2: Active Learning#
This tutorial demonstrates how to use FEgrow in combination with active learning to optimise the predicted pK of designed compounds against the main protease of SARS-CoV-2. See our preprint for more details.
import prody
from rdkit import Chem
import fegrow
from fegrow import ChemSpace, Linkers, RGroups
from fegrow.al import Model, Query
rgroups = RGroups()
linkers = Linkers()
MolGridWidget(grid_id='m2')
MolGridWidget(grid_id='m1')
from dask.distributed import LocalCluster
lc = LocalCluster(processes=True, n_workers=None, threads_per_worker=1)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/distributed/node.py:187: UserWarning: Port 8787 is already in use.
Perhaps you already have a cluster running?
Hosting the HTTP server on port 34625 instead
warnings.warn(
2025-03-14 21:18:29,667 - distributed.nanny - WARNING - Restarting worker
2025-03-14 21:18:44,750 - distributed.nanny - WARNING - Restarting worker
2025-03-14 21:19:01,168 - distributed.nanny - WARNING - Restarting worker
2025-03-14 21:19:30,586 - distributed.nanny - WARNING - Restarting worker
# create the chemical space
cs = ChemSpace(dask_cluster=lc)
cs
Dask can be watched on http://127.0.0.1:34625/status
| Smiles | score | h | Training | Success | enamine_searched | enamine_id | 2D |
|---|
# turn on the caching in RAM (optional)
cs.set_dask_caching()
Read in the protonated ligand core:
init_mol = Chem.SDMolSupplier("sarscov2/5R83_core.sdf", removeHs=False)[0]
# get the FEgrow representation of the rdkit Mol
scaffold = fegrow.RMol(init_mol)
scaffold.rep2D(idx=True, size=(500, 500))
# specify the attachment point (in this case hydrogen atom number 6)
attachmentid = 6
scaffold.GetAtomWithIdx(attachmentid).SetAtomicNum(0)
cs.add_scaffold(scaffold)
cs
| Smiles | score | h | Training | Success | enamine_searched | enamine_id | 2D |
|---|
# load the receptor structure
sys = prody.parsePDB("sarscov2/5R83_final.pdb")
# remove any unwanted molecules
rec = sys.select("not (nucleic or hetatm or water)")
# save the processed protein
prody.writePDB("rec.pdb", rec)
# fix the receptor file (missing residues, protonation, etc)
fegrow.fix_receptor("rec.pdb", "rec_final.pdb")
cs.add_protein("rec_final.pdb")
@> 4656 atoms and 1 coordinate set(s) were parsed in 0.04s.
Build a chemical space to explore with active learning (this will take a few minutes). Here, we pick 50 of each of the most common linkers and R-groups, giving us 2500 molecules in total, but these can be increased:
numlinkers = 50
numrgroups = 50
for i in range(numlinkers):
if i % 10 == 0:
print(i)
for j in range(numrgroups):
cs.add_rgroups(linkers.Mol[i], rgroups.Mol[j])
0
10
20
30
40
# The chemical space now includes our 2500 small molecules:
cs
| Smiles | score | h | Training | Success | enamine_searched | enamine_id | 2D | |
|---|---|---|---|---|---|---|---|---|
| 0 | [H]OC([H])([H])c1c([H])nc([H])c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN |  |
| 1 | [H]c1nc([H])c(C([H])([H])OC([H])([H])[H])c([H]... | <NA> | 6 | False | NaN | False | NaN |  |
| 2 | [H]c1nc([H])c(C([H])([H])N([H])[H])c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN |  |
| 3 | [H]c1nc([H])c(C([H])([H])Cl)c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN |  |
| 4 | [H]c1nc([H])c(C([H])([H])F)c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN |  |
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 2495 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2N2C... | <NA> | 6 | False | NaN | False | NaN |  |
| 2496 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2N2C... | <NA> | 6 | False | NaN | False | NaN |  |
| 2497 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2-c2... | <NA> | 6 | False | NaN | False | NaN |  |
| 2498 | [H]Oc1c([H])c([H])c([H])c(-c2c([H])c([H])c([H]... | <NA> | 6 | False | NaN | False | NaN |  |
| 2499 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2C([... | <NA> | 6 | False | NaN | False | NaN |  |
2500 rows × 8 columns
cs[0].rep2D()
The active learning model initially has no data, so the first 50 molecules are selected at random:
# Pick 50 random molecules
random1 = cs.active_learning(50, first_random=True)
/home/dresio/code/fegrow/fegrow/package.py:1376: UserWarning: Selecting randomly the first samples to be studied (no score data yet).
warnings.warn(
# now evaluate the first selection, note that dask is used to parallelise the calculation
# molecules that cannot be built assigned a predicted affinity of 0
random1_results = cs.evaluate(
random1, num_conf=50, gnina_gpu=True, penalty=0.0, al_ignore_penalty=False
)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Generated 4 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 6 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 33%|███████▋ | 2/6 [00:04<00:08, 2.23s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 100%|███████████████████████| 6/6 [00:14<00:00, 2.35s/it]
Generated 36 conformers.
Removed 15 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s] Optimising conformer: 100%|███████████████████████| 3/3 [00:19<00:00, 6.65s/it] Optimising conformer: 100%|███████████████████████| 3/3 [00:19<00:00, 6.64s/it]
Generated 13 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/11 [00:00<?, ?it/s]2025-03-14 21:18:02,602 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-c7dc0479-f8a4-424d-868f-731ce545f28e
State: executing
Task: <Task '_evaluate_atomic-c7dc0479-f8a4-424d-868f-731ce545f28e' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 9%|██ | 1/11 [00:04<00:43, 4.32s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 14%|███▏ | 3/21 [00:08<00:44, 2.49s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 45%|██████████ | 5/11 [00:14<00:15, 2.60s/it]
Generated 36 conformers.
Removed 15 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s]
Generated 4 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/34 [00:00<?, ?it/s]
Generated 45 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:12<00:00, 3.18s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 91%|███████████████████ | 10/11 [00:32<00:03, 3.51s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 100%|█████████████████████| 11/11 [00:37<00:00, 3.42s/it]
Generated 22 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 57%|████████████ | 12/21 [00:38<00:33, 3.75s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 15%|███▏ | 5/34 [00:20<01:41, 3.51s/it]
Generated 25 conformers.
