chembfn-webui 0.1.0__tar.gz → 0.2.0__tar.gz

{chembfn_webui-0.1.0 → chembfn_webui-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chembfn_webui
-Version: 0.1.0
+Version: 0.2.0
 Summary: WebUI for ChemBFN
 Home-page: https://github.com/Augus1999/ChemBFN-WebUI
 Author: Nianze A. Tao
@@ -122,9 +122,16 @@ $ chembfn
 
 Under "advanced control" tab
 
-* You can control semi-autoregressive behaviours by key in `F` for switch off SAR, `T` for switch on SAR, and prompt like `F,F,T,...` to individually control the SAR in an ensemble model.
+* You can control semi-autoregressive behaviours by key in `F` for switching off SAR, `T` for switching on SAR, and prompt like `F,F,T,...` to individually control the SAR in an ensemble model.
 * You can add unwanted tokens, e.g., `[Cu],p,[Si]`.
 
 ### 6. Generate molecules
 
 Click "RUN" then here you go! If error occured, please check your prompts and settings.
+
+## Where to obtain the models?
+
+* Pretrained models: [https://huggingface.co/suenoomozawa/ChemBFN](https://huggingface.co/suenoomozawa/ChemBFN)
+* ChemBFN source code: [https://github.com/Augus1999/bayesian-flow-network-for-chemistry](https://github.com/Augus1999/bayesian-flow-network-for-chemistry)
+* ChemBFN document: [https://augus1999.github.io/bayesian-flow-network-for-chemistry/](https://augus1999.github.io/bayesian-flow-network-for-chemistry/)
+* ChemBFN package: [https://pypi.org/project/bayesianflow-for-chem/](https://pypi.org/project/bayesianflow-for-chem/)

{chembfn_webui-0.1.0 → chembfn_webui-0.2.0}/README.md

@@ -87,9 +87,16 @@ $ chembfn
 
 Under "advanced control" tab
 
-* You can control semi-autoregressive behaviours by key in `F` for switch off SAR, `T` for switch on SAR, and prompt like `F,F,T,...` to individually control the SAR in an ensemble model.
+* You can control semi-autoregressive behaviours by key in `F` for switching off SAR, `T` for switching on SAR, and prompt like `F,F,T,...` to individually control the SAR in an ensemble model.
 * You can add unwanted tokens, e.g., `[Cu],p,[Si]`.
 
 ### 6. Generate molecules
 
 Click "RUN" then here you go! If error occured, please check your prompts and settings.
+
+## Where to obtain the models?
+
+* Pretrained models: [https://huggingface.co/suenoomozawa/ChemBFN](https://huggingface.co/suenoomozawa/ChemBFN)
+* ChemBFN source code: [https://github.com/Augus1999/bayesian-flow-network-for-chemistry](https://github.com/Augus1999/bayesian-flow-network-for-chemistry)
+* ChemBFN document: [https://augus1999.github.io/bayesian-flow-network-for-chemistry/](https://augus1999.github.io/bayesian-flow-network-for-chemistry/)
+* ChemBFN package: [https://pypi.org/project/bayesianflow-for-chem/](https://pypi.org/project/bayesianflow-for-chem/)

{chembfn_webui-0.1.0 → chembfn_webui-0.2.0}/chembfn_webui/bin/app.py

@@ -24,7 +24,7 @@ from bayesianflow_for_chem.data import (
     aa2vec,
     split_selfies,
 )
-from bayesianflow_for_chem.tool import sample, inpaint, adjust_lora_
+from bayesianflow_for_chem.tool import sample, inpaint, adjust_lora_, quantise_model_
 from lib.utilities import (
     find_model,
     find_vocab,
@@ -41,6 +41,16 @@ cache_dir = Path(__file__).parent.parent / "cache"
 
 
 def selfies2vec(sel: str, vocab_dict: Dict[str, int]) -> List[int]:
+    """
+    Tokeniser SELFIES string.
+
+    :param sel: SELFIES string
+    :param vocab_dict: vocabulary dictionary
+    :type sel: str
+    :type vocab_dict: dict
+    :return: a list of token indices
+    :rtype: list
+    """
     s = split_selfies(sel)
     unknown_id = None
     for key, idx in vocab_dict.items():
@@ -55,6 +65,23 @@ def refresh(
 ) -> Tuple[
     List[str], List[str], List[List[str]], List[List[str]], gr.Dropdown, gr.Dropdown
 ]:
+    """
+    Refresh model file list.
+
+    :param model_selected: the selected model name
+    :param vocab_selected: the selected vocabulary name
+    :param tokeniser_selected: the selected tokeniser name
+    :type model_selected: str
+    :type vocab_selected: str
+    :type tokeniser_selected: str
+    :return: a list of vocabulary names \n
+             a list of base model files \n
+             a list of standalone model files \n
+             a list of LoRA model files \n
+             Gradio Dropdown item \n
+             Gradio Dropdown item \n
+    :rtype: tuple
+    """
     global vocabs, models
     vocabs = find_vocab()
     models = find_model()
@@ -77,6 +104,16 @@ def refresh(
 
