Modify function to load .cml graph data where an outer cml element is added to the data file (dataset ACE).

gklearn/dataset/file_managers.py

@@ -537,16 +537,18 @@ class DataLoader():
 
 
 	def load_cml(self, filename): # @todo: directed graphs.
+		# @todo: what is "atomParity" and "bondStereo" in the data file?
 		from os.path import basename
 		import networkx as nx
 		import xml.etree.ElementTree as ET
 
+		xmlns = '{http://www.xml-cml.org/schema}' # @todo: why this has to be added?
 		tree = ET.parse(filename)
 		root = tree.getroot()
 		index = 0
-		g = nx.Graph(filename=basename(filename), name=root.attrib['id'])
+		g_id = root.find(xmlns + 'molecule').attrib['id']
+		g = nx.Graph(filename=basename(filename), name=g_id)
 		dic = {}  # used to retrieve incident nodes of edges
-		xmlns = '{http://www.xml-cml.org/schema}' # @todo: why this has to be added?
 		for atom in root.iter(xmlns + 'atom'):
 			dic[atom.attrib['id']] = index
 			labels = {}

gklearn/dataset/metadata.py

@@ -33,6 +33,7 @@ GREYC_META = {
 		'train_valid_test': [],
 		'stereoisomerism': True,
 		'load_files': ['data.ds'],
+		'extra_params': {'gformat': 'cml'}
 	},
 	'Acyclic': {
 		'database': 'greyc',
@@ -224,7 +225,8 @@ GREYC_META = {
 		'domain': 'small molecules',
 		'train_valid_test': [],
 		'stereoisomerism': True,
-		'load_files': [],
+		'load_files': ['data.txt'],
+		'extra_params': {'gformat': 'cml'}
 	},
 }