Removed 5 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 13 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 21%|████▌ | 7/34 [00:28<01:46, 3.95s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 20%|████▍ | 4/20 [00:14<00:56, 3.52s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 25%|█████▌ | 5/20 [00:17<00:50, 3.38s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 100%|███████████████████████| 5/5 [00:21<00:00, 4.25s/it]
Optimising conformer: 100%|█████████████████████| 21/21 [01:04<00:00, 3.08s/it]
Optimising conformer: 50%|██████████▌ | 10/20 [00:29<00:25, 2.58s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 78%|█████████████████▉ | 7/9 [00:37<00:08, 4.35s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 38%|████████ | 13/34 [00:54<01:15, 3.62s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 9/9 [00:43<00:00, 4.82s/it]
Optimising conformer: 67%|██████████████ | 14/21 [01:07<00:33, 4.75s/it]
Generated 22 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 47%|█████████▉ | 16/34 [01:05<01:03, 3.54s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 90%|██████████████████▉ | 18/20 [00:47<00:04, 2.35s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 20/20 [00:52<00:00, 2.61s/it]
Optimising conformer: 59%|████████████▎ | 20/34 [01:17<00:43, 3.12s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 46%|██████████▏ | 6/13 [00:18<00:19, 2.77s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 69%|███████████████▏ | 9/13 [00:24<00:08, 2.19s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 92%|███████████████████▍ | 12/13 [00:31<00:02, 2.26s/it]
Generated 34 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 13/13 [00:33<00:00, 2.55s/it]
Optimising conformer: 5%|█ | 1/20 [00:04<01:22, 4.32s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/3 [00:00<?, ?it/s]
Generated 4 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 15%|███▎ | 3/20 [00:08<00:42, 2.51s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 21/21 [01:50<00:00, 5.24s/it]
Optimising conformer: 67%|███████████████▎ | 2/3 [00:08<00:04, 4.39s/it]
Generated 15 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 3/3 [00:13<00:00, 4.35s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 38 conformers.
Removed 22 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 30%|██████▌ | 6/20 [00:25<01:24, 6.07s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 50%|██████████▌ | 10/20 [00:34<00:30, 3.02s/it]
Generated 19 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/1 [00:00<?, ?it/s]
Generated 11 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 1/1 [00:04<00:00, 4.13s/it]
Optimising conformer: 75%|███████████████▊ | 15/20 [00:44<00:11, 2.27s/it]
Generated 21 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 31%|██████▉ | 5/16 [00:24<00:47, 4.27s/it]
Generated 12 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 34/34 [02:22<00:00, 4.19s/it]
Optimising conformer: 62%|█████████████▌ | 8/13 [00:16<00:09, 1.90s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 20/20 [00:55<00:00, 2.76s/it]
Optimising conformer: 92%|███████████████████▍ | 12/13 [00:24<00:01, 1.83s/it]
Generated 4 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 8/8 [00:44<00:00, 5.53s/it]
Optimising conformer: 100%|█████████████████████| 13/13 [00:26<00:00, 2.06s/it]
Optimising conformer: 25%|█████▊ | 2/8 [00:18<00:53, 8.97s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 80%|██████████████████▍ | 4/5 [00:21<00:05, 5.10s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 2/2 [00:12<00:00, 6.40s/it]
2025-03-14 21:21:10,726 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-e8c4dd50-5235-46cc-85d3-3de91766df5c
State: executing
Task: <Task '_evaluate_atomic-e8c4dd50-5235-46cc-85d3-3de91766df5c' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Generated 10 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/8 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 5/5 [00:25<00:00, 5.18s/it]
2025-03-14 21:21:12,952 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-8d556f51-effa-4a17-9d16-933ca3c13141
State: executing
Task: <Task '_evaluate_atomic-8d556f51-effa-4a17-9d16-933ca3c13141' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Optimising conformer: 0%| | 0/10 [00:00<?, ?it/s]
Generated 24 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 62%|██████████████▍ | 5/8 [00:36<00:19, 6.53s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 88%|████████████████████▏ | 7/8 [00:19<00:02, 2.59s/it]
Generated 2 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 8/8 [00:21<00:00, 2.65s/it]
Optimising conformer: 50%|███████████▌ | 1/2 [00:04<00:04, 4.59s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/__init__.py:59: UserWarning: Dependency not satisfied, torchani.ase will not be available
warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Optimising conformer: 60%|█████████████▏ | 6/10 [00:24<00:14, 3.61s/it]Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Optimising conformer: 100%|███████████████████████| 8/8 [00:55<00:00, 6.95s/it]
Optimising conformer: 100%|███████████████████████| 2/2 [00:07<00:00, 3.55s/it]
Optimising conformer: 100%|█████████████████████| 10/10 [00:30<00:00, 3.04s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 16/16 [01:24<00:00, 5.30s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/5 [00:00<?, ?it/s]
Generated 8 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 23 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/10 [00:00<?, ?it/s]
Generated 33 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/22 [00:00<?, ?it/s]
Generated 37 conformers.
Removed 22 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 10%|██▏ | 1/10 [00:04<00:40, 4.47s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 20%|████▍ | 2/10 [00:06<00:24, 3.04s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 5/5 [00:13<00:00, 2.67s/it]
Optimising conformer: 50%|███████████ | 5/10 [00:13<00:11, 2.38s/it]
Generated 15 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 36%|████████ | 8/22 [00:22<00:44, 3.20s/it]
Generated 21 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [00:25<00:00, 2.51s/it]
Optimising conformer: 5%|█ | 1/21 [00:05<01:45, 5.28s/it]
Generated 44 conformers.
Removed 29 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 40%|████████▊ | 6/15 [00:31<00:48, 5.38s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 33%|███████▎ | 7/21 [00:21<00:38, 2.73s/it]
Generated 24 conformers.
