Grammar update and minor fixes in translation

glyles/glycans/mono/reactor.py

@@ -65,7 +65,7 @@
     "Thr": "N[C@@H](C(=O)O)[C@@H](O)C",
     "triN": "N=[N+]=[N-]",
     "Troc": "C(=O)OCC(Cl)(Cl)Cl",
-    "Ts": "S(=O)(=O)c2ccc(C)cc2",
+    "Ts": "OS(=O)(=O)c2ccc(C)cc2",
     "Ulo": "OC(c2ccccc2)(c2ccccc2(Cl))CCN(C)C",
 
     # COH land
@@ -137,32 +137,32 @@
     "tBu": "OC(C)(C)C",
 
     # Methan, Ethan, Propan, ...
-    "Me": "C" * 1,
-    "Et": "C" * 2,
-    "Pr": "C" * 3,
-    "Prop": "C" * 3,
-    "Bu": "C" * 4,
-    "Pe": "C" * 5,
-    "Hx": "C" * 6,
-    "Hp": "C" * 7,
-    "Oc": "C" * 8,
-    "Nn": "C" * 9,
-    "Dec": "C" * 10,
-    "Und": "C" * 11,
-    "Dod": "C" * 12,
-    # "Me": "O" + "C" * 1,
-    # "Et": "O" + "C" * 2,
-    # "Pr": "O" + "C" * 3,
-    # "Prop": "O" + "C" * 3,
-    # "Bu": "O" + "C" * 4,
-    # "Pe": "O" + "C" * 5,
-    # "Hx": "O" + "C" * 6,
-    # "Hp": "O" + "C" * 7,
-    # "Oc": "O" + "C" * 8,
-    # "Nn": "O" + "C" * 9,
-    # "Dec": "O" + "C" * 10,
-    # "Und": "O" + "C" * 11,
-    # "Dod": "O" + "C" * 12,
+    # "Me": "C" * 1,
+    # "Et": "C" * 2,
+    # "Pr": "C" * 3,
+    # "Prop": "C" * 3,
+    # "Bu": "C" * 4,
+    # "Pe": "C" * 5,
+    # "Hx": "C" * 6,
+    # "Hp": "C" * 7,
+    # "Oc": "C" * 8,
+    # "Nn": "C" * 9,
+    # "Dec": "C" * 10,
+    # "Und": "C" * 11,
+    # "Dod": "C" * 12,
+    "Me": "O" + "C" * 1,
+    "Et": "O" + "C" * 2,
+    "Pr": "O" + "C" * 3,
+    "Prop": "O" + "C" * 3,
+    "Bu": "O" + "C" * 4,
+    "Pe": "O" + "C" * 5,
+    "Hx": "O" + "C" * 6,
+    "Hp": "O" + "C" * 7,
+    "Oc": "O" + "C" * 8,
+    "Nn": "O" + "C" * 9,
+    "Dec": "O" + "C" * 10,
+    "Und": "O" + "C" * 11,
+    "Dod": "O" + "C" * 12,
     # ... and their acids
     "But": "OC(=O)" + "C" * 2,
     "Vl": "OC(=O)" + "C" * 4,

glyles/glycans/poly/walker.py

@@ -160,7 +160,8 @@ def __add_edge(self, parent, child, con) -> bool:
                 con = con[0] + bond + con[1:]
             con = "(" + con + ")"
         self.g.add_edge(parent, child, type=con)
-        return "?" not in con
+        # Identify standard and narrow wildcard connections
+        return "?" not in con and "/" not in con
 
     def build_recipe(self, node):
         recipe = []

glyles/grammar/Glycan.g4

@@ -37,7 +37,7 @@ modi:
     | HEADD DASH
     | DASH END;
 qnum:
-	QMARK | NUM;
+	QMARK | NUM (SLASH NUM)*;
 typi:
 	TYPE | QMARK;
 bridge:
@@ -67,7 +67,7 @@ FG:
     | 'MOM' | 'Mon' | 'Myr' | 'NAP' | 'Ner' | 'Nno' | 'Non' | 'Oco' | 'Ole' | 'oNB' | 'Orn' | 'Pam' | 'Pic' | 'Piv'
     | 'PMB' | 'PMP' | 'Poc' | 'Pro' | 'Pyr' | 'Ser' | 'Sin' | 'Ste' | 'TBS' | 'tBu' | 'TCA' | 'TES' | 'TFA' | 'THP'
     | 'Thr' | 'Tig' | 'TMS' | 'Udo' | 'Ulo' | 'ulo' | 'Und' | 'Vac' | 'Ac' | 'Al' | 'Am' | 'Bn' | 'Br' | 'Bu' | 'Bz'
-    | 'Cl' | 'Cm' | 'DD' | 'DL' | 'en' | 'Et' | 'Fo' | 'Gc' | 'Hp' | 'Hx' | 'LD' | 'LL' | 'Me' | 'N3' | 'Nn' | 'Ns'
+    | 'Cl' | 'Cm' | 'DD' | 'DL' | 'en' | 'Et' | 'Fo' | 'Gc' | 'Hp' | 'Hx' | 'LD' | 'LL' | 'Me' | 'Nn' | 'Ns'
     | 'Oc' | 'Pe' | 'Ph' | 'Pp' | 'Pr' | 'Tf' | 'Tr' | 'Ts' | 'Vl' | 'A' | 'F' | 'I' | 'S';
 ANHYDRO:
     'Anhydro';
@@ -117,6 +117,8 @@ EQ:
 	'=';
 I:
 	'i';
+SLASH:
+    '/';
 QMARK:
 	'?';
 

glyles/grammar/Glycan.tokens

@@ -30,7 +30,8 @@ E=29
 T=30
 EQ=31
 I=32
-QMARK=33
+SLASH=33
+QMARK=34
 '#'=1
 ' '=2
 'C'=4
@@ -55,4 +56,5 @@ QMARK=33
 't'=30
 '='=31
 'i'=32
-'?'=33
+'/'=33
+'?'=34

glyles/grammar/GlycanLexer.tokens

@@ -30,7 +30,8 @@ E=29
 T=30
 EQ=31
 I=32
-QMARK=33
+SLASH=33
+QMARK=34
 '#'=1
 ' '=2
 'C'=4
@@ -55,4 +56,5 @@ QMARK=33
 't'=30
 '='=31
 'i'=32
-'?'=33
+'/'=33
+'?'=34