bayesianflow-for-chem 2.0.3__py3-none-any.whl → 2.0.5__py3-none-any.whl

bayesianflow_for_chem/__init__.py

@@ -18,7 +18,7 @@ __all__ = [
     "MLP",
     "EnsembleChemBFN",
 ]
-__version__ = "2.0.3"
+__version__ = "2.0.5"
 __author__ = "Nianze A. Tao (Omozawa Sueno)"
 
 

bayesianflow_for_chem/cli.py

@@ -130,10 +130,11 @@ def parse_cli(version: str) -> argparse.Namespace:
     """
     parser = argparse.ArgumentParser(
         description="Madmol: a CLI molecular design tool for "
-        "de novo design and R-group replacement, "
+        "de novo design, R-group replacement, and sequence in-filling, "
         "based on generative route of ChemBFN method. "
         "Let's make some craziest molecules.",
-        epilog=f"Madmol {version}, developed in Hiroshima University",
+        epilog=f"Madmol {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(
@@ -376,9 +377,7 @@ def main_script(version: str) -> None:
 
         def selfies2token(s):
             return torch.tensor(
-                [1]
-                + [vocab_dict.get(i, default=unknown_idx) for i in split_selfies(s)]
-                + [2],
+                [1] + [vocab_dict.get(i, unknown_idx) for i in split_selfies(s)] + [2],
                 dtype=torch.long,
             )
 

bayesianflow_for_chem/model.py

@@ -1038,6 +1038,19 @@ class EnsembleChemBFN(ChemBFN):
         self.__delattr__("lora_enabled")
         self.__delattr__("lora_param")
         self.__delattr__("hparam")
+        # ------- merge LoRA parameters to reduce the latency -------
+        for _, v in self.models.items():
+            for module in v.modules():
+                if hasattr(module, "lora_A"):
+                    module.weight.data += (
+                        module.lora_B @ module.lora_A
+                    ) * module.scaling
+                    module.lora_enabled = False
+                    module.lora_A = None
+                    module.lora_B = None
+                    module.scaling = None
+                    module.lora_dropout = None
+            v.lora_enabled = False
 
     def construct_y(
         self, c: Union[List[Tensor], Dict[str, Tensor]]

bayesianflow_for_chem/tool.py

@@ -470,7 +470,7 @@ class GeometryConverter:
         spin: float = 0.0,
     ) -> Tuple[List[str], np.ndarray]:
         """
-        Guess the 3D geometry from SMILES string via MMFF conformer search.
+        Guess the 3D geometry from SMILES string via conformer search.
 
         :param smiles: a valid SMILES string
         :param num_conformers: number of initial conformers

bayesianflow_for_chem/train.py

@@ -134,7 +134,7 @@ class Regressor(LightningModule):
         hparam: Dict[str, Union[str, int, float, bool]] = DEFAULT_REGRESSOR_HPARAM,
     ) -> None:
         """
-        A `~lightning.LightningModule` wrapper of bayesian flow network for chemistry regression model.\n
+        A `~lightning.LightningModule` wrapper of bayesian flow network for chemistry regression or classification model.\n
         This module is used in training stage only. By calling `Regressor(...).export_model(YOUR_WORK_DIR)` after training,
         the models will be saved to `YOUR_WORK_DIR/model_ft.pt` (if LoRA is enabled then `YOUR_WORK_DIR/lora.pt`)
         and `YOUR_WORK_DIR/readout.pt`.

{bayesianflow_for_chem-2.0.3.dist-info → bayesianflow_for_chem-2.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bayesianflow_for_chem
-Version: 2.0.3
+Version: 2.0.5
 Summary: Bayesian flow network framework for Chemistry
 Home-page: https://augus1999.github.io/bayesian-flow-network-for-chemistry/
 Author: Nianze A. Tao
@@ -50,7 +50,7 @@ Dynamic: summary
 
 This is the repository of the PyTorch implementation of ChemBFN model.
 