Removed 16 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 5/5 [00:33<00:00, 6.72s/it]
2025-03-14 21:22:37,278 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-7d4b0a9e-8e03-420c-99d5-e8d513049206
State: executing
Task: <Task '_evaluate_atomic-7d4b0a9e-8e03-420c-99d5-e8d513049206' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Optimising conformer: 86%|██████████████████▏ | 19/22 [00:55<00:11, 3.75s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 67%|██████████████ | 14/21 [00:39<00:18, 2.71s/it]
Generated 25 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 22/22 [01:05<00:00, 2.96s/it]
Optimising conformer: 80%|████████████████▊ | 12/15 [00:43<00:09, 3.33s/it]
Generated 11 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 76%|████████████████ | 16/21 [00:50<00:19, 3.89s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 35 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 8/8 [00:31<00:00, 3.96s/it]
Optimising conformer: 100%|█████████████████████| 15/15 [01:16<00:00, 5.11s/it]
Optimising conformer: 0%| | 0/6 [00:00<?, ?it/s]
Generated 16 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 15/15 [00:56<00:00, 3.74s/it]
Optimising conformer: 22%|█████ | 2/9 [00:12<00:42, 6.12s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 10%|██ | 2/21 [00:13<02:07, 6.72s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 21/21 [01:11<00:00, 3.42s/it]
Optimising conformer: 33%|███████▋ | 2/6 [00:10<00:19, 4.90s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 29%|██████▎ | 6/21 [00:25<00:51, 3.41s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 14/14 [00:40<00:00, 2.93s/it]
Optimising conformer: 43%|█████████▍ | 9/21 [00:31<00:28, 2.36s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 6/6 [00:25<00:00, 4.30s/it]
Optimising conformer: 0%| | 0/28 [00:00<?, ?it/s]
Generated 31 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 9/9 [00:38<00:00, 4.26s/it]
Optimising conformer: 11%|██▎ | 3/28 [00:07<00:56, 2.26s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 14 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/19 [00:00<?, ?it/s]
Generated 22 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 41 conformers.
Removed 20 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/4 [00:00<?, ?it/s]
Generated 20 conformers.
Removed 16 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 16%|███▍ | 3/19 [00:11<00:59, 3.75s/it]
Generated 22 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 21/21 [01:19<00:00, 3.79s/it]
Optimising conformer: 100%|█████████████████████| 14/14 [00:39<00:00, 2.85s/it]
Optimising conformer: 100%|███████████████████████| 4/4 [00:24<00:00, 6.22s/it]
Optimising conformer: 100%|███████████████████████| 4/4 [00:17<00:00, 4.33s/it]
2025-03-14 21:24:32,726 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-63bf20f8-e3eb-43f8-b5fe-c5b816674f3f
State: executing
Task: <Task '_evaluate_atomic-63bf20f8-e3eb-43f8-b5fe-c5b816674f3f' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Generated 19 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/11 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 38%|████████▍ | 8/21 [00:30<00:44, 3.42s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 48%|██████████ | 10/21 [00:35<00:30, 2.76s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 58%|████████████▏ | 11/19 [00:37<00:21, 2.73s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/6 [00:00<?, ?it/s]
Generated 18 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 17 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 64%|██████████████ | 7/11 [00:25<00:13, 3.49s/it]
Generated 28 conformers.
Removed 20 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 19/19 [01:01<00:00, 3.21s/it]
Optimising conformer: 100%|█████████████████████| 11/11 [00:38<00:00, 3.48s/it]
Optimising conformer: 100%|███████████████████████| 6/6 [00:32<00:00, 5.44s/it]
Optimising conformer: 100%|█████████████████████| 21/21 [01:15<00:00, 3.58s/it]
Optimising conformer: 67%|███████████████▎ | 6/9 [00:39<00:18, 6.13s/it]
Generated 6 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 8/8 [00:30<00:00, 3.78s/it]
Optimising conformer: 100%|███████████████████████| 9/9 [00:48<00:00, 5.43s/it]
2025-03-14 21:25:30,885 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-19a5eda1-ae99-4707-908b-938c0181882e
State: executing
Task: <Task '_evaluate_atomic-19a5eda1-ae99-4707-908b-938c0181882e' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Optimising conformer: 80%|██████████████████▍ | 4/5 [00:09<00:02, 2.03s/it]
Generated 43 conformers.
Removed 29 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 5/5 [00:10<00:00, 2.17s/it]
Optimising conformer: 14%|███▏ | 2/14 [00:03<00:20, 1.70s/it]
Generated 13 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 7/7 [00:22<00:00, 3.26s/it]
Optimising conformer: 100%|█████████████████████| 14/14 [00:31<00:00, 2.26s/it]
Optimising conformer: 64%|█████████████▌ | 18/28 [02:25<01:06, 6.68s/it]
Generated 14 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 2/2 [00:07<00:00, 3.55s/it]
2025-03-14 21:26:19,735 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-08e5b3e7-f8f6-4c50-85b3-6a7e5e04c351
State: executing
Task: <Task '_evaluate_atomic-08e5b3e7-f8f6-4c50-85b3-6a7e5e04c351' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Optimising conformer: 100%|█████████████████████| 28/28 [02:41<00:00, 5.78s/it]
