Add tqdm dependency for progress bar feature

pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "ml-collections",
     "dm-tree",
     "openmm",
+    "tqdm",
 ]
 
 # Note: pdbfixer is not on PyPI, install via conda:

src/graphrelax/LigandMPNN/data_utils.py

@@ -2,12 +2,18 @@
 # This is vendored code from LigandMPNN - style issues are preserved from upstream
 from __future__ import print_function
 
+import logging
+
 import numpy as np
 import torch
 import torch.utils
+
+# Completely disable all logging during prody import to suppress debug messages
+logging.disable(logging.CRITICAL)
 from prody import *
 
 confProDy(verbosity="none")
+logging.disable(logging.NOTSET)
 
 restype_1to3 = {
     "A": "ALA",

src/graphrelax/LigandMPNN/openfold/np/relax/amber_minimize.py

@@ -30,6 +30,7 @@
     residue_constants,
 )
 from openfold.np.relax import cleanup, utils
+from tqdm import tqdm
 
 try:
     from simtk import openmm, unit
@@ -487,11 +488,14 @@ def _run_one_iteration(
     start = time.perf_counter()
     minimized = False
     attempts = 0
+
     while not minimized and attempts < max_attempts:
         attempts += 1
         try:
             logging.info(
-                "Minimizing protein, attempt %d of %d.", attempts, max_attempts
+                "Minimizing protein, attempt %d of %d.",
+                attempts,
+                max_attempts,
             )
             ret = _openmm_minimize(
                 pdb_string,
@@ -506,6 +510,7 @@ def _run_one_iteration(
         except Exception as e:  # pylint: disable=broad-except
             print(e)
             logging.info(e)
+
     if not minimized:
         raise ValueError(f"Minimization failed after {max_attempts} attempts.")
     ret["opt_time"] = time.perf_counter() - start
@@ -525,6 +530,7 @@ def run_pipeline(
     max_attempts: int = 100,
     checks: bool = True,
     exclude_residues: Optional[Sequence[int]] = None,
+    pbar: Optional[tqdm] = None,
 ):
     """Run iterative amber relax.
 
@@ -548,6 +554,7 @@ def run_pipeline(
       checks: Whether to perform cleaning checks.
       exclude_residues: An optional list of zero-indexed residues to exclude from
           restraints.
+      pbar: Optional progress bar for status updates.
 
     Returns:
       out: A dictionary of output values.
@@ -607,6 +614,7 @@ def run_pipeline(
             ret["num_exclusions"],
         )
         iteration += 1
+
     return ret
 
 

src/graphrelax/LigandMPNN/openfold/np/relax/relax.py

@@ -16,11 +16,12 @@
 # limitations under the License.
 
 """Amber relaxation."""
-from typing import Any, Dict, Sequence, Tuple
+from typing import Any, Dict, Optional, Sequence, Tuple
 
 import numpy as np
 from openfold.np import protein
 from openfold.np.relax import amber_minimize, utils
+from tqdm import tqdm
 
 
 class AmberRelaxation(object):
@@ -61,7 +62,7 @@ def __init__(
         self._use_gpu = use_gpu
 
     def process(
-        self, *, prot: protein.Protein
+        self, *, prot: protein.Protein, pbar: Optional[tqdm] = None
     ) -> Tuple[str, Dict[str, Any], np.ndarray]:
         """Runs Amber relax on a prediction, adds hydrogens, returns PDB string."""
         out = amber_minimize.run_pipeline(
@@ -72,6 +73,7 @@ def process(
             exclude_residues=self._exclude_residues,
             max_outer_iterations=self._max_outer_iterations,
             use_gpu=self._use_gpu,
+            pbar=pbar,
         )
         min_pos = out["pos"]
         start_pos = out["posinit"]

src/graphrelax/LigandMPNN/sc_utils.py

@@ -1,6 +1,7 @@
 # flake8: noqa
 # This is vendored code from LigandMPNN - style issues are preserved from upstream
 import sys
+from typing import Optional
 
 import numpy as np
 import torch
@@ -27,6 +28,7 @@
 )
 from openfold.utils import feats
 from openfold.utils.rigid_utils import Rigid
+from tqdm import tqdm
 
 torch_pi = torch.tensor(np.pi, device="cpu")
 
