Update function gklearn.utils.graph_file.load_ct() for CTFile V2000.

gklearn/utils/graph_files.py

@@ -127,7 +127,7 @@ def save_dataset(Gn, y, gformat='gxl', group=None, filename='gfile', xparams=Non
 			fgroup.close()
 
 
-def load_ct(filename):
+def load_ct(filename): # @todo: this function is only tested on CTFile V2000; header not considered; only simple cases (atoms and bonds are considered.)
 	"""load data from a Chemical Table (.ct) file.
 
 	Notes
@@ -154,30 +154,65 @@ def load_ct(filename):
 	g = nx.Graph()
 	with open(filename) as f:
 		content = f.read().splitlines()
-		g = nx.Graph(
-			name = str(content[0]),
-			filename = basename(filename))  # set name of the graph
-		tmp = content[1].split(" ")
-		if tmp[0] == '':
-			nb_nodes = int(tmp[1])  # number of the nodes
-			nb_edges = int(tmp[2])  # number of the edges
-		else:
-			nb_nodes = int(tmp[0])
-			nb_edges = int(tmp[1])
-			# patch for compatibility : label will be removed later
-		for i in range(0, nb_nodes):
-			tmp = content[i + 2].split(" ")
+		g = nx.Graph(name=str(content[0]), filename=basename(filename))  # set name of the graph
+
+		# read the counts line.
+		tmp = content[1].split(' ')
+		tmp = [x for x in tmp if x != '']
+		nb_atoms = int(tmp[0].strip())  # number of atoms
+		nb_bonds = int(tmp[1].strip())  # number of bonds
+		count_line_tags = ['number_of_atoms', 'number_of_bonds', 'number_of_atom_lists', '', 'chiral_flag', 'number_of_stext_entries', '', '', '', '', 'number_of_properties', 'CT_version']
+		i = 0
+		while i < len(tmp):
+			if count_line_tags[i] != '': # if not obsoleted
+				g.graph[count_line_tags[i]] = tmp[i].strip()
+			i += 1
+		
+		# read the atom block.
+		atom_tags = ['x', 'y', 'z', 'atom_symbol', 'mass_difference', 'charge', 'atom_stereo_parity', 'hydrogen_count_plus_1', 'stereo_care_box', 'valence', 'h0_designator', '', '', 'atom_atom_mapping_number', 'inversion_retention_flag', 'exact_change_flag']
+		for i in range(0, nb_atoms):
+			tmp = content[i + 2].split(' ')
 			tmp = [x for x in tmp if x != '']
-			g.add_node(i, atom=tmp[3].strip(), 
-					   label=[item.strip() for item in tmp[3:]], 
-					   attributes=[item.strip() for item in tmp[0:3]])
-		for i in range(0, nb_edges):
-			tmp = content[i + g.number_of_nodes() + 2].split(" ")
+			g.add_node(i)
+			j = 0
+			while j < len(tmp):
+				if atom_tags[j] != '':
+					g.nodes[i][atom_tags[j]] = tmp[j].strip()
+				j += 1
+				
+		# read the bond block.
+		bond_tags = ['first_atom_number', 'second_atom_number', 'bond_type', 'bond_stereo', '', 'bond_topology', 'reacting_center_status']
+		for i in range(0, nb_bonds):
+			tmp = content[i + g.number_of_nodes() + 2].split(' ')
 			tmp = [x for x in tmp if x != '']
-			g.add_edge(int(tmp[0]) - 1, int(tmp[1]) - 1,
-					   bond_type=tmp[2].strip(),
-					   label=[item.strip() for item in tmp[2:]])
-	return g
+			n1, n2 = int(tmp[0].strip()) - 1, int(tmp[1].strip()) - 1
+			g.add_edge(n1, n2)
+			j = 2
+			while j < len(tmp):
+				if bond_tags[j] != '':
+					g.edges[(n1, n2)][bond_tags[j]] = tmp[j].strip()
+				j += 1
+				
+	# get label names.
+	label_names = {'node_labels': [], 'edge_labels': [], 'node_attrs': [], 'edge_attrs': []}
+	atom_symbolic = [0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, None, None, 1, 1, 1]
+	for nd in g.nodes():
+		for key in g.nodes[nd]:
+			if atom_symbolic[atom_tags.index(key)] == 1:
+				label_names['node_labels'].append(key)
+			else:
+				label_names['node_attrs'].append(key)
+		break
+	bond_symbolic = [None, None, 1, 1, None, 1, 1]
+	for ed in g.edges():
+		for key in g.edges[ed]:
+			if bond_symbolic[bond_tags.index(key)] == 1:
+				label_names['edge_labels'].append(key)
+			else:
+				label_names['edge_attrs'].append(key)
+		break
+		
+	return g, label_names
 
 
 def load_gxl(filename): # @todo: directed graphs.
@@ -678,11 +713,7 @@ def load_from_ds(filename, filename_targets):
 