Generated 15 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 7/7 [00:07<00:00, 1.05s/it]
Check the scores (in pK units), note that they were updated in the master dataframe too:
random1_results
| Smiles | Mol | score | h | Training | Success | enamine_searched | enamine_id | |
|---|---|---|---|---|---|---|---|---|
| 2347 | [H]c1nc([H])c(C([H])([H])S(=O)(=O)c2c([H])c([H... | <fegrow.package.RMol object at 0x7bdc601d3740> | 4.204 | 6 | True | True | False | NaN |
| 2184 | [H]c1nc([H])c(N(OC([H])([H])c2c([H])c([H])c([H... | <fegrow.package.RMol object at 0x7bdd80f25a30> | 4.312 | 6 | True | True | False | NaN |
| 1693 | [H]c1nc([H])c(N2C([H])([H])C([H])([H])N(N([H])... | <fegrow.package.RMol object at 0x7bdc9c6bb2e0> | 4.549 | 6 | True | True | False | NaN |
| 1286 | [H]c1nc([H])c(SC([H])([H])C([H])([H])c2c([H])c... | <fegrow.package.RMol object at 0x7bdd80f26520> | 4.408 | 6 | True | True | False | NaN |
| 516 | [H]c1nc([H])c(N([H])S(=O)(=O)OC([H])([H])C([H]... | <fegrow.package.RMol object at 0x7bdc6053cef0> | 0.0 | 6 | True | False | False | NaN |
| 2132 | [H]c1nc([H])c(-c2noc(-c3c([H])c([H])c(Cl)c([H]... | <fegrow.package.RMol object at 0x7bdc9c1ab560> | 0.0 | 6 | True | False | False | NaN |
| 33 | [H]c1nc([H])c(C([H])([H])N2C([H])([H])C([H])([... | <fegrow.package.RMol object at 0x7bdc60708db0> | 4.025 | 6 | True | True | False | NaN |
| 1810 | [H]c1nc([H])c(C2([H])C([H])([H])C([H])([H])N(C... | <fegrow.package.RMol object at 0x7bdd80f93f10> | 4.527 | 6 | True | True | False | NaN |
| 629 | [H]c1nc([H])c(C([H])([H])N([H])N([H])C(=O)C([H... | <fegrow.package.RMol object at 0x7bdd80faebb0> | 3.904 | 6 | True | True | False | NaN |
| 1403 | [H]c1nc([H])c(N([H])[C@]([H])(Cl)C([H])([H])[H... | <fegrow.package.RMol object at 0x7bdd80fad210> | 3.697 | 6 | True | True | False | NaN |
| 493 | [H]c1nc([H])c(S(=O)(=O)N([H])N([H])c2c([H])c([... | <fegrow.package.RMol object at 0x7bdd80fac3b0> | 4.108 | 6 | True | True | False | NaN |
| 771 | [H]c1nc([H])c(C([H])([H])C([H])([H])C(C([H])([... | <fegrow.package.RMol object at 0x7bdc605985e0> | 4.214 | 6 | True | True | False | NaN |
| 1283 | [H]c1nc([H])c(SN2C([H])([H])C([H])([H])N(C([H]... | <fegrow.package.RMol object at 0x7bdc60211cb0> | 3.966 | 6 | True | True | False | NaN |
| 1707 | [H]OC(=O)[C@]([H])(c1c([H])nc([H])c([H])c1[H])... | <fegrow.package.RMol object at 0x7bdd810f4db0> | 0.0 | 6 | True | False | False | NaN |
| 519 | [H]c1nc([H])c(N([H])S(=O)(=O)N2C([H])([H])C([H... | <fegrow.package.RMol object at 0x7bdc846e79c0> | 4.215 | 6 | True | True | False | NaN |
| 2013 | [H]C(=Nc1c([H])c([H])nc([H])c1[H])c1c([H])nc([... | <fegrow.package.RMol object at 0x7bdd80fafb50> | 3.912 | 6 | True | True | False | NaN |
| 160 | [H]c1nc([H])c(N([H])C([H])(C([H])([H])[H])C([H... | <fegrow.package.RMol object at 0x7bdc60211e40> | 3.572 | 6 | True | True | False | NaN |
| 1511 | [H]c1nc([H])c(OC(=O)C([H])([H])c2c([H])c([H])c... | <fegrow.package.RMol object at 0x7bdd810bc040> | 4.466 | 6 | True | True | False | NaN |
| 1623 | [H]c1nc([H])c(C([H])([H])OC(=O)c2c([H])c([H])c... | <fegrow.package.RMol object at 0x7bdd80f922f0> | 4.198 | 6 | True | True | False | NaN |
| 1599 | [H]c1nc([H])c(C(=O)OC([H])([H])C([H])([H])N2C(... | <fegrow.package.RMol object at 0x7bdc9c6724d0> | 4.061 | 6 | True | True | False | NaN |
| 2143 | [H]c1nc([H])c(-c2noc(N([H])c3c([H])c([H])c([H]... | <fegrow.package.RMol object at 0x7bdd80f628e0> | 4.771 | 6 | True | True | False | NaN |
| 2313 | [H]c1nc([H])c(C([H])([H])S(=O)(=O)c2c([H])c([H... | <fegrow.package.RMol object at 0x7bdd80fec720> | 4.107 | 6 | True | True | False | NaN |
| 2141 | [H]c1nc([H])c(-c2noc(Oc3c([H])c([H])c([H])c([H... | <fegrow.package.RMol object at 0x7bdc601baa70> | 4.649 | 6 | True | True | False | NaN |
| 987 | [H]c1nc([H])c(C(=O)C([H])([H])N2C([H])([H])C([... | <fegrow.package.RMol object at 0x7bdd80fad2b0> | 4.271 | 6 | True | True | False | NaN |
| 1331 | [H]C(C(=O)C([H])([H])[H])=C([H])c1c([H])nc([H]... | <fegrow.package.RMol object at 0x7bdc602138d0> | 3.539 | 6 | True | True | False | NaN |
| 1794 | [H]c1nc([H])c(N2C([H])([H])C([H])([H])C([H])(S... | <fegrow.package.RMol object at 0x7bdc9c5100e0> | 4.379 | 6 | True | True | False | NaN |
| 1036 | [H]c1nc([H])c(C([H])([H])C(=O)C([H])([H])C([H]... | <fegrow.package.RMol object at 0x7bdc2044ce50> | 4.195 | 6 | True | True | False | NaN |
| 999 | [H]c1nc([H])c(C(=O)C([H])([H])C([H])([H])N2C([... | <fegrow.package.RMol object at 0x7bdd80f24bd0> | 4.202 | 6 | True | True | False | NaN |
| 1439 | [H]c1nc([H])c(N([H])[C@@]([H])(C([H])([H])[H])... | <fegrow.package.RMol object at 0x7bdc2044d580> | 3.816 | 6 | True | True | False | NaN |
| 1044 | [H]c1nc([H])c(C([H])([H])C(=O)S(=O)(=O)C([H])(... | <fegrow.package.RMol object at 0x7bdd810ad990> | 3.847 | 6 | True | True | False | NaN |
| 1254 | [H]c1nc([H])c(SF)c([H])c1[H] | <fegrow.package.RMol object at 0x7bdc2044e070> | 3.752 | 6 | True | True | False | NaN |
| 1387 | [H]c1nc([H])c([C@@]([H])(N([H])N2C([H])([H])C(... | <fegrow.package.RMol object at 0x7bdc2044e3e0> | 4.476 | 6 | True | True | False | NaN |
| 2379 | [H]c1nc([H])c(C(=O)N(N([H])C(=O)C([H])([H])[H]... | <fegrow.package.RMol object at 0x7bdc2044e7a0> | 4.054 | 6 | True | True | False | NaN |
