preceded by A
EXECPT_EHD = rule.Rule(-2, "E", False, -1) # Never cut after D, preceded by H, preceded by E
EXECPT_EAD = rule.Rule(-2, "E", False, -1) # Never cleaves after D, preceded by A, preceded by E
EXECPT_IEHD = rule.Rule(-3, "I", True, -1) # Always cut after D, preceded by H, preceded by E, preceded by I
EXECPT_IEAD = rule.Rule(-3, "I", True, -1) # Always cleaves after D, preceded by A, preceded by E, preceded by I
# Add exception to cutting rules: ...preceded by L/W
EXECPT_EHD.rules.append(EXECPT_IEHD)
EXECPT_EAD.rules.append(EXECPT_IEAD)
EXECPT_AD.rules.append(EXECPT_EHD)
EXECPT_AD.rules.append(EXECPT_EAD)
# Add exception to cutting rules
AFTER_D.rules.append(EXECPT_AD)
......@@ -714,44 +714,44 @@ CPT_ENZ += 1
# RULES: after K if preceded by D/E D/E D/E D/E (P5 not in expasy)
ENZ = []
# Cutting rule
AFTER_K = rule.Rule(0, "K", False, 1) # Never cut after K, except...
AFTER_K = rule.Rule(0, "K", False, 1) # Never cleaves after K, except...
# Exceptions
EXECPT_DK = rule.Rule(-1, "D", False, -1) # Never cut after K, preceded by D
EXECPT_EK = rule.Rule(-1, "E", False, -1) # Never cut after K, preceded by E
EXECPT_DDK = rule.Rule(-2, "D", False, -1) # Never cut after K, preceded by D, preceded by D
EXECPT_DEK = rule.Rule(-2, "D", False, -1) # Never cut after K, preceded by E, preceded by D
EXECPT_EDK = rule.Rule(-2, "E", False, -1) # Never cut after K, preceded by D, preceded by E
EXECPT_EEK = rule.Rule(-2, "E", False, -1) # Never cut after K, preceded by E, preceded by E
EXECPT_DDDK = rule.Rule(-3, "D", False, -1) # Never cut after K, preceded by D, preceded by D, preceded by D
EXECPT_DDEK = rule.Rule(-3, "D", False, -1) # Never cut after K, preceded by E, preceded by D, preceded by D
EXECPT_DEDK = rule.Rule(-3, "D", False, -1) # Never cut after K, preceded by D, preceded by E, preceded by D
EXECPT_DEEK = rule.Rule(-3, "D", False, -1) # Never cut after K, preceded by E, preceded by E, preceded by D
EXECPT_EDDK = rule.Rule(-3, "E", False, -1) # Never cut after K, preceded by D, preceded by D, preceded by E
EXECPT_EDEK = rule.Rule(-3, "E", False, -1) # Never cut after K, preceded by E, preceded by D, preceded by E
EXECPT_EEDK = rule.Rule(-3, "E", False, -1) # Never cut after K, preceded by D, preceded by E, preceded by E
EXECPT_EEEK = rule.Rule(-3, "E", False, -1) # Never cut after K, preceded by E, preceded by E, preceded by E
EXECPT_DK = rule.Rule(-1, "D", False, -1) # Never cleaves after K, preceded by D
EXECPT_EK = rule.Rule(-1, "E", False, -1) # Never cleaves after K, preceded by E
EXECPT_DDK = rule.Rule(-2, "D", False, -1) # Never cleaves after K, preceded by D, preceded by D
EXECPT_DEK = rule.Rule(-2, "D", False, -1) # Never cleaves after K, preceded by E, preceded by D
EXECPT_EDK = rule.Rule(-2, "E", False, -1) # Never cleaves after K, preceded by D, preceded by E
EXECPT_EEK = rule.Rule(-2, "E", False, -1) # Never cleaves after K, preceded by E, preceded by E
EXECPT_DDDK = rule.Rule(-3, "D", False, -1) # Never cleaves after K, preceded by D, preceded by D, preceded by D
EXECPT_DDEK = rule.Rule(-3, "D", False, -1) # Never cleaves after K, preceded by E, preceded by D, preceded by D
EXECPT_DEDK = rule.Rule(-3, "D", False, -1) # Never cleaves after K, preceded by D, preceded by E, preceded by D
EXECPT_DEEK = rule.Rule(-3, "D", False, -1) # Never cleaves after K, preceded by E, preceded by E, preceded by D
EXECPT_EDDK = rule.Rule(-3, "E", False, -1) # Never cleaves after K, preceded by D, preceded by D, preceded by E