 
 def select_lora(evt: gr.SelectData, prompt: str) -> str:
+    """
+    Select LoRA model name from Dataframe object.
+
+    :param evt: `~gradio.SelectData` instance
+    :param prompt: prompt string
+    :type evt: gradio.SelectData
+    :type prompt: str
+    :return: new prompt string
+    :rtype: str
+    """
     global lora_selected
     if lora_selected:  # avoid double select
         lora_selected = False
@@ -104,7 +141,49 @@ def run(
     scaffold: str,
     sar_control: str,
     exclude_token: str,
+    quantise: str,
+    jited: str,
 ) -> Tuple[List, List[str], str, str, str]:
+    """
+    Run generation or inpainting.
+
+    :param model_name: model name
+    :param token_name: tokeniser name
+    :param vocab_fn: customised vocabulary name
+    :param step: number of sampling steps
+    :param batch_size: batch-size
+    :param sequence_size: maximum sequence length
+    :param guidance_strength: guidance strength of conditioning
+    :param method: `"BFN"` or `"ODE"`
+    :param temperature: sampling temperature while ODE-solver used
+    :param prompt: prompt string
+    :param scaffold: molecular scaffold
+    :param sar_control: semi-autoregressive behaviour flags
+    :param exclude_token: unwanted tokens
+    :param quantise: `"on"` or `"off"`
+    :param jited: `"on"` or `"off"`
+    :type model_name: str
+    :type token_name: str
+    :type vocab_fn: str
+    :type step: int
+    :type batch_size: int
+    :type sequence_size: int
+    :type guidance_strength: float
+    :type method: str
+    :type temperature: float
+    :type prompt: str
+    :type scaffold: str
+    :type sar_control: str
+    :type exclude_token: str
+    :type quantise: str
+    :type jited: str
+    :return: list of images \n
+             list of generated molecules \n
+             Chemfig code \n
+             messages \n
+             cache file path
+    :rtype: tuple
+    """
     _message = []
     base_model_dict = dict(models["base"])
     standalone_model_dict = dict([[i[0], i[1]] for i in models["standalone"]])
@@ -113,6 +192,7 @@ def run(
     lora_label_dict = dict([[i[0], i[2] != []] for i in models["lora"]])
     standalone_lmax_dict = dict([[i[0], i[3]] for i in models["standalone"]])
     lora_lmax_dict = dict([[i[0], i[3]] for i in models["lora"]])
+    # ------- build tokeniser -------
     if token_name == "SMILES & SAFE":
         vocab_keys = VOCAB_KEYS
         tokeniser = smiles2vec
@@ -139,7 +219,7 @@ def run(
     # ------- build model -------
     prompt_info = parse_prompt(prompt)
     sar_flag = parse_sar_control(sar_control)
-    print(prompt_info)
+    print("Prompt summary:", prompt_info)  # show prompt info
     if not prompt_info["lora"]:
         if model_name in base_model_dict:
             lmax = sequence_size
@@ -166,6 +246,10 @@ def run(
                 y = None
             _message.append(f"Sequence length is set to {lmax} from model metadata.")
         bfn.semi_autoregressive = sar_flag[0]
+        if quantise == "on":
+            quantise_model_(bfn)
+        if jited == "on":
+            bfn.compile()
     elif len(prompt_info["lora"]) == 1:
         lmax = lora_lmax_dict[prompt_info["lora"][0]]
         if model_name in base_model_dict:
@@ -194,6 +278,10 @@ def run(
             adjust_lora_(bfn, prompt_info["lora_scaling"][0])
         _message.append(f"Sequence length is set to {lmax} from model metadata.")
         bfn.semi_autoregressive = sar_flag[0]
+        if quantise == "on":
+            quantise_model_(bfn)
+        if jited == "on":
+            bfn.compile()
     else:
         lmax = max([lora_lmax_dict[i] for i in prompt_info["lora"]])
         if model_name in base_model_dict:
@@ -211,6 +299,10 @@ def run(
             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"]]
+        if quantise == "on":
+            bfn.quantise()
+        if jited == "on":
+            bfn.compile()
         _message.append(f"Sequence length is set to {lmax} from model metadata.")
     # ------- inference -------
     allowed_tokens = parse_exclude_token(exclude_token, vocab_keys)
@@ -366,6 +458,8 @@ with gr.Blocks(title="ChemBFN WebUI") as app:
                     label="exclude tokens",
                     placeholder="key in unwanted tokens separated by comma.",
                 )
+                quantise = gr.Radio(["on", "off"], value="off", label="quantisation")
+                jited = gr.Radio(["on", "off"], value="off", label="JIT")
     # ------ user interaction events -------
     btn.click(
         fn=run,
@@ -383,6 +477,8 @@ with gr.Blocks(title="ChemBFN WebUI") as app:
             scaffold,
             sar_control,
             exclude_token,
+            quantise,
+            jited,
         ],
         outputs=[img, result, chemfig, message, btn_download],
     )
@@ -426,6 +522,12 @@ with gr.Blocks(title="ChemBFN WebUI") as app:
 
