More bug fixes in parsing

kalininalab · Feb 21, 2025 · 5a7f82d · 5a7f82d
1 parent c2d7e37
commit 5a7f82d
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Showing 5 changed files with 10 additions and 17 deletions.
diff --git a/glyles/converter.py b/glyles/converter.py
@@ -5,8 +5,8 @@
 from joblib import Parallel, delayed, parallel_backend
 
 from glyles.glycans.poly.gwb_glycan import GWBGlycan
-from glyles.glycans.utils import ParseError
 from glyles.glycans.poly.glycan import Glycan
+from glyles.glycans.utils import ParseError
 
 
 def preprocess_glycans(glycan, glycan_list, glycan_file):
@@ -207,4 +207,4 @@ def generate(glycan, full):
 
 if __name__ == "__main__":
     # print(convert("GalNAc"))
-    print(Glycan("GalNAc").get_smiles())
+    print(Glycan("GalNAc").to_iupac())
diff --git a/glyles/glycans/poly/glycan.py b/glyles/glycans/poly/glycan.py
@@ -414,7 +414,3 @@ def parse(self):
                           f"Error message: {msg}")
             self.glycan_smiles = ""
             raise e
-
-
-if __name__ == "__main__":
-    print(Glycan("dTal").get_smiles())
diff --git a/glyles/glycans/poly/gwb_glycan.py b/glyles/glycans/poly/gwb_glycan.py
@@ -3,12 +3,12 @@
 from antlr4 import CommonTokenStream, InputStream
 import networkx as nx
 
-from glyles.glycans.poly.gwb_walker import GWBTreeWalker
+from glyles.glycans.poly.glycan import Glycan, prepare
 from glyles.glycans.poly.merger import Merger
+from glyles.glycans.poly.gwb_walker import GWBTreeWalker
 from glyles.glycans.utils import ParseError
 from glyles.gwb.GWBLexer import GWBLexer
 from glyles.gwb.GWBParser import GWBParser
-from glyles.glycans.poly.glycan import Glycan, prepare
 
 
 def graph_to_string_int(graph: nx.DiGraph, node2label: callable) -> str:
@@ -78,7 +78,7 @@ def parse(self):
             if "$" in self.iupac:
                 self.iupac = self.iupac[:self.iupac.index("$")]
             self.iupac += "$"
-            prepare(self.iupac)
+            self.iupac = prepare(self.iupac)
             stream = InputStream(data=self.iupac)
             lexer = GWBLexer(stream)
             token = CommonTokenStream(lexer)
@@ -106,7 +106,3 @@ def parse(self):
                           f"Error message: {msg}")
             self.glycan_smiles = ""
             raise e
-
-
-if __name__ == "__main__":
-    print(GWBGlycan("freeEnd--?b1D-GlcNAc,p(--6a1L-Fuc,p)--4b1D-GlcNAc,p--4b1D-Man,p(--3a1D-Man,p(--??1D-GlcNAc,p--??1D-Gal,p--??2D-NeuAc,p)--??1D-GlcNAc,p--??1D-Gal,p--??2D-NeuAc,p--??2D-NeuAc,p)--6a1D-Man,p(--??1D-Man,p)--??1D-Man,p$MONO,Und,-2H,0,freeEnd").to_iupac(slim=True))
diff --git a/glyles/glycans/poly/gwb_walker.py b/glyles/glycans/poly/gwb_walker.py
@@ -71,7 +71,7 @@ def add_edge(self, parent, child, con, floating: bool = False) -> bool:
                 return True
             self.g.add_edge(parent, child, type=con)
             return "?" not in con and "/" not in con
-        return False
+        return True  # parent == -1 and not floating
 
     def update_node(self, node_id):
         recipe = self.g.nodes[node_id]["update"]

diff --git a/glyles/glycans/poly/walker.py b/glyles/glycans/poly/walker.py
@@ -2,6 +2,7 @@
 from antlr4 import ErrorNode, TerminalNode
 
 from glyles.glycans.utils import UnreachableError, ketoses2
+from glyles.gwb.GWBParser import GWBParser
 from glyles.iupac.IUPACLexer import IUPACLexer
 from glyles.iupac.IUPACParser import IUPACParser
 from glyles.gwb.GWBLexer import GWBLexer
@@ -165,12 +166,12 @@ def build_recipe(self, node):
         recipe = []
         for c in node.getChildren():
             if isinstance(c, TerminalNode):
-                recipe.append((str(c), IUPACLexer.SAC if isinstance(node, IUPACParser.SaciContext) else c.symbol.type))
+                recipe.append((str(c), IUPACLexer.SAC if isinstance(node, (IUPACParser.SaciContext, GWBParser.SaciContext)) else c.symbol.type))
             else:
                 tmp = self.build_recipe(c)
-                if isinstance(c, IUPACParser.ModiContext):
+                if isinstance(c, (IUPACParser.ModiContext, GWBParser.ModiContext)):
                     recipe.append(("".join([x[0] for x in tmp]), IUPACLexer.MOD))
-                elif isinstance(c, IUPACParser.SaciContext):
+                elif isinstance(c, (IUPACParser.SaciContext, GWBParser.SaciContext)):
                     recipe += [(x[0], IUPACLexer.SAC) for x in tmp]
                 else:
                     recipe += tmp