Spaces:
Runtime error
Runtime error
File size: 8,675 Bytes
6b59850 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 |
import os
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
from rdkit.Geometry import Point3D
from rdkit import RDLogger
import imageio
import networkx as nx
import numpy as np
import rdkit.Chem
import wandb
import matplotlib.pyplot as plt
class MolecularVisualization:
def __init__(self, remove_h, dataset_infos):
self.remove_h = remove_h
self.dataset_infos = dataset_infos
def mol_from_graphs(self, node_list, adjacency_matrix):
"""
Convert graphs to rdkit molecules
node_list: the nodes of a batch of nodes (bs x n)
adjacency_matrix: the adjacency_matrix of the molecule (bs x n x n)
"""
# dictionary to map integer value to the char of atom
atom_decoder = self.dataset_infos.atom_decoder
# create empty editable mol object
mol = Chem.RWMol()
# add atoms to mol and keep track of index
node_to_idx = {}
for i in range(len(node_list)):
if node_list[i] == -1:
continue
a = Chem.Atom(atom_decoder[int(node_list[i])])
molIdx = mol.AddAtom(a)
node_to_idx[i] = molIdx
for ix, row in enumerate(adjacency_matrix):
for iy, bond in enumerate(row):
# only traverse half the symmetric matrix
if iy <= ix:
continue
if bond == 1:
bond_type = Chem.rdchem.BondType.SINGLE
elif bond == 2:
bond_type = Chem.rdchem.BondType.DOUBLE
elif bond == 3:
bond_type = Chem.rdchem.BondType.TRIPLE
elif bond == 4:
bond_type = Chem.rdchem.BondType.AROMATIC
else:
continue
mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type)
try:
mol = mol.GetMol()
except rdkit.Chem.KekulizeException:
print("Can't kekulize molecule")
mol = None
return mol
def visualize(self, path: str, molecules: list, num_molecules_to_visualize: int, log='graph'):
# define path to save figures
if not os.path.exists(path):
os.makedirs(path)
# visualize the final molecules
print(f"Visualizing {num_molecules_to_visualize} of {len(molecules)}")
if num_molecules_to_visualize > len(molecules):
print(f"Shortening to {len(molecules)}")
num_molecules_to_visualize = len(molecules)
for i in range(num_molecules_to_visualize):
file_path = os.path.join(path, 'molecule_{}.png'.format(i))
mol = self.mol_from_graphs(molecules[i][0].numpy(), molecules[i][1].numpy())
try:
Draw.MolToFile(mol, file_path)
if wandb.run and log is not None:
print(f"Saving {file_path} to wandb")
wandb.log({log: wandb.Image(file_path)}, commit=True)
except rdkit.Chem.KekulizeException:
print("Can't kekulize molecule")
def visualize_chain(self, path, nodes_list, adjacency_matrix, trainer=None):
RDLogger.DisableLog('rdApp.*')
# convert graphs to the rdkit molecules
mols = [self.mol_from_graphs(nodes_list[i], adjacency_matrix[i]) for i in range(nodes_list.shape[0])]
# find the coordinates of atoms in the final molecule
final_molecule = mols[-1]
AllChem.Compute2DCoords(final_molecule)
coords = []
for i, atom in enumerate(final_molecule.GetAtoms()):
positions = final_molecule.GetConformer().GetAtomPosition(i)
coords.append((positions.x, positions.y, positions.z))
# align all the molecules
for i, mol in enumerate(mols):
AllChem.Compute2DCoords(mol)
conf = mol.GetConformer()
for j, atom in enumerate(mol.GetAtoms()):
x, y, z = coords[j]
conf.SetAtomPosition(j, Point3D(x, y, z))
# draw gif
save_paths = []
num_frams = nodes_list.shape[0]
for frame in range(num_frams):
file_name = os.path.join(path, 'fram_{}.png'.format(frame))
Draw.MolToFile(mols[frame], file_name, size=(300, 300), legend=f"Frame {frame}")
save_paths.append(file_name)