@@ -66,6 +68,7 @@ def pack_side_chains(
     num_samples=10,
     repack_everything=True,
     num_context_atoms=16,
+    pbar: Optional[tqdm] = None,
 ):
     device = feature_dict["X"].device
     torsion_dict = make_torsion_features(feature_dict, repack_everything)
@@ -101,6 +104,7 @@ def pack_side_chains(
     feature_dict["h_V"] = h_V
     feature_dict["h_E"] = h_E
     feature_dict["E_idx"] = E_idx
+
     for step in range(num_denoising_steps):
         mean, concentration, mix_logits = model_sc.decode(feature_dict)
         mix = D.Categorical(logits=mix_logits)

src/graphrelax/cli.py

@@ -16,9 +16,36 @@ def setup_logging(verbose: bool):
         level=level,
         format="%(asctime)s [%(levelname)s] %(message)s",
         datefmt="%Y-%m-%d %H:%M:%S",
+        force=True,  # Override any existing configuration
     )
 
 
+def configure_third_party_loggers(verbose: bool):
+    """Configure third-party loggers after they've been imported."""
+    from prody import confProDy
+
+    if verbose:
+        # Enable ProDy logging when verbose
+        confProDy(verbosity="debug")
+        for name in [
+            "prody",
+            "prody.proteins",
+            "prody.atomic",
+            "prody.dynamics",
+        ]:
+            logging.getLogger(name).setLevel(logging.DEBUG)
+    else:
+        # Ensure ProDy stays silent (already silenced at import, but reinforce)
+        confProDy(verbosity="none")
+        for name in [
+            "prody",
+            "prody.proteins",
+            "prody.atomic",
+            "prody.dynamics",
+        ]:
+            logging.getLogger(name).setLevel(logging.ERROR)
+
+
 def _check_for_ligands(input_path: Path, fmt) -> bool:
     """
     Check if input structure has ligands (non-water HETATM records).
@@ -319,6 +346,9 @@ def main(args=None) -> int:
     from graphrelax.pipeline import Pipeline
     from graphrelax.structure_io import detect_format
 
+    # Configure third-party loggers after import
+    configure_third_party_loggers(opts.verbose)
+
     # Determine mode
     if opts.repack_only:
         mode = PipelineMode.REPACK_ONLY

src/graphrelax/designer.py

@@ -8,6 +8,7 @@
 
 import numpy as np
 import torch
+from tqdm import tqdm
 
 from graphrelax.config import DesignConfig
 from graphrelax.resfile import ALL_AAS, DesignSpec, ResidueMode
@@ -130,6 +131,7 @@ def design(
         pdb_path: Path,
         design_spec: Optional[DesignSpec] = None,
         design_all: bool = False,
+        pbar: Optional[tqdm] = None,
     ) -> dict:
         """
         Run sequence design on a structure.
@@ -138,6 +140,7 @@ def design(
             pdb_path: Path to input PDB
             design_spec: Specification of which residues to design/fix
             design_all: If True, design all residues (full redesign)
+            pbar: Optional progress bar for status updates
 
         Returns:
             Dictionary with designed sequence, structure, and scores
@@ -214,6 +217,7 @@ def design(
                     self.config.sc_num_denoising_steps,
                     self.config.sc_num_samples,
                     repack_everything=False,
+                    pbar=pbar,
                 )
                 output_dict.update(sc_dict)
 
@@ -249,13 +253,15 @@ def repack(
         self,
         pdb_path: Path,
         design_spec: Optional[DesignSpec] = None,
+        pbar: Optional[tqdm] = None,
     ) -> dict:
         """
         Repack side chains without changing sequence.
 
         Args:
             pdb_path: Path to input PDB
             design_spec: Specification (NATRO residues excluded from repacking)
+            pbar: Optional progress bar for status updates
 
         Returns:
             Dictionary with repacked structure
@@ -299,6 +305,7 @@ def repack(
                 self.config.sc_num_denoising_steps,
                 self.config.sc_num_samples,
                 repack_everything=True,
+                pbar=pbar,
             )
 
         # Get sequence