| 2318 | [H]OC([H])([H])S(=O)(=O)C([H])([H])c1c([H])nc(... | <fegrow.package.RMol object at 0x7bdd80fff510> | 0.0 | 6 | True | False | False | NaN |
| 410 | [H]c1nc([H])c(S(=O)(=O)C([H])(C([H])([H])[H])C... | <fegrow.package.RMol object at 0x7bdc843264d0> | 3.812 | 6 | True | True | False | NaN |
| 877 | [H]c1nc([H])c(C([H])([H])C(=O)N([H])C(=O)OC([H... | <fegrow.package.RMol object at 0x7bdc9c3ce890> | 4.185 | 6 | True | True | False | NaN |
| 2084 | [H]c1nc([H])c(-c2nc(OC([H])([H])c3c([H])c([H])... | <fegrow.package.RMol object at 0x7bdd80fefc40> | 0.0 | 6 | True | False | False | NaN |
| 548 | [H]Oc1c([H])c([H])c([H])c(S(=O)(=O)N([H])c2c([... | <fegrow.package.RMol object at 0x7bdc9c3cf1f0> | 0.0 | 6 | True | False | False | NaN |
| 875 | [H]OC(=O)C([H])([H])N([H])C(=O)C([H])([H])c1c(... | <fegrow.package.RMol object at 0x7bdc2044f8d0> | 3.226 | 6 | True | True | False | NaN |
| 2345 | [H]c1nc([H])c(C([H])([H])S(=O)(=O)N2C([H])([H]... | <fegrow.package.RMol object at 0x7bdc60120a40> | 4.236 | 6 | True | True | False | NaN |
| 133 | [H]c1nc([H])c(N([H])C(=O)N2C([H])([H])C([H])([... | <fegrow.package.RMol object at 0x7bdc2044ff10> | 4.202 | 6 | True | True | False | NaN |
| 2016 | [H]C(=NOC([H])([H])C([H])([H])[H])c1c([H])nc([... | <fegrow.package.RMol object at 0x7bdc2044f330> | 3.267 | 6 | True | True | False | NaN |
| 627 | [H]c1nc([H])c(C([H])([H])N([H])C(=O)OC([H])([H... | <fegrow.package.RMol object at 0x7bdc2044fe20> | 3.571 | 6 | True | True | False | NaN |
| 2033 | [H]C(=NN1C([H])([H])C([H])([H])N(C([H])([H])[H... | <fegrow.package.RMol object at 0x7bdc20458ae0> | 3.41 | 6 | True | True | False | NaN |
| 1975 | [H]OC(=O)C([H])([H])C([H])=Nc1c([H])nc([H])c([... | <fegrow.package.RMol object at 0x7bdc20458ea0> | 3.487 | 6 | True | True | False | NaN |
| 2028 | [H]C(=NC([H])([H])C([H])([H])C([H])([H])C([H])... | <fegrow.package.RMol object at 0x7bdd810a8bd0> | 3.363 | 6 | True | True | False | NaN |
| 2130 | [H]c1nc([H])c(-c2noc(N([H])C([H])([H])[H])n2)c... | <fegrow.package.RMol object at 0x7bdc2044f9c0> | 4.033 | 6 | True | True | False | NaN |
| 1107 | [H]OC(=O)C([H])([H])Sc1c([H])nc([H])c([H])c1[H] | <fegrow.package.RMol object at 0x7bdc84669c60> | 0.0 | 6 | True | False | False | NaN |
| 490 | [H]c1nc([H])c(S(=O)(=O)N([H])c2c([H])c([H])c(C... | <fegrow.package.RMol object at 0x7bdc2044d760> | 5.187 | 6 | True | True | False | NaN |
| 1728 | [H]c1nc([H])c([C@]([H])(C([H])([H])[H])C([H])(... | <fegrow.package.RMol object at 0x7bdc20459df0> | 3.503 | 6 | True | True | False | NaN |
Note that molecules that have a steric clash with the receptor (and therefore cannot be built) are assigned a score of zero. Occasionally a molecule cannot be built with RDKit or assigned force field parameters, and in these cases the molecule is discarded completely.
computed = cs.df[~cs.df.score.isna()]
print("Computed cases in total: ", len(computed))
Computed cases in total: 50
Active learning cycles:#
In this example we use a Gaussian process model, with a UCB acquisition function
# The query methods available in modAL.acquisition are made available, these include
# Query.greedy(),
# Query.PI(tradeoff=0) - highest probability of improvement
# Query.EI(tradeoff=0) - highest expected improvement
# Query.UCB(beta=1) - highest upper confidence bound (employes modAL.models.BayesianOptimizer)
# Models include the scikit:
# Model.linear()
# Model.elastic_net()
# Model.random_forest()
# Model.gradient_boosting_regressor()
# Model.mlp_regressor()
# Model.gaussian_process() # uses a TanimotoKernel by default, meaning that it
# # compares the fingerprints of all the training dataset
# # with the cases not yet studied, which can be expensive
# # computationally
cs.model = Model.gaussian_process()
cs.query = Query.UCB(beta=1)
Perform 3 cycles of active learning, with 50 picks per cycle:
for cycle in range(3):
picks = cs.active_learning(50)
picks_results = cs.evaluate(
picks, num_conf=50, gnina_gpu=True, penalty=0.0, al_ignore_penalty=False
)
# save the new results
picks_results.to_csv(f"notebook_iteration{cycle}_results.csv")
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/18 [00:00<?, ?it/s]
Generated 18 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 6%|█▏ | 1/18 [00:03<01:01, 3.62s/it]
Generated 38 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 4%|▊ | 1/26 [00:03<01:28, 3.53s/it]
Generated 30 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/23 [00:00<?, ?it/s] Optimising conformer: 17%|███▋ | 3/18 [00:08<00:38, 2.60s/it]
Generated 30 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/23 [00:00<?, ?it/s]
Generated 31 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 22%|████▉ | 4/18 [00:10<00:33, 2.39s/it]
Generated 44 conformers.
Removed 29 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 28%|██████ | 5/18 [00:13<00:34, 2.62s/it]
Generated 40 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/7 [00:00<?, ?it/s]
Generated 14 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 23%|█████ | 5/22 [00:13<00:46, 2.72s/it]
Generated 19 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 78%|████████████████▎ | 14/18 [00:38<00:10, 2.66s/it]
Generated 28 conformers.
Removed 17 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 18/18 [00:51<00:00, 2.84s/it]
Optimising conformer: 86%|██████████████████▏ | 19/22 [00:47<00:07, 2.46s/it]
Generated 26 conformers.
