[Example] Add chem example - Synthemol #1204

huhaohao525 · 2025-08-19T06:55:20Z

PR types

New Features

PR changes

Others

Describe

Add chem example Generative AI for designing and validating easily synthesizable and structurally novel antibiotics

paddle-bot · 2025-08-19T06:55:26Z

Thanks for your contribution!

HydrogenSulfate · 2025-08-19T08:31:56Z

ppsci/arch/chemprop_molecule.py

一些注释内容可以删除一下，比如# import paddle_aux

HydrogenSulfate · 2025-08-19T08:33:31Z

ppsci/arch/chemprop_molecule.py

+        """
+        :param args: A :class:`~chemprop.args.TrainArgs` object containing model arguments.
+        :param atom_fdim: Atom feature vector dimension.
+        :param bond_fdim: Bond feature vector dimension.
+        :param hidden_size: Hidden layers dimension
+        :param bias: Whether to add bias to linear layers
+        :param depth: Number of message passing steps
+        """


__init__的docstring请移动到类的下方

HydrogenSulfate · 2025-08-19T08:37:20Z

ppsci/arch/chemprop_molecule.py

+        :param mol_graph: A :class:`~chemprop.features.featurization.BatchMolGraph` representing
+                          a batch of molecular graphs.
+        :param atom_descriptors_batch: A list of numpy arrays containing additional atomic descriptors
+        :return: A PyTorch tensor of shape :code:`(num_molecules, hidden_size)` containing the encoding of each molecule.


类似的“PyTorch”字眼请替换成Paddle，整个PR都检查一遍

HydrogenSulfate · 2025-08-19T08:37:42Z

ppsci/arch/chemprop_molecule.py

+        # print(self.device)
+        # f_atoms, f_bonds, a2b, b2a, b2revb, a_scope, b_scope = (mol_graph.
+        #    get_components(atom_messages=self.atom_messages))


这些是调试代码吗？如果不用的话可以删除

HydrogenSulfate · 2025-08-19T08:38:19Z

ppsci/arch/chemprop_molecule.py

+        # print("message", message)
+        # print("b2revb", b2revb)


同上，是否可以删除

HydrogenSulfate · 2025-08-19T08:38:37Z

ppsci/arch/chemprop_molecule.py

+        """
+        :param args: A :class:`~chemprop.args.TrainArgs` object containing model arguments.
+        :param atom_fdim: Atom feature vector dimension.
+        :param bond_fdim: Bond feature vector dimension.
+        """


__init__的docstring请移动一下

HydrogenSulfate · 2025-08-19T08:38:54Z

ppsci/arch/chemprop_molecule.py

+        :param atom_descriptors_batch: A list of numpy arrays containing additional atom descriptors.
+        :param atom_features_batch: A list of numpy arrays containing additional atom features.
+        :param bond_features_batch: A list of numpy arrays containing additional bond features.
+        :return: A PyTorch tensor of shape :code:`(num_molecules, hidden_size)` containing the encoding of each molecule.


问题同上

HydrogenSulfate · 2025-08-19T08:46:12Z

ppsci/arch/chemprop_molecule.py

+
+# import paddle_aux
+import paddle
+from rdkit import Chem


rdkit只是这个案例的依赖项，而不是PaddleScience的依赖，请参考如下代码进行处理，否则其它的案例都会无法运行

PaddleScience/ppsci/arch/cfdgcn.py

Lines 32 to 35 in 94f81a2

try:

import pgl

except ModuleNotFoundError:

pass

HydrogenSulfate · 2025-08-20T09:18:55Z

examples/synthemol/features/features_generators.py

@@ -0,0 +1,163 @@
+from typing import Callable


Suggested change

from typing import Callable

from __future__ import annotations

from typing import Callable

HydrogenSulfate · 2025-08-20T09:20:30Z

ppsci/data/dataset/synthemol_dataset.py

+from examples.synthemol.features import atom_features_zeros
+from examples.synthemol.features import get_bond_fdim
+from examples.synthemol.features import get_features_generator
+from examples.synthemol.features import map_reac_to_prod


从正常代码设计逻辑来讲，模块代码不应该依赖案例代码，即ppsci/下的内容不应该依赖examples/下的代码，建议把这四个函数迁移到ppsci/data/dataset/synthemol_dataset.py下，然后examples的代码要使用时，从synthemol_dataset导入这几个函数

HydrogenSulfate · 2025-08-20T09:21:49Z

ppsci/data/dataset/synthemol_dataset.py

+
+# Copyright 2024 Kyle Swanson
+
+import threading


Suggested change

import threading

from __future__ import annotations

import threading

HydrogenSulfate · 2025-08-20T09:27:34Z

ppsci/data/dataset/synthemol_dataset.py

+    )
+
+
+class MoleculeDatasetIter(io.IterableDataset):


