add a negation decorator to refine motif definitions

build/lib/glycowork/glycan_data/glycan_motifs.csv

@@ -125,12 +125,12 @@ Gala_series,Gal(a1-4)Gal1Cer,"['flexible', 'terminal']"
 LPS_core,Kdo(a2-4)Kdo(a2-6)GlcN(b1-6)GlcN,"['flexible', 'flexible', 'flexible', 'terminal']"
 Nglycan_complex,GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc,"['flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'terminal']"
 Nglycan_complex2,GlcNAc(b1-4)Man(a1-3)[GlcNAc(b1-4)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc,"['flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'terminal']"
-Oglycan_core1,Gal(b1-3)GalNAc,"['flexible', 'terminal']"
+Oglycan_core1,Gal(b1-3)[!GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'terminal']"
 Oglycan_core2,Gal(b1-3)[GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'flexible']"
-Oglycan_core3,GlcNAc(b1-3)GalNAc,"['flexible', 'terminal']"
+Oglycan_core3,GlcNAc(b1-3)[!GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'terminal']"
 Oglycan_core4,GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'flexible']"
 Oglycan_core5,GalNAc(a1-3)GalNAc,"['flexible', 'terminal']"
-Oglycan_core6,GlcNAc(b1-6)GalNAc,"['flexible', 'terminal']"
+Oglycan_core6,GlcNAc(b1-6)[!GlcNAc(b1-3)]GalNAc,"['flexible', 'flexible', 'terminal']"
 Oglycan_core7,GalNAc(a1-6)GalNAc,"['flexible', 'terminal']"
 Xylogalacturonan,Xyl(a1-3)GalA(a1-4)[Xyl(a1-3)]GalA,"['flexible', 'flexible', 'flexible', 'flexible']"
 Sialosylparagloboside,Sia(a2-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)Glc1Cer,"['terminal', 'flexible', 'flexible', 'flexible', 'terminal']"

build/lib/glycowork/motif/graph.py

@@ -248,6 +248,18 @@ def expand_termini_list(motif, termini_list):
   return t_list
 
 
+def handle_negation(original_func):
+  def wrapper(glycan, motif, *args, **kwargs):
+    if isinstance(motif, str) and '!' in motif:
+      return subgraph_isomorphism_with_negation(glycan, motif, *args, **kwargs)
+    elif hasattr(motif, 'nodes') and any('!' in data.get('string_labels', '') for _, data in motif.nodes(data = True)):
+      return subgraph_isomorphism_with_negation(glycan, motif, *args, **kwargs)
+    else:
+      return original_func(glycan, motif, *args, **kwargs)
+  return wrapper
+
+
+@handle_negation
 def subgraph_isomorphism(glycan, motif, termini_list = [], count = False, return_matches = False):
   """returns True if motif is in glycan and False if not\n
   | Arguments:
@@ -264,6 +276,8 @@ def subgraph_isomorphism(glycan, motif, termini_list = [], count = False, return
   if isinstance(glycan, str) and isinstance(motif, str):
     if motif.count('(') > glycan.count('('):
       return (0, []) if return_matches else 0 if count else False
+    if not count and not return_matches and motif in glycan:
+      return True
     motif_comp = min_process_glycans([motif, glycan])
     if 'O' in glycan + motif:
       glycan, motif = [re.sub(r"(?<=[a-zA-Z])\d+(?=[a-zA-Z])", 'O', g).replace('NeuOAc', 'Neu5Ac').replace('NeuOGc', 'Neu5Gc') for g in [glycan, motif]]
@@ -322,6 +336,46 @@ def subgraph_isomorphism(glycan, motif, termini_list = [], count = False, return
   return False if not return_matches else (0, [])
 