-## Build State
+### Build State
 
 [![PyPI](https://img.shields.io/pypi/v/bayesianflow-for-chem?color=ff69b4)](https://pypi.org/project/bayesianflow-for-chem/)
 ![pytest](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/actions/workflows/pytest.yml/badge.svg)

bayesianflow_for_chem-2.0.5.dist-info/RECORD

@@ -0,0 +1,15 @@
+bayesianflow_for_chem/__init__.py,sha256=U8ExDm5IRa-OPOLgt8VfjMDAiCmARiJonIKnZ8AVDQ0,612
+bayesianflow_for_chem/cli.py,sha256=g5pjXymycpchlgRE6SKr0LjTBjUl6MFHnFdQiKjcE3Q,22803
+bayesianflow_for_chem/data.py,sha256=Pl0gGWHmMKTKHpsxznvLgYPCwwlLNL7nqH19Vipjkxs,6584
+bayesianflow_for_chem/model.py,sha256=QF15BLpUjEpUCneTOHoU6MswvxArPfbFMiOHjwJ9JrM,52230
+bayesianflow_for_chem/scorer.py,sha256=gQFUlkyxitch02ntqcRh1ZS8aondKLynW5U6NfTQTb4,4084
+bayesianflow_for_chem/spectra.py,sha256=Ba9ib1aDvTtDYbH3b4d-lIty3ZSQMu7jwehuV2KmhwA,1781
+bayesianflow_for_chem/tool.py,sha256=JSlKrar1vVouTRUJBYU6lc5AQmAIaexvpUA3W3oQcKs,21284
+bayesianflow_for_chem/train.py,sha256=jYkhSguW50lrcTEydCQ20yig_mmc1j7WH9KmVwBCTAo,9727
+bayesianflow_for_chem/vocab.txt,sha256=HgtAZmpWYk4y8PqEVC4vqut1vE75DfRKE_10s2UW0rU,790
+bayesianflow_for_chem-2.0.5.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
+bayesianflow_for_chem-2.0.5.dist-info/METADATA,sha256=qCd0LnD66eQbWlTvKDpHZHtJKmy9NQogm_k9_amEt2s,6057
+bayesianflow_for_chem-2.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bayesianflow_for_chem-2.0.5.dist-info/entry_points.txt,sha256=N63RMoJsr8rxuKxc7Fj802SL8J5AlpCoPkS8E3IFPLI,54
+bayesianflow_for_chem-2.0.5.dist-info/top_level.txt,sha256=KHsanI3BMCt8D9Qpze2ycrF6nMa3PyojgO6eS1c8kco,22
+bayesianflow_for_chem-2.0.5.dist-info/RECORD,,

bayesianflow_for_chem-2.0.3.dist-info/RECORD

@@ -1,15 +0,0 @@
-bayesianflow_for_chem/__init__.py,sha256=D4bOlPLzpGhxTdr4Zb96Xtoc5y5BftiiuQT-SL86a7s,612
-bayesianflow_for_chem/cli.py,sha256=decINvgtoDNUZy-wJvUE41ggUb-7RKZZh3Vbu0v_nSk,22695
-bayesianflow_for_chem/data.py,sha256=Pl0gGWHmMKTKHpsxznvLgYPCwwlLNL7nqH19Vipjkxs,6584
-bayesianflow_for_chem/model.py,sha256=bswVv3DiQTF3u37A80lrj_UPzklYtRH06woFfMXy84k,51643
-bayesianflow_for_chem/scorer.py,sha256=gQFUlkyxitch02ntqcRh1ZS8aondKLynW5U6NfTQTb4,4084
-bayesianflow_for_chem/spectra.py,sha256=Ba9ib1aDvTtDYbH3b4d-lIty3ZSQMu7jwehuV2KmhwA,1781
-bayesianflow_for_chem/tool.py,sha256=8fNe8pL5veUHHnnqV02AQXDe76miKRrZzypjb9Nu_hA,21289
-bayesianflow_for_chem/train.py,sha256=hGKyhGhLch-exSYPZdLXrLn3gf39Q1VLSJs2qtuikQE,9709
-bayesianflow_for_chem/vocab.txt,sha256=HgtAZmpWYk4y8PqEVC4vqut1vE75DfRKE_10s2UW0rU,790
-bayesianflow_for_chem-2.0.3.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-bayesianflow_for_chem-2.0.3.dist-info/METADATA,sha256=eR9Kn7lM9xsALxC5y2cThQQ5iiGX-atOl_sBaLdg_NM,6056
-bayesianflow_for_chem-2.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bayesianflow_for_chem-2.0.3.dist-info/entry_points.txt,sha256=N63RMoJsr8rxuKxc7Fj802SL8J5AlpCoPkS8E3IFPLI,54
-bayesianflow_for_chem-2.0.3.dist-info/top_level.txt,sha256=KHsanI3BMCt8D9Qpze2ycrF6nMa3PyojgO6eS1c8kco,22
-bayesianflow_for_chem-2.0.3.dist-info/RECORD,,