def __init__(self, smiles):
DGLGraph.__init__(self)
self.nodes_dict = {}
if smiles is None:
return
self.smiles = smiles
self.mol = get_mol(smiles)
# Stereo Generation
mol = Chem.MolFromSmiles(smiles)
self.smiles3D = Chem.MolToSmiles(mol, isomericSmiles=True)
self.smiles2D = Chem.MolToSmiles(mol)
self.stereo_cands = decode_stereo(self.smiles2D)
# cliques: a list of list of atom indices
cliques, edges = tree_decomp(self.mol)
root = 0
for i, c in enumerate(cliques):
cmol = get_clique_mol(self.mol, c)
csmiles = get_smiles(cmol)
self.nodes_dict[i] = dict(
smiles=csmiles,
mol=get_mol(csmiles),
clique=c,
)
if min(c) == 0:
root = i
self.add_nodes(len(cliques))
# The clique with atom ID 0 becomes root
if root > 0:
for attr in self.nodes_dict[0]:
self.nodes_dict[0][attr], self.nodes_dict[root][attr] = \
self.nodes_dict[root][attr], self.nodes_dict[0][attr]
src = np.zeros((len(edges) * 2, ), dtype='int')
dst = np.zeros((len(edges) * 2, ), dtype='int')
for i, (_x, _y) in enumerate(edges):
x = 0 if _x == root else root if _x == 0 else _x
y = 0 if _y == root else root if _y == 0 else _y
src[2 * i] = x
dst[2 * i] = y
src[2 * i + 1] = y
dst[2 * i + 1] = x
self.add_edges(src, dst)
for i in self.nodes_dict:
self.nodes_dict[i]['nid'] = i + 1
if self.out_degree(i) > 1: # Leaf node mol is not marked
set_atommap(self.nodes_dict[i]['mol'],
self.nodes_dict[i]['nid'])
self.nodes_dict[i]['is_leaf'] = (self.out_degree(i) == 1)
def __init__(self, smiles):
DGLGraph.__init__(self)
self.nodes_dict = {}
if smiles is None:
return
self.smiles = smiles
self.mol = get_mol(smiles)
"""Stereo Generation."""
mol = Chem.MolFromSmiles(smiles)
self.smiles2D = Chem.MolToSmiles(mol)
self.smiles3D = Chem.MolToSmiles(mol, isomericSmiles=True)
self.stereo_cands = decode_stereo(self.smiles2D)
"""Cliques: [[Neighbor Indices] for Atom in Atoms]"""
cliques, edges = tree_decomp(self.mol)
root = 0
for i, clique in enumerate(cliques):
cmol = get_clique_mol(self.mol, clique)
csmiles = get_smiles(cmol)
self.nodes_dict[i] = dict(smiles=csmiles,
mol=get_mol(csmiles),
clique=clique)
if min(clique) == 0:
root = i
self.add_nodes(len(cliques))
if root > 0:
for attr in self.nodes_dict[0]:
self.nodes_dict[0][attr] = self.nodes_dict[root][attr]
self.nodes_dict[root][attr] = self.nodes_dict[0][attr]
"""Generate Edges."""
src = np.zeros((len(edges) * 2, ), dtype='int')
dst = np.zeros((len(edges) * 2, ), dtype='int')
for i, (_x, _y) in enumerate(edges):
x = 0 if _x == root else root if _x == 0 else _x
y = 0 if _y == root else root if _y == 0 else _y
src[2 * i], dst[2 * i] = x, y
src[2 * i + 1], dst[2 * i + 1] = y, x
self.add_edges(src, dst)
for i in self.nodes_dict:
self.nodes_dict[i]['nid'] = i + 1
if self.out_degree(i) > 1:
set_atommap(self.nodes_dict[i]['mol'],
self.nodes_dict[i]['nid'])
self.nodes_dict[i]['is_leaf'] = (self.out_degree(i) == 1)
def __init__(self, num_nodes: int, num_relations: int,
triplets: np.ndarray):
Object.__init__(self)
DGLGraph.__init__(self)
assert triplets.shape[0] == 3
src, rel, dst = triplets
self.add_nodes(num_nodes)
self.add_edges(src, dst)
self.set_n_initializer(zero_initializer)
self.set_e_initializer(zero_initializer)
self.logger.info(
f"Constructed graph with {num_nodes} nodes and {num_relations} relation types."
)
def __init__(self, smiles):
DGLGraph.__init__(self)
self.smiles = smiles
self.mol = get_mol(smiles)
# Stereo Generation
mol = Chem.MolFromSmiles(smiles)
self.smiles3D = Chem.MolToSmiles(mol, isomericSmiles=True)
self.smiles2D = Chem.MolToSmiles(mol)
self.stereo_cands = decode_stereo(self.smiles2D)
# cliques: a list of list of atom indices
cliques, edges = tree_decomp(self.mol)
root = 0
for i, c in enumerate(cliques):
cmol = get_clique_mol(self.mol, c)
csmiles = get_smiles(cmol)
self.add_node(
i,
smiles=csmiles,
mol=get_mol(csmiles),
clique=c,
)
if min(c) == 0:
root = i
# The clique with atom ID 0 becomes root
if root > 0:
for attr in self.nodes[0]:
self.nodes[0][attr], self.nodes[root][attr] = \
self.nodes[root][attr], self.nodes[0][attr]
for _x, _y in edges:
x = 0 if _x == root else root if _x == 0 else _x
y = 0 if _y == root else root if _y == 0 else _y
self.add_edge(x, y)
self.add_edge(y, x)
for i in self.nodes:
self.nodes[i]['nid'] = i + 1
if len(self[i]) > 1: # Leaf node mol is not marked
set_atommap(self.nodes[i]['mol'], self.nodes[i]['nid'])
self.nodes[i]['is_leaf'] = (len(self[i]) == 1)