 
+def subgraph_isomorphism_with_negation(glycan, motif, termini_list = [], count = False, return_matches = False):
+  """returns True if motif is in glycan and False if not\n
+  | Arguments:
+  | :-
+  | glycan (string or networkx): glycan in IUPAC-condensed format or as graph in NetworkX format
+  | motif (string or networkx): glycan motif in IUPAC-condensed format or as graph in NetworkX format
+  | termini_list (list): list of monosaccharide positions (from 'terminal', 'internal', and 'flexible')
+  | count (bool): whether to return the number or absence/presence of motifs; default:False
+  | return_matches (bool): whether the matched subgraphs in input glycan should be returned as node lists as an additional output; default:False\n
+  | Returns:
+  | :-
+  | Returns True if motif is in glycan and False if not
+  """
+  if isinstance(motif, str):
+    temp = motif[motif.index('!'):]
+    motif_stub = (motif[:motif.index('!')] + temp[temp.index(')')+1:]).replace('[]', '')
+  else:
+    motif_stub = motif.copy()
+    nodes_to_remove = {node for node, data in motif_stub.nodes(data = True)
+                       if '!' in data.get('string_labels', '')}
+    nodes_to_remove.update({node + 1 for node in nodes_to_remove if node + 1 in motif_stub})
+    motif_stub.remove_nodes_from(nodes_to_remove)
+  res = subgraph_isomorphism(glycan, motif_stub, termini_list = termini_list, count = count, return_matches = return_matches)
+  if not res or (isinstance(res, tuple) and not res[0]):
+    return res
+  else:
+    if isinstance(motif, str):
+      motif_too_large = motif.replace('!', '')
+    else:
+      motif_too_large = motif.copy()
+      for node, data in motif_too_large.nodes(data = True):
+        if '!' in data.get('string_labels', ''):
+          motif_too_large.nodes[node]['string_labels'] = data['string_labels'].replace('!', '')
+    res2 = subgraph_isomorphism(glycan, motif_too_large, termini_list = termini_list, count = count, return_matches = return_matches)
+    if res2:
+      return (0, []) if return_matches else 0 if count else False
+    else:
+      return res
+
+
 def generate_graph_features(glycan, glycan_graph = True, label = 'network'):
     """compute graph features of glycan\n
     | Arguments:

glycowork/glycan_data/glycan_motifs.csv

@@ -125,12 +125,12 @@ Gala_series,Gal(a1-4)Gal1Cer,"['flexible', 'terminal']"
 LPS_core,Kdo(a2-4)Kdo(a2-6)GlcN(b1-6)GlcN,"['flexible', 'flexible', 'flexible', 'terminal']"
 Nglycan_complex,GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc,"['flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'terminal']"
 Nglycan_complex2,GlcNAc(b1-4)Man(a1-3)[GlcNAc(b1-4)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc,"['flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'flexible', 'terminal']"
-Oglycan_core1,Gal(b1-3)GalNAc,"['flexible', 'terminal']"
+Oglycan_core1,Gal(b1-3)[!GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'terminal']"
 Oglycan_core2,Gal(b1-3)[GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'flexible']"
-Oglycan_core3,GlcNAc(b1-3)GalNAc,"['flexible', 'terminal']"
+Oglycan_core3,GlcNAc(b1-3)[!GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'terminal']"
 Oglycan_core4,GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc,"['flexible', 'flexible', 'flexible']"
 Oglycan_core5,GalNAc(a1-3)GalNAc,"['flexible', 'terminal']"
-Oglycan_core6,GlcNAc(b1-6)GalNAc,"['flexible', 'terminal']"
+Oglycan_core6,GlcNAc(b1-6)[!GlcNAc(b1-3)]GalNAc,"['flexible', 'flexible', 'terminal']"
 Oglycan_core7,GalNAc(a1-6)GalNAc,"['flexible', 'terminal']"
 Xylogalacturonan,Xyl(a1-3)GalA(a1-4)[Xyl(a1-3)]GalA,"['flexible', 'flexible', 'flexible', 'flexible']"
 Sialosylparagloboside,Sia(a2-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)Glc1Cer,"['terminal', 'flexible', 'flexible', 'flexible', 'terminal']"

glycowork/motif/graph.py

@@ -248,6 +248,18 @@ def expand_termini_list(motif, termini_list):
   return t_list
 