请添加到dataset.md中

HydrogenSulfate · 2025-08-20T09:28:15Z

ppsci/arch/chemprop_molecule.py

+        module.train()
+
+
+class MoleculeModel(paddle.nn.Layer):


请将MoleculeModel添加到arch.md和ppsci/arch/__init__.py中

HydrogenSulfate · 2025-08-21T09:38:37Z

ppsci/arch/chemprop_molecule_utils.py

+        self.ADDING_H = False
+
+
+PARAMS = Featurization_parameters()


这个是否能延迟初始化？否则一旦在任何位置导入这个文件，会报错找不到Chem

HydrogenSulfate · 2025-08-21T10:22:48Z

@huhaohao525 后续的PR可以关注一下

，里面如果出现报错信息，仍然需要解决一下

huhaohao525 · 2025-08-22T09:18:30Z

@huhaohao525 后续的PR可以关注一下，里面如果出现报错信息，仍然需要解决一下

为啥我加了 from future import annotations ，在CL的时候还是会看到，找不到Chem未定义的NameError呢

HydrogenSulfate · 2025-08-22T09:26:30Z

ppsci/arch/chemprop_molecule_utils.py

+Molecule = Union[str, Chem.Mol]
+FeaturesGenerator = Callable[[Molecule], np.ndarray]


因为你这里进行了实际的类型赋值操作，所以annotations是没用的，给类加上引号可以解决这个问题

Suggested change

Molecule = Union[str, Chem.Mol]

FeaturesGenerator = Callable[[Molecule], np.ndarray]

Molecule = Union[str, "Chem.Mol"]

FeaturesGenerator = Callable[[Molecule], np.ndarray]

好的好的

leeleolay · 2025-08-31T05:40:24Z

训练模型报错了

leeleolay · 2025-08-31T05:43:13Z

md文档显示代码那里有点问题
systhmol模型的训练代码在哪里呢，只看到训练chemprop的

leeleolay

可合入

examples/synthemol/synthemol/resources/real/building_blocks.csv

HydrogenSulfate · 2025-09-11T12:58:40Z

examples/synthemol/synthemol/resources/real/reaction_to_building_blocks.pkl

数据相关文件请 @leeleolay 帮忙上传下

两个文件已打包上传，文档已修改，多余的数据文件已从PR里删除了

huhaohao525 added 3 commits August 19, 2025 09:42

pre-commit check

2350cd6

refactor: remove unused code

15a37af

doc: fix line num

7de57d8

paddle-bot bot added the contributor label Aug 19, 2025

HydrogenSulfate reviewed Aug 19, 2025

View reviewed changes

fix: review problems

cc23de9

HydrogenSulfate reviewed Aug 20, 2025

View reviewed changes

refactor: extract dependency

7dd26ad

HydrogenSulfate reviewed Aug 21, 2025

View reviewed changes

huhaohao525 added 3 commits August 22, 2025 15:51

refactor: arch/class init

255614b

fix: import error

b217289

fix: annotation error

43c0819

HydrogenSulfate reviewed Aug 22, 2025

View reviewed changes

huhaohao525 added 4 commits August 22, 2025 17:33

fix: annotation error

2b0c84d

Merge remote-tracking branch 'upstream/develop' into sythemol-pre-commit

bc2ef55

fix: depency import

0f54767

fix: depency import

377dc02

huhaohao525 added 6 commits September 1, 2025 14:13

fix: use paddle3.0 dtype

d9f650b

Merge remote-tracking branch 'upstream/develop' into sythemol-pre-commit

93f691c

feat: chemprop eval

34f7378

Merge remote-tracking branch 'upstream/develop' into sythemol-pre-commit

2daaced

Merge remote-tracking branch 'upstream/develop' into sythemol-pre-commit

4825629

Merge branch 'develop' into sythemol-pre-commit

1ee6373

leeleolay approved these changes Sep 11, 2025

View reviewed changes

HydrogenSulfate reviewed Sep 11, 2025

View reviewed changes

huhaohao525 added 4 commits September 12, 2025 10:39

doc: pretrained args

f3e7ff6

Merge remote-tracking branch 'upstream/develop' into sythemol-pre-commit

5b5821d

doc: use uploaded data

9840e5c

doc: fix typo

8dfb419

		Molecule = Union[str, Chem.Mol]
		FeaturesGenerator = Callable[[Molecule], np.ndarray]

		)


		class MoleculeDatasetIter(io.IterableDataset):

[Example] Add chem example - Synthemol #1204

Are you sure you want to change the base?

[Example] Add chem example - Synthemol #1204

Conversation

huhaohao525 commented Aug 19, 2025

PR types

PR changes

Describe

Uh oh!

paddle-bot bot commented Aug 19, 2025

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

HydrogenSulfate commented Aug 21, 2025

Uh oh!

huhaohao525 commented Aug 22, 2025

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

leeleolay commented Aug 31, 2025

Uh oh!

leeleolay commented Aug 31, 2025

Uh oh!

leeleolay left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!