chembfn-webui 0.6.0__tar.gz → 1.1.0__tar.gz

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chembfn_webui
-Version: 0.6.0
+Version: 1.1.0
 Summary: WebUI for ChemBFN
 Home-page: https://github.com/Augus1999/ChemBFN-WebUI
 Author: Nianze A. Tao
@@ -20,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: bayesianflow_for_chem>=2.1.0
+Requires-Dist: bayesianflow_for_chem>=2.2.2
 Requires-Dist: mol2chemfigPy3>=1.5.11
 Requires-Dist: gradio>=5.32.1
 Requires-Dist: torch>=2.7.0
@@ -83,6 +83,21 @@ For example,
             └───moses_selfies_vocab.txt
 ```
 
+> Note:
+>
+> >The file `config.json` is automatically saved by CLI tool `Madmol` provided in `bayesianflow-for-chem` package. If you train models via Python API, you need to manually create that file for your models by filling in the tempate:
+> >```json
+> >{
+> >    "padding_index": 0,
+> >    "start_index": 1,
+> >    "end_index": 2,
+> >    "padding_strategy": "static",
+> >    "padding_length": PADDING_LENGTH,
+> >    "label": [LABEL_NAME_I, LABEL_NAME_II, ...],
+> >    "name": JOB_NAME
+> >}
+> >```
+
 If placed correctly, all these files can be seen in the "model explorer" tab.
 
 > You can use an external folder to host the models if it follows the same structure as [`chembfn_webui/model`](https://github.com/Augus1999/ChemBFN-WebUI/tree/main/chembfn_webui/model). See the next section for the method.

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/README.md

@@ -48,6 +48,21 @@ For example,
             └───moses_selfies_vocab.txt
 ```
 
+> [!NOTE]
+>
+> >The file `config.json` is automatically saved by CLI tool `Madmol` provided in `bayesianflow-for-chem` package. If you train models via Python API, you need to manually create that file for your models by filling in the tempate:
+> >```json
+> >{
+> >    "padding_index": 0,
+> >    "start_index": 1,
+> >    "end_index": 2,
+> >    "padding_strategy": "static",
+> >    "padding_length": PADDING_LENGTH,
+> >    "label": [LABEL_NAME_I, LABEL_NAME_II, ...],
+> >    "name": JOB_NAME
+> >}
+> >```
+
 If placed correctly, all these files can be seen in the "model explorer" tab.
 
 > You can use an external folder to host the models if it follows the same structure as [`chembfn_webui/model`](./chembfn_webui/model). See the next section for the method.

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/chembfn_webui/bin/app.py

@@ -10,7 +10,7 @@ from functools import partial
 from typing import Tuple, List, Dict, Union
 
 sys.path.append(str(Path(__file__).parent.parent))
-from rdkit.Chem import Draw, MolFromSmiles
+from rdkit.Chem import Draw, MolFromSmiles  # type: ignore
 from mol2chemfigPy3 import mol2chemfig
 import gradio as gr
 import torch
@@ -18,10 +18,10 @@ from selfies import decoder
 from bayesianflow_for_chem import ChemBFN, MLP, EnsembleChemBFN
 from bayesianflow_for_chem.data import (
     VOCAB_KEYS,
-    AA_VOCAB_KEYS,
+    FASTA_VOCAB_KEYS,
     load_vocab,
     smiles2vec,
-    aa2vec,
+    fasta2vec,
     split_selfies,
 )
 from bayesianflow_for_chem.tool import (
@@ -42,7 +42,8 @@ from lib.version import __version__
 
 vocabs = find_vocab()
 models = find_model()
-lora_selected = False  # lora select flag
+_lora_selected = False  # lora select flag
+_run_in_public = False  # public flag
 cache_dir = Path(__file__).parent.parent / "cache"
 