 
+def handle_negation(original_func):
+  def wrapper(glycan, motif, *args, **kwargs):
+    if isinstance(motif, str) and '!' in motif:
+      return subgraph_isomorphism_with_negation(glycan, motif, *args, **kwargs)
+    elif hasattr(motif, 'nodes') and any('!' in data.get('string_labels', '') for _, data in motif.nodes(data = True)):
+      return subgraph_isomorphism_with_negation(glycan, motif, *args, **kwargs)
+    else:
+      return original_func(glycan, motif, *args, **kwargs)
+  return wrapper
+
+
+@handle_negation
 def subgraph_isomorphism(glycan, motif, termini_list = [], count = False, return_matches = False):
   """returns True if motif is in glycan and False if not\n
   | Arguments:
@@ -264,6 +276,8 @@ def subgraph_isomorphism(glycan, motif, termini_list = [], count = False, return
   if isinstance(glycan, str) and isinstance(motif, str):
     if motif.count('(') > glycan.count('('):
       return (0, []) if return_matches else 0 if count else False
+    if not count and not return_matches and motif in glycan:
+      return True
     motif_comp = min_process_glycans([motif, glycan])
     if 'O' in glycan + motif:
       glycan, motif = [re.sub(r"(?<=[a-zA-Z])\d+(?=[a-zA-Z])", 'O', g).replace('NeuOAc', 'Neu5Ac').replace('NeuOGc', 'Neu5Gc') for g in [glycan, motif]]
@@ -322,6 +336,46 @@ def subgraph_isomorphism(glycan, motif, termini_list = [], count = False, return
   return False if not return_matches else (0, [])
 
 
+def subgraph_isomorphism_with_negation(glycan, motif, termini_list = [], count = False, return_matches = False):
+  """returns True if motif is in glycan and False if not\n
+  | Arguments:
+  | :-
+  | glycan (string or networkx): glycan in IUPAC-condensed format or as graph in NetworkX format
+  | motif (string or networkx): glycan motif in IUPAC-condensed format or as graph in NetworkX format
+  | termini_list (list): list of monosaccharide positions (from 'terminal', 'internal', and 'flexible')
+  | count (bool): whether to return the number or absence/presence of motifs; default:False
+  | return_matches (bool): whether the matched subgraphs in input glycan should be returned as node lists as an additional output; default:False\n
+  | Returns:
+  | :-
+  | Returns True if motif is in glycan and False if not
+  """
+  if isinstance(motif, str):
+    temp = motif[motif.index('!'):]
+    motif_stub = (motif[:motif.index('!')] + temp[temp.index(')')+1:]).replace('[]', '')
+  else:
+    motif_stub = motif.copy()
+    nodes_to_remove = {node for node, data in motif_stub.nodes(data = True)
+                       if '!' in data.get('string_labels', '')}
+    nodes_to_remove.update({node + 1 for node in nodes_to_remove if node + 1 in motif_stub})
+    motif_stub.remove_nodes_from(nodes_to_remove)
+  res = subgraph_isomorphism(glycan, motif_stub, termini_list = termini_list, count = count, return_matches = return_matches)
+  if not res or (isinstance(res, tuple) and not res[0]):
+    return res
+  else:
+    if isinstance(motif, str):
+      motif_too_large = motif.replace('!', '')
+    else:
+      motif_too_large = motif.copy()
+      for node, data in motif_too_large.nodes(data = True):
+        if '!' in data.get('string_labels', ''):
+          motif_too_large.nodes[node]['string_labels'] = data['string_labels'].replace('!', '')
+    res2 = subgraph_isomorphism(glycan, motif_too_large, termini_list = termini_list, count = count, return_matches = return_matches)
+    if res2:
+      return (0, []) if return_matches else 0 if count else False
+    else:
+      return res
+
+
 def generate_graph_features(glycan, glycan_graph = True, label = 'network'):
     """compute graph features of glycan\n
     | Arguments:

glycowork/motif/regex.py

@@ -339,10 +339,7 @@ def process_pattern(p, p2, ggraph, glycan, match_location):
   | :-
   | Returns list of matches as list of node indices
   """
-  if isinstance(p2, dict):
-    return process_complex_pattern(p, p2, ggraph, glycan, match_location)
-  else:
-    return process_simple_pattern(p2, ggraph, match_location)
+  return process_complex_pattern(p, p2, ggraph, glycan, match_location) if isinstance(p2, dict) else process_simple_pattern(p2, ggraph, match_location)
 
 
 def match_it_up(pattern_components, glycan, ggraph):