imgs = [imageio.imread(fn) for fn in save_paths]
gif_path = os.path.join(os.path.dirname(path), '{}.gif'.format(path.split('/')[-1]))
imgs.extend([imgs[-1]] * 10)
imageio.mimsave(gif_path, imgs, subrectangles=True, duration=20)
if wandb.run:
print(f"Saving {gif_path} to wandb")
wandb.log({"chain": wandb.Video(gif_path, fps=5, format="gif")}, commit=True)
# draw grid image
try:
img = Draw.MolsToGridImage(mols, molsPerRow=10, subImgSize=(200, 200))
img.save(os.path.join(path, '{}_grid_image.png'.format(path.split('/')[-1])))
except Chem.rdchem.KekulizeException:
print("Can't kekulize molecule")
return mols
class NonMolecularVisualization:
def to_networkx(self, node_list, adjacency_matrix):
"""
Convert graphs to networkx graphs
node_list: the nodes of a batch of nodes (bs x n)
adjacency_matrix: the adjacency_matrix of the molecule (bs x n x n)
"""
graph = nx.Graph()
for i in range(len(node_list)):
if node_list[i] == -1:
continue
graph.add_node(i, number=i, symbol=node_list[i], color_val=node_list[i])
rows, cols = np.where(adjacency_matrix >= 1)
edges = zip(rows.tolist(), cols.tolist())
for edge in edges:
edge_type = adjacency_matrix[edge[0]][edge[1]]
graph.add_edge(edge[0], edge[1], color=float(edge_type), weight=3 * edge_type)
return graph
def visualize_non_molecule(self, graph, pos, path, iterations=100, node_size=100, largest_component=False):
if largest_component:
CGs = [graph.subgraph(c) for c in nx.connected_components(graph)]
CGs = sorted(CGs, key=lambda x: x.number_of_nodes(), reverse=True)
graph = CGs[0]
# Plot the graph structure with colors
if pos is None:
pos = nx.spring_layout(graph, iterations=iterations)
# Set node colors based on the eigenvectors
w, U = np.linalg.eigh(nx.normalized_laplacian_matrix(graph).toarray())
vmin, vmax = np.min(U[:, 1]), np.max(U[:, 1])
m = max(np.abs(vmin), vmax)
vmin, vmax = -m, m
plt.figure()
nx.draw(graph, pos, font_size=5, node_size=node_size, with_labels=False, node_color=U[:, 1],
cmap=plt.cm.coolwarm, vmin=vmin, vmax=vmax, edge_color='grey')
plt.tight_layout()
plt.savefig(path)
plt.close("all")
def visualize(self, path: str, graphs: list, num_graphs_to_visualize: int, log='graph'):
# define path to save figures
if not os.path.exists(path):
os.makedirs(path)
# visualize the final molecules
for i in range(num_graphs_to_visualize):
file_path = os.path.join(path, 'graph_{}.png'.format(i))
graph = self.to_networkx(graphs[i][0].numpy(), graphs[i][1].numpy())
self.visualize_non_molecule(graph=graph, pos=None, path=file_path)
im = plt.imread(file_path)
if wandb.run and log is not None:
wandb.log({log: [wandb.Image(im, caption=file_path)]})
def visualize_chain(self, path, nodes_list, adjacency_matrix):
# convert graphs to networkx
graphs = [self.to_networkx(nodes_list[i], adjacency_matrix[i]) for i in range(nodes_list.shape[0])]
# find the coordinates of atoms in the final molecule
final_graph = graphs[-1]
final_pos = nx.spring_layout(final_graph, seed=0)
# draw gif
save_paths = []
num_frams = nodes_list.shape[0]
for frame in range(num_frams):
file_name = os.path.join(path, 'fram_{}.png'.format(frame))
self.visualize_non_molecule(graph=graphs[frame], pos=final_pos, path=file_name)
save_paths.append(file_name)
imgs = [imageio.imread(fn) for fn in save_paths]
gif_path = os.path.join(os.path.dirname(path), '{}.gif'.format(path.split('/')[-1]))
imgs.extend([imgs[-1]] * 10)
imageio.mimsave(gif_path, imgs, subrectangles=True, duration=20)
if wandb.run:
wandb.log({'chain': [wandb.Video(gif_path, caption=gif_path, format="gif")]})
|