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)