def __init__(self, smiles):
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, edges = tree_decomp(self.mol)
self.nodes = []
root = 0
for i, c in enumerate(cliques):
cmol = get_clique_mol(self.mol, c)
node = MolTreeNode(get_smiles(cmol), c)
self.nodes.append(node)
if min(c) == 0:
root = i
for x, y in edges:
self.nodes[x].add_neighbor(self.nodes[y])
self.nodes[y].add_neighbor(self.nodes[x])
if root > 0:
self.nodes[0], self.nodes[root] = self.nodes[root], self.nodes[0]
for i, node in enumerate(self.nodes):
node.nid = i + 1
if len(node.neighbors) > 1: #Leaf node mol is not marked
set_atommap(node.mol, node.nid)
node.is_leaf = (len(node.neighbors) == 1)
def __init__(self, smiles):
self.smiles = smiles
self.mol = get_mol(smiles)
self.mol_graph = self.build_mol_graph()
self.cliques, self.edges = tree_decomp(self.mol)
self.mol_tree = self.build_mol_tree()
self.order = []
self.set_anchor()
def __init__(self, smiles):
DGLGraph.__init__(self)
self.nodes_dict = {}
if smiles is None:
return
self.smiles = smiles
self.mol = get_mol(smiles)
mol = Chem.MolFromSmiles(smiles)
self.smiles3D = Chem.MolToSmiles(mol, isomericSmiles=True)
self.smiles2D = Chem.MolToSmiles(mol)
self.stereo_cands = decode_stereo(self.smiles2D)
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))
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:
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):
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)
self.node_pair2bond = {}
cliques, edges = tree_decomp(self.mol)
self.nodes = []
root = 0
for i, c in enumerate(cliques):
cmol = get_clique_mol(self.mol, c)
node = MolTreeNode(get_smiles(cmol), c)
self.nodes.append(node)
if min(c) == 0:
root = i
self.n_edges = 0
self.n_virtual_edges = 0
for x, y in edges:
self.nodes[x].add_neighbor(self.nodes[y])
self.nodes[y].add_neighbor(self.nodes[x])
xy_bond = self.nodes[x].add_neighbor_bond(self.nodes[y], self.mol)
yx_bond = self.nodes[y].add_neighbor_bond(self.nodes[x], self.mol)
self.node_pair2bond[(x, y)] = xy_bond
self.node_pair2bond[(y, x)] = yx_bond
if isinstance(xy_bond, RDKitBond) or isinstance(
yx_bond, RDKitBond):
self.n_virtual_edges += 1
self.n_edges += 1
# change
if root > 0:
self.nodes[0], self.nodes[root] = self.nodes[root], self.nodes[0]
for i, node in enumerate(self.nodes):
node.nid = i + 1
if len(node.neighbors) > 1: # Leaf node mol is not marked
set_atommap(node.mol, node.nid)
node.is_leaf = (len(node.neighbors) == 1)