Removed 16 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 7/7 [00:44<00:00, 6.40s/it]
Optimising conformer: 100%|█████████████████████| 22/22 [00:53<00:00, 2.45s/it]
Optimising conformer: 73%|███████████████▍ | 11/15 [00:55<00:21, 5.32s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 30%|██████▌ | 3/10 [00:13<00:30, 4.41s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 15/15 [00:53<00:00, 3.54s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 23/23 [01:13<00:00, 3.18s/it]
Optimising conformer: 100%|█████████████████████| 15/15 [01:17<00:00, 5.15s/it]
Optimising conformer: 96%|████████████████████▏| 25/26 [01:27<00:02, 2.87s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 11/11 [00:54<00:00, 4.94s/it]
Optimising conformer: 100%|█████████████████████| 27/27 [01:20<00:00, 2.99s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 23/23 [01:28<00:00, 3.86s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 26/26 [01:36<00:00, 3.72s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 80%|█████████████████▌ | 8/10 [00:48<00:11, 5.59s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 90%|███████████████████▊ | 9/10 [00:51<00:04, 4.71s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [00:58<00:00, 5.85s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 25 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 59%|████████████▎ | 10/17 [00:22<00:13, 1.91s/it]
Generated 30 conformers.
Removed 5 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/9 [00:00<?, ?it/s]
Generated 36 conformers.
Removed 25 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 40 conformers.
Removed 31 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 17/17 [00:34<00:00, 2.03s/it]
Optimising conformer: 28%|██████▏ | 7/25 [00:15<00:33, 1.89s/it]
Generated 11 conformers.
Removed 5 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 33%|███████▋ | 3/9 [00:12<00:23, 3.87s/it]
Generated 8 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 17%|███▊ | 1/6 [00:03<00:19, 3.96s/it]
Generated 32 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 5%|█▏ | 1/19 [00:04<01:15, 4.21s/it]
Generated 41 conformers.
Removed 27 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 36%|███████▉ | 9/25 [00:25<00:51, 3.20s/it]
Generated 49 conformers.
Removed 38 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 2/2 [00:07<00:00, 3.66s/it]
Optimising conformer: 40%|████████▍ | 10/25 [00:27<00:42, 2.86s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 6/6 [00:13<00:00, 2.20s/it]
Optimising conformer: 14%|███▏ | 2/14 [00:09<00:52, 4.33s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 89%|████████████████████▍ | 8/9 [00:32<00:03, 3.97s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 9/9 [00:36<00:00, 4.04s/it]
Optimising conformer: 0%| | 0/13 [00:00<?, ?it/s]
Generated 47 conformers.
Removed 34 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 80%|████████████████▊ | 20/25 [00:50<00:11, 2.24s/it]
Generated 24 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/10 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 11/11 [00:47<00:00, 4.33s/it]
Optimising conformer: 57%|████████████▌ | 8/14 [00:36<00:27, 4.63s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 25/25 [01:05<00:00, 2.62s/it]
Optimising conformer: 91%|███████████████████ | 10/11 [00:50<00:04, 4.35s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 11/11 [00:53<00:00, 4.83s/it]
Optimising conformer: 100%|█████████████████████| 14/14 [00:54<00:00, 3.92s/it]
Optimising conformer: 100%|█████████████████████| 19/19 [01:09<00:00, 3.64s/it]
Generated 22 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s]
Generated 10 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 90%|███████████████████▊ | 9/10 [00:41<00:04, 4.49s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 33%|███████▋ | 1/3 [00:04<00:08, 4.31s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 3/3 [00:08<00:00, 2.70s/it]
Optimising conformer: 100%|█████████████████████| 10/10 [00:46<00:00, 4.69s/it]
Optimising conformer: 14%|███▏ | 3/21 [00:08<00:50, 2.81s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/26 [00:00<?, ?it/s]
Generated 30 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 33%|███████▎ | 7/21 [00:18<00:32, 2.33s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 4%|▊ | 1/26 [00:04<01:55, 4.62s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 13/13 [01:06<00:00, 5.08s/it]
Optimising conformer: 0%| | 0/15 [00:00<?, ?it/s]
Generated 19 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 7%|█▍ | 1/15 [00:06<01:31, 6.55s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/31 [00:00<?, ?it/s]
Generated 34 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 27%|█████▊ | 4/15 [00:12<00:26, 2.43s/it]
Generated 38 conformers.
Removed 21 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 50%|██████████▌ | 13/26 [00:32<00:29, 2.26s/it]
Generated 45 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 21/21 [00:51<00:00, 2.45s/it]
Optimising conformer: 4%|▊ | 1/27 [00:08<03:28, 8.01s/it]
Generated 8 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 77%|████████████████▏ | 20/26 [00:46<00:11, 1.97s/it]
Generated 38 conformers.
Removed 19 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 15/15 [00:43<00:00, 2.87s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 22%|████▉ | 6/27 [00:25<01:15, 3.60s/it]
Generated 29 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 96%|████████████████████▏| 25/26 [00:59<00:02, 2.31s/it]
Generated 25 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 26/26 [01:02<00:00, 2.40s/it]
Optimising conformer: 32%|██████▉ | 6/19 [00:17<00:39, 3.03s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 8/8 [00:29<00:00, 3.71s/it]
Optimising conformer: 19%|████▏ | 4/21 [00:12<00:48, 2.83s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 42%|█████████▎ | 8/19 [00:26<00:34, 3.15s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/4 [00:00<?, ?it/s]
Generated 33 conformers.
Removed 29 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 19/19 [01:02<00:00, 3.31s/it]
Optimising conformer: 100%|█████████████████████| 21/21 [00:58<00:00, 2.77s/it]
Optimising conformer: 89%|██████████████████▋ | 24/27 [01:25<00:09, 3.01s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 19/19 [01:00<00:00, 3.18s/it]
Optimising conformer: 100%|█████████████████████| 31/31 [01:46<00:00, 3.45s/it]
Optimising conformer: 93%|███████████████████▍ | 25/27 [01:28<00:06, 3.18s/it]
Generated 38 conformers.
Removed 32 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:30<00:00, 7.52s/it]
Optimising conformer: 96%|████████████████████▏| 26/27 [01:38<00:05, 5.04s/it]
Generated 29 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 27/27 [01:40<00:00, 3.73s/it]
Optimising conformer: 17%|███▊ | 1/6 [00:12<01:01, 12.40s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 5%|█▏ | 1/19 [00:04<01:18, 4.33s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/13 [00:00<?, ?it/s]
Generated 41 conformers.
Removed 28 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 50%|███████████▌ | 3/6 [00:21<00:19, 6.45s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 8%|█▋ | 1/13 [00:05<01:11, 5.96s/it]
Generated 44 conformers.