 
 def main() -> None:
+    """
+    Main function.
+
+    :return:
+    :rtype: None
+    """
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "--public", default=False, help="open to public", action="store_true"

chembfn_webui-0.2.0/chembfn_webui/cache/results.csv

@@ -0,0 +1,7 @@
+CC(C)(CC#N)C#N
+CCC(C)(C#N)C#N
+C1C(C)(C#N)C1C#N
+C(C)(C)C(C#N)C#N
+C(C)CC(C#N)C#N
+CCC(C)(C#N)C#N
+CC(C)(C#N)C#N

{chembfn_webui-0.1.0 → chembfn_webui-0.2.0}/chembfn_webui/lib/utilities.py

@@ -15,6 +15,12 @@ if "CHEMBFN_WEBUI_MODEL_DIR" in os.environ:
 
 
 def find_vocab() -> Dict[str, str]:
+    """
+    Find customised vocabulary files.
+
+    :return: {file_name: file_path}
+    :rtype: dict
+    """
     vocab_fns = glob(str(_model_path / "vocab/*.txt"))
     return {
         os.path.basename(i).replace(".txt", ""): i
@@ -24,6 +30,17 @@ def find_vocab() -> Dict[str, str]:
 
 
 def find_model() -> Dict[str, List[List[Union[str, int, List[str], Path]]]]:
+    """
+    Find model files.
+
+    :return: ```
+            {
+              "base": [[name1, path1], [name2, path2], ...],
+              "standalone": [[name1, parent_path1, label1, pad_len1], ...],
+              "lora": [[name1, parent_path1, label1, pad_len1], ...]
+            }```
+    :rtype: dict
+    """
     models = {}
     # find base models
     base_fns = glob(str(_model_path / "base_model/*.pt"))
@@ -61,7 +78,21 @@ def find_model() -> Dict[str, List[List[Union[str, int, List[str], Path]]]]:
     return models
 
 
-def _get_lora_info(prompt: str) -> Tuple[str, List[float], List[float]]:
+def _get_lora_info(prompt: str) -> Tuple[str, List[float], float]:
+    """
+    Parse sub-prompt string containing LoRA info.
+
+    :param prompt: LoRA sub-pompt: \n
+                   case I. `"<name:A>"` \n
+                   case II. `"<name>"` \n
+                   case III. `"<name:A>:[a,b,...]"` \n
+                   case IV. `"<name>:[a,b,c,...]"`
+    :type prompt: str
+    :return: LoRA name \n
+             objective values \n
+             LoRA scaling
+    :rtype: tuple
+    """
     s = prompt.split(">")
     s1 = s[0].replace("<", "")
     lora_info = s1.split(":")
@@ -83,6 +114,27 @@ def _get_lora_info(prompt: str) -> Tuple[str, List[float], List[float]]:
 def parse_prompt(
     prompt: str,
 ) -> Dict[str, Union[List[str], List[float], List[List[float]]]]:
+    """
+    Parse propmt.
+
+    :param prompt: prompt string: \n
+                   case I. empty string `""` --> `{"lora": [], "objective": [], "lora_scaling": []}`\n
+                   case II. one condition `"[a,b,c,...]"` --> `{"lora": [], "objective": [[a, b, c, ...]], "lora_scaling": []}`\n
+                   case III. one LoRA `"<name:A>"` --> `{"lora": [name], "objective": [], "lora_scaling": [A]}`\n
+                   case IV. one LoRA `"<name>"` --> `{"lora": [name], "objective": [], "lora_scaling": [1]}`\n
+                   case V. one LoRA with condition `"<name:A>:[a,b,...]"` --> `{"lora": [name], "objective": [[a, b, ...]], "lora_scaling": [A]}`\n
+                   case VI. one LoRA with condition `"<name>:[a,b,...]"` --> `{"lora": [name], "objective": [[a, b, ...]], "lora_scaling": [1]}`\n
+                   case VII. several LoRAs with conditions `"<name1:A1>:[a1,b1,...];<name2>:[a2,b2,c2,...]"` --> `{"lora": [name1, name2], "objective": [[a1, b1, ...], [a2, b2, c2, ...]], "lora_scaling": [A1, 1]}`\n
+                   case VIII. other cases --> `{"lora": [], "objective": [], "lora_scaling": []}`\n
+    :type prompt: str
+    :return: ```
+            {
+              "lora": [name1, name2, ...],
+              "objective": [obj1, obj2, ...],
+              "lora_scaling": [s1, s2, ...]
+            }```
+    :rtype: dict
+    """
     prompt_group = prompt.strip().replace("\n", "").split(";")
     prompt_group = [i for i in prompt_group if i]
     info = {"lora": [], "objective": [], "lora_scaling": []}
@@ -114,6 +166,16 @@ def parse_prompt(
 