 HTML_STYLE = gr.InputHTMLAttributes(
@@ -130,12 +131,12 @@ def select_lora(evt: gr.SelectData, prompt: str) -> str:
     :return: new prompt string
     :rtype: str
     """
-    global lora_selected
-    if lora_selected:  # avoid double select
-        lora_selected = False
+    global _lora_selected
+    if _lora_selected and not _run_in_public:  # avoid double select
+        _lora_selected = False
         return prompt
     selected_lora = evt.value
-    lora_selected = True
+    _lora_selected = True
     if evt.index[1] != 0:
         return prompt
     if not prompt:
@@ -246,8 +247,8 @@ def run(
         img_fn = lambda x: [Draw.MolToImage(MolFromSmiles(i), (500, 500)) for i in x]
         chemfig_fn = lambda x: [mol2chemfig(i, "-r", inline=True) for i in x]
     if token_name == "FASTA":
-        vocab_keys = AA_VOCAB_KEYS
-        tokeniser = aa2vec
+        vocab_keys = FASTA_VOCAB_KEYS
+        tokeniser = fasta2vec
         trans_fn = lambda x: x
         img_fn = lambda _: None  # senseless to provide dumb 2D images
         chemfig_fn = lambda _: [""]  # senseless to provide very long Chemfig code
@@ -344,7 +345,11 @@ def run(
         if len(sar_flag) == 1:
             sar_flag = [sar_flag[0] for _ in range(len(weights))]
         bfn = EnsembleChemBFN(base_model_dir, lora_dir, mlps, weights)
-        y = [torch.tensor([i], dtype=torch.float32) for i in prompt_info["objective"]]
+        y = (
+            [torch.tensor([i], dtype=torch.float32) for i in prompt_info["objective"]]
+            if prompt_info["objective"]
+            else None
+        )
         if quantise == "on":
             bfn.quantise()
         if jited == "on":
@@ -417,7 +422,6 @@ def run(
         imgs,
         mols,
         "\n\n".join(chemfigs),
-        # "\n".join(_message),
         gr.TextArea("\n".join(_message), label="message", lines=len(_message)),
         str(cache_dir / "results.csv"),
     )
@@ -610,12 +614,19 @@ def main() -> None:
     :return:
     :rtype: None
     """
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(
+        description="A web-based visualisation tool for ChemBFN method.",
+        epilog=f"ChemBFN WebUI {__version__}, developed in Hiroshima University by chemists for chemists. "
+        "Visit https://augus1999.github.io/bayesian-flow-network-for-chemistry/ for more details.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
     parser.add_argument(
-        "--public", default=False, help="open to public", action="store_true"
+        "-P", "--public", default=False, help="open to public", action="store_true"
     )
     parser.add_argument("-V", "--version", action="version", version=__version__)
     args = parser.parse_args()
+    global _run_in_public
+    _run_in_public = args.public
     app.launch(share=args.public, allowed_paths=[cache_dir.absolute().__str__()])
 
 

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/chembfn_webui/lib/version.py

@@ -4,5 +4,5 @@
 Version info.
 """
 
-__version__ = "0.6.0"
+__version__ = "1.1.0"
 __author__ = "Nianze A. TAO"

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/chembfn_webui.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chembfn_webui
-Version: 0.6.0
+Version: 1.1.0
 Summary: WebUI for ChemBFN
 Home-page: https://github.com/Augus1999/ChemBFN-WebUI
 Author: Nianze A. Tao
@@ -20,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: bayesianflow_for_chem>=2.1.0
+Requires-Dist: bayesianflow_for_chem>=2.2.2
 Requires-Dist: mol2chemfigPy3>=1.5.11
 Requires-Dist: gradio>=5.32.1
 Requires-Dist: torch>=2.7.0
@@ -83,6 +83,21 @@ For example,
             └───moses_selfies_vocab.txt
 ```
 
+> Note:
+>
+> >The file `config.json` is automatically saved by CLI tool `Madmol` provided in `bayesianflow-for-chem` package. If you train models via Python API, you need to manually create that file for your models by filling in the tempate:
+> >```json
+> >{
+> >    "padding_index": 0,
+> >    "start_index": 1,
+> >    "end_index": 2,
+> >    "padding_strategy": "static",
+> >    "padding_length": PADDING_LENGTH,
+> >    "label": [LABEL_NAME_I, LABEL_NAME_II, ...],
+> >    "name": JOB_NAME
+> >}
+> >```
+
 If placed correctly, all these files can be seen in the "model explorer" tab.
 
 > You can use an external folder to host the models if it follows the same structure as [`chembfn_webui/model`](https://github.com/Augus1999/ChemBFN-WebUI/tree/main/chembfn_webui/model). See the next section for the method.

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/chembfn_webui.egg-info/requires.txt

@@ -1,4 +1,4 @@
-bayesianflow_for_chem>=2.1.0
+bayesianflow_for_chem>=2.2.2
 mol2chemfigPy3>=1.5.11
 gradio>=5.32.1
 torch>=2.7.0

{chembfn_webui-0.6.0 → chembfn_webui-1.1.0}/setup.py

@@ -35,6 +35,7 @@ long_description = long_description.replace(
     r"(./chembfn_webui/",
     r"(https://github.com/Augus1999/ChemBFN-WebUI/tree/main/chembfn_webui/",
 )
+long_description = long_description.replace(r"> [!NOTE]", r"> Note:")
 
 setup(
     name="chembfn_webui",
@@ -55,7 +56,7 @@ setup(
     packages=find_packages(),
     python_requires=">=3.11",
     install_requires=[
-        "bayesianflow_for_chem>=2.1.0",
+        "bayesianflow_for_chem>=2.2.2",
         "mol2chemfigPy3>=1.5.11",
         "gradio>=5.32.1",
         "torch>=2.7.0",