Removed 39 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 5/5 [00:19<00:00, 3.82s/it]
Optimising conformer: 100%|███████████████████████| 6/6 [00:46<00:00, 7.74s/it]
Optimising conformer: 79%|████████████████▌ | 15/19 [00:42<00:10, 2.66s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 69%|███████████████▏ | 9/13 [00:37<00:16, 4.10s/it]
Generated 23 conformers.
Removed 16 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/7 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 84%|█████████████████▋ | 16/19 [00:46<00:09, 3.09s/it]
Generated 41 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 77%|████████████████▏ | 10/13 [00:41<00:12, 4.03s/it]
Generated 43 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 19/19 [00:53<00:00, 2.84s/it]
Optimising conformer: 92%|███████████████████▍ | 12/13 [00:48<00:03, 3.73s/it]
Generated 35 conformers.
Removed 15 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 13/13 [00:51<00:00, 3.94s/it]
Optimising conformer: 18%|███▉ | 6/34 [00:17<01:10, 2.50s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 24%|█████▏ | 8/34 [00:21<00:59, 2.29s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 94%|███████████████████▊ | 16/17 [03:06<00:12, 12.87s/it]
Generated 47 conformers.
Removed 30 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 17/17 [03:12<00:00, 11.30s/it]
Optimising conformer: 0%| | 0/18 [00:00<?, ?it/s]
Generated 41 conformers.
Removed 23 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 7/7 [00:42<00:00, 6.05s/it]
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 35 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/15 [00:00<?, ?it/s]
Generated 19 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 20/20 [00:48<00:00, 2.45s/it]
Optimising conformer: 39%|████████▌ | 7/18 [00:26<00:37, 3.37s/it]
Generated 30 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 9%|█▉ | 2/23 [00:11<02:12, 6.32s/it]
Generated 31 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 34/34 [01:24<00:00, 2.50s/it]
Optimising conformer: 100%|█████████████████████| 15/15 [00:43<00:00, 2.90s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [01:10<00:00, 3.94s/it]
Optimising conformer: 100%|█████████████████████| 17/17 [01:20<00:00, 4.72s/it]
Optimising conformer: 56%|███████████▋ | 10/18 [00:35<00:23, 2.91s/it]
Generated 40 conformers.
Removed 16 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 23/23 [00:56<00:00, 2.45s/it]
Optimising conformer: 12%|██▊ | 3/24 [00:11<01:13, 3.50s/it]
Generated 20 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 21/21 [01:20<00:00, 3.81s/it]
Optimising conformer: 100%|█████████████████████| 33/33 [02:12<00:00, 4.00s/it]
Optimising conformer: 100%|███████████████████████| 9/9 [00:17<00:00, 1.94s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [01:06<00:00, 3.72s/it]
Optimising conformer: 100%|█████████████████████| 24/24 [00:53<00:00, 2.24s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 18 conformers.
Removed 1 conformers.
Using force field
Optimising conformer: 100%|█████████████████████| 17/17 [00:12<00:00, 1.37it/s]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 19 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/18 [00:00<?, ?it/s]
Generated 18 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/18 [00:00<?, ?it/s]
Generated 16 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/25 [00:00<?, ?it/s]
Generated 40 conformers.
Removed 15 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/20 [00:00<?, ?it/s]
Generated 23 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 47%|██████████▎ | 7/15 [00:16<00:17, 2.19s/it]
Generated 16 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/17 [00:00<?, ?it/s]
Generated 40 conformers.
Removed 23 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/17 [00:00<?, ?it/s]
Generated 27 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 87%|██████████████████▏ | 13/15 [00:32<00:05, 2.54s/it]
Generated 37 conformers.
Removed 36 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 15/15 [00:36<00:00, 2.45s/it]
Optimising conformer: 61%|████████████▊ | 11/18 [00:43<00:25, 3.71s/it]
Generated 15 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 1/1 [00:11<00:00, 11.35s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [00:49<00:00, 2.74s/it]
Optimising conformer: 0%| | 0/4 [00:00<?, ?it/s]
Generated 38 conformers.
Removed 34 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 83%|█████████████████▌ | 15/18 [00:58<00:11, 3.67s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 75%|█████████████████▎ | 6/8 [00:42<00:14, 7.25s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 8/8 [00:56<00:00, 7.06s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [01:18<00:00, 4.37s/it]
Optimising conformer: 100%|█████████████████████| 20/20 [01:14<00:00, 3.71s/it]
Optimising conformer: 100%|█████████████████████| 17/17 [00:55<00:00, 3.29s/it]
Optimising conformer: 100%|█████████████████████| 15/15 [00:46<00:00, 3.07s/it]
Optimising conformer: 100%|█████████████████████| 25/25 [01:19<00:00, 3.17s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 4/4 [00:53<00:00, 13.31s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 65%|█████████████▌ | 11/17 [01:28<00:38, 6.43s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 71%|██████████████▊ | 12/17 [01:31<00:26, 5.32s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 76%|████████████████ | 13/17 [01:33<00:16, 4.19s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 88%|██████████████████▌ | 15/17 [01:36<00:05, 2.84s/it]
Generated 36 conformers.
Removed 24 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/12 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray. coords = np.asanyarray(value, dtype=np.float64)
Generated 16 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 94%|███████████████████▊ | 16/17 [01:39<00:02, 2.80s/it]
Generated 46 conformers.
Removed 25 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s]
Generated 46 conformers.
Removed 31 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 17/17 [01:40<00:00, 5.94s/it]
Optimising conformer: 10%|██ | 2/21 [00:09<01:26, 4.53s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 83%|█████████████████▌ | 10/12 [00:31<00:05, 2.52s/it]
Generated 27 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 12/12 [00:36<00:00, 3.04s/it]
Optimising conformer: 100%|███████████████████████| 8/8 [00:37<00:00, 4.65s/it]
Optimising conformer: 52%|███████████ | 11/21 [00:44<00:45, 4.53s/it]
Generated 29 conformers.
Removed 23 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/6 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 57%|████████████ | 12/21 [00:48<00:37, 4.15s/it]
Generated 50 conformers.
Removed 28 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 17%|███▊ | 1/6 [00:09<00:48, 9.61s/it]
Generated 32 conformers.
Removed 25 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/17 [00:00<?, ?it/s]
Generated 38 conformers.