 
 def parse_exclude_token(tokens: str, vocab_keys: List[str]) -> List[str]:
+    """
+    Parse exclude token string.
+
+    :param tokens: unwanted token string in the format `"token1,token2,..."`
+    :param vocab_keys: vocabulary elements
+    :type tokens: str
+    :type vocab_keys: list
+    :return: a list of allowed vocabulary
+    :rtype: list
+    """
     tokens = tokens.strip().replace("\n", "").split(",")
     tokens = [i for i in tokens if i]
     if not tokens:
@@ -121,7 +183,21 @@ def parse_exclude_token(tokens: str, vocab_keys: List[str]) -> List[str]:
     tokens = [i for i in vocab_keys if i not in tokens]
     return tokens
 
+
 def parse_sar_control(sar_control: str) -> List[bool]:
+    """
+    Parse semi-autoregression control string.
+
+    :param sar_control: semi-autoregression control string: \n
+                        case I. `""` --> `[False]` \n
+                        case II. `"F"` --> `[False]` \n
+                        case III. `"T"` --> `[True]` \n
+                        case IV. `F,T,...` --> `[False, True, ...]` \n
+                        case V. other cases --> `[False, False, ...]` \n
+    :type sar_control: str
+    :return: a list of SAR flag
+    :rtype: list
+    """
     sar_flag = sar_control.strip().replace("\n", "").split(",")
     sar_flag = [i for i in sar_flag if i]
     if not sar_flag:

{chembfn_webui-0.1.0 → chembfn_webui-0.2.0}/chembfn_webui/lib/version.py

@@ -4,5 +4,5 @@
 Version info.
 """
 
-__version__ = "0.1.0"
+__version__ = "0.2.0"
 __author__ = "Nianze A. TAO"

{chembfn_webui-0.1.0 → chembfn_webui-0.2.0}/chembfn_webui.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chembfn_webui
-Version: 0.1.0
+Version: 0.2.0
 Summary: WebUI for ChemBFN
 Home-page: https://github.com/Augus1999/ChemBFN-WebUI
 Author: Nianze A. Tao
@@ -122,9 +122,16 @@ $ chembfn
 
 Under "advanced control" tab
 
-* You can control semi-autoregressive behaviours by key in `F` for switch off SAR, `T` for switch on SAR, and prompt like `F,F,T,...` to individually control the SAR in an ensemble model.
+* You can control semi-autoregressive behaviours by key in `F` for switching off SAR, `T` for switching on SAR, and prompt like `F,F,T,...` to individually control the SAR in an ensemble model.
 * You can add unwanted tokens, e.g., `[Cu],p,[Si]`.
 
 ### 6. Generate molecules
 
 Click "RUN" then here you go! If error occured, please check your prompts and settings.
+
+## Where to obtain the models?
+
+* Pretrained models: [https://huggingface.co/suenoomozawa/ChemBFN](https://huggingface.co/suenoomozawa/ChemBFN)
+* ChemBFN source code: [https://github.com/Augus1999/bayesian-flow-network-for-chemistry](https://github.com/Augus1999/bayesian-flow-network-for-chemistry)
+* ChemBFN document: [https://augus1999.github.io/bayesian-flow-network-for-chemistry/](https://augus1999.github.io/bayesian-flow-network-for-chemistry/)
+* ChemBFN package: [https://pypi.org/project/bayesianflow-for-chem/](https://pypi.org/project/bayesianflow-for-chem/)

chembfn_webui-0.1.0/chembfn_webui/cache/results.csv

@@ -1,15 +0,0 @@
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][O]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][=Branch1][C][=O][N][C][C][C]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][N][C][C][Branch1][=Branch2][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=C][C][=C][C][=C][Ring1][=Branch1]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][O]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
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-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
-[O][=C][Branch2][Ring1][C][N][N][C][=Branch1][C][=O][C][=C][C][=C][Branch1][C][Cl][C][=C][Ring1][#Branch1][C][=C][C][=C][C][=C][Ring1][=Branch1]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][=Branch1][C][=O][O]
-[C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C]
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