 	Note these graph formats are checked automatically by the extensions of 
 	graph files.
-	"""
-	def append_label_names(label_names, new_names):
-		for key, val in label_names.items():
-			label_names[key] += [name for name in new_names[key] if name not in val]
-		
+	"""		
 	dirname_dataset = dirname(filename)
 	data = []
 	y = []
@@ -694,8 +725,9 @@ def load_from_ds(filename, filename_targets):
 			for i in range(0, len(content)):
 				tmp = content[i].split(' ')
 				# remove the '#'s in file names
-				data.append(
-					load_ct(dirname_dataset + '/' + tmp[0].replace('#', '', 1)))
+				g, l_names = load_ct(dirname_dataset + '/' + tmp[0].replace('#', '', 1))
+				data.append(g)
+				__append_label_names(label_names, l_names)
 				y.append(float(tmp[1]))
 		elif extension == 'gxl':
 			for i in range(0, len(content)):
@@ -703,22 +735,23 @@ def load_from_ds(filename, filename_targets):
 				# remove the '#'s in file names
 				g, l_names = load_gxl(dirname_dataset + '/' + tmp[0].replace('#', '', 1))
 				data.append(g)
-				append_label_names(label_names, l_names)
+				__append_label_names(label_names, l_names)
 				y.append(float(tmp[1]))
 	else:  # y in a seperate file
 		if extension == 'ct':
 			for i in range(0, len(content)):
 				tmp = content[i]
 				# remove the '#'s in file names
-				data.append(
-					load_ct(dirname_dataset + '/' + tmp.replace('#', '', 1)))
+				g, l_names = load_ct(dirname_dataset + '/' + tmp.replace('#', '', 1))
+				data.append(g)
+				__append_label_names(label_names, l_names)
 		elif extension == 'gxl':
 			for i in range(0, len(content)):
 				tmp = content[i]
 				# remove the '#'s in file names
-				g, l_names = load_gxl(dirname_dataset + '/' + tmp[0].replace('#', '', 1))
+				g, l_names = load_gxl(dirname_dataset + '/' + tmp.replace('#', '', 1))
 				data.append(g)
-				append_label_names(label_names, l_names)
+				__append_label_names(label_names, l_names)
 															   
 		content_y = open(filename_targets).read().splitlines()
 		# assume entries in filename and filename_targets have the same order.
@@ -728,7 +761,12 @@ def load_from_ds(filename, filename_targets):
 			y.append(float(tmp[2]))
 			
 	return data, y, label_names
-			
+
+
+def __append_label_names(label_names, new_names):
+	for key, val in label_names.items():
+		label_names[key] += [name for name in new_names[key] if name not in val]
+		
 			
 if __name__ == '__main__':	
 #	### Load dataset from .ds file.
@@ -736,24 +774,24 @@ if __name__ == '__main__':
 #	ds = {'name': 'Alkane', 'dataset': '../../datasets/Alkane/dataset.ds',
 #		'dataset_y': '../../datasets/Alkane/dataset_boiling_point_names.txt'}
 #	Gn, y = loadDataset(ds['dataset'], filename_y=ds['dataset_y'])
-##	ds = {'name': 'Acyclic', 'dataset': '../../datasets/acyclic/dataset_bps.ds'}  # node symb
-##	Gn, y = loadDataset(ds['dataset'])
+	ds_file = '../../datasets/acyclic/dataset_bps.ds'  # node symb
+	Gn, targets, label_names = load_dataset(ds_file)
 ##	ds = {'name': 'MAO', 'dataset': '../../datasets/MAO/dataset.ds'} # node/edge symb
 ##	Gn, y = loadDataset(ds['dataset'])
 ##	ds = {'name': 'PAH', 'dataset': '../../datasets/PAH/dataset.ds'} # unlabeled
 ##	Gn, y = loadDataset(ds['dataset'])
-#	print(Gn[1].nodes(data=True))
-#	print(Gn[1].edges(data=True))
-#	print(y[1])
-	
-	# .gxl file.
-	ds = {'name': 'monoterpenoides', 
-		  'dataset': '../../datasets/monoterpenoides/dataset_10+.ds'}  # node/edge symb
-	Gn, y, label_names = load_dataset(ds['dataset'])
 	print(Gn[1].graph)
 	print(Gn[1].nodes(data=True))
 	print(Gn[1].edges(data=True))
-	print(y[1])
+	print(targets[1])
+	
+# 	# .gxl file.
+# 	ds_file = '../../datasets/monoterpenoides/dataset_10+.ds'  # node/edge symb
+# 	Gn, y, label_names = load_dataset(ds_file)
+# 	print(Gn[1].graph)
+# 	print(Gn[1].nodes(data=True))
+# 	print(Gn[1].edges(data=True))
+# 	print(y[1])
 	
 #	### Convert graph from one format to another.
 #	# .gxl file.