Add 7 enzymes

docs/enzymes.rst

@@ -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)

tests/test_RapidPeptidesGenerator.py

@@ -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]"