Removed 21 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 14%|███ | 3/22 [00:18<01:35, 5.02s/it]
Generated 24 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 15/15 [01:10<00:00, 4.70s/it]
Optimising conformer: 100%|█████████████████████| 17/17 [00:48<00:00, 2.85s/it]
Optimising conformer: 100%|█████████████████████| 21/21 [01:21<00:00, 3.88s/it]
Generated 43 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 86%|███████████████████▋ | 6/7 [00:31<00:04, 4.85s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/24 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 36 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 7/7 [00:35<00:00, 5.02s/it]
Optimising conformer: 33%|███████▎ | 5/15 [00:22<00:47, 4.73s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 17%|███▋ | 4/24 [00:16<01:23, 4.17s/it]
Generated 37 conformers.
Removed 16 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 53%|███████████▋ | 8/15 [00:36<00:36, 5.16s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 16 conformers.
Removed 0 conformers.
Using force field
Optimising conformer: 50%|██████████▌ | 11/22 [01:03<00:54, 4.98s/it]
Generated 14 conformers.
Removed 0 conformers.
Using force field
Optimising conformer: 100%|█████████████████████| 16/16 [00:13<00:00, 1.22it/s]
Optimising conformer: 100%|█████████████████████| 14/14 [00:10<00:00, 1.39it/s]
Optimising conformer: 100%|█████████████████████| 15/15 [01:04<00:00, 4.28s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 50%|██████████▌ | 12/24 [00:50<00:50, 4.20s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 68%|██████████████▎ | 15/22 [01:36<00:49, 7.12s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 64%|█████████████▍ | 16/25 [01:18<00:31, 3.50s/it]
Generated 28 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/23 [00:00<?, ?it/s]
Generated 41 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 21/21 [01:04<00:00, 3.09s/it]
Optimising conformer: 100%|█████████████████████| 24/24 [01:24<00:00, 3.52s/it]
Optimising conformer: 100%|█████████████████████| 22/22 [02:04<00:00, 5.68s/it]
Optimising conformer: 26%|█████▋ | 6/23 [00:15<00:38, 2.24s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 30%|██████▋ | 7/23 [00:17<00:34, 2.13s/it]2025-03-14 21:43:14,213 - distributed.worker - ERROR - Compute Failed
Key: _evaluate_atomic-755b3c3f-4940-4b87-a749-caf607e74788
State: executing
Task: <Task '_evaluate_atomic-755b3c3f-4940-4b87-a749-caf607e74788' apply(...)>
Exception: "Exception('No Conformers')"
Traceback: ' File "/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/dask/utils.py", line 77, in apply\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File "/home/dresio/code/fegrow/fegrow/package.py", line 1830, in _evaluate_atomic\n raise Exception("No Conformers")\n'
Optimising conformer: 84%|█████████████████▋ | 21/25 [01:51<00:29, 7.29s/it]
Generated 40 conformers.
Removed 30 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/10 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 57%|███████████▊ | 13/23 [00:45<00:47, 4.71s/it]
Generated 41 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 75%|███████████████▊ | 12/16 [00:55<00:15, 3.89s/it]
Generated 33 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 25/25 [02:21<00:00, 5.64s/it]
Optimising conformer: 94%|███████████████████▋ | 15/16 [01:09<00:04, 4.08s/it]
Generated 33 conformers.
Removed 23 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [01:12<00:00, 4.54s/it]
Optimising conformer: 90%|███████████████████▊ | 9/10 [00:42<00:04, 4.64s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 35 conformers.
Removed 28 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 10/10 [00:45<00:00, 4.52s/it]
Optimising conformer: 41%|████████▌ | 11/27 [00:30<00:41, 2.58s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 14%|███▎ | 1/7 [00:07<00:46, 7.83s/it]
Generated 29 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 36 conformers.
Removed 36 conformers.
Warning: no conformers so cannot optimise_in_receptor. Ignoring.
Generated 25 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 23/23 [01:27<00:00, 3.82s/it]
Optimising conformer: 63%|█████████████▏ | 17/27 [00:42<00:21, 2.11s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 6/6 [03:33<00:00, 35.58s/it]
Optimising conformer: 21%|████▋ | 4/19 [00:17<01:02, 4.18s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 31%|██████▉ | 5/16 [00:19<00:44, 4.07s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [00:44<00:00, 4.48s/it]
Optimising conformer: 100%|███████████████████████| 7/7 [00:39<00:00, 5.60s/it]
Optimising conformer: 100%|█████████████████████| 27/27 [01:06<00:00, 2.46s/it]
Optimising conformer: 68%|██████████████▎ | 13/19 [00:41<00:14, 2.39s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 69%|██████████████▍ | 11/16 [00:40<00:16, 3.31s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 79%|████████████████▌ | 15/19 [00:48<00:11, 2.88s/it]
Generated 33 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/20 [00:00<?, ?it/s] Optimising conformer: 29%|██████▍ | 5/17 [03:55<04:24, 22.07s/it]
Generated 15 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/6 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 22/22 [01:21<00:00, 3.70s/it]
Optimising conformer: 100%|█████████████████████| 16/16 [00:51<00:00, 3.24s/it]
Optimising conformer: 100%|█████████████████████| 19/19 [01:01<00:00, 3.24s/it]
Generated 42 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/39 [00:00<?, ?it/s]
Generated 20 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 50%|███████████▌ | 3/6 [00:14<00:14, 4.79s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 15%|███▎ | 3/20 [00:17<01:22, 4.86s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 6/6 [00:24<00:00, 4.13s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 17/17 [04:28<00:00, 15.81s/it]
Optimising conformer: 35%|███████▋ | 7/20 [00:33<00:55, 4.29s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 53%|███████████ | 10/19 [00:22<00:18, 2.10s/it]
Generated 43 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 68%|██████████████▎ | 13/19 [00:29<00:13, 2.23s/it]
Generated 48 conformers.
Removed 26 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 9%|██ | 3/33 [00:10<01:34, 3.14s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/25 [00:00<?, ?it/s]
Generated 30 conformers.
Removed 5 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 19/19 [00:44<00:00, 2.33s/it]
Optimising conformer: 0%| | 0/15 [00:00<?, ?it/s]
Generated 50 conformers.
Removed 35 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 74%|███████████████▌ | 29/39 [01:12<00:21, 2.13s/it]
Generated 45 conformers.
Removed 37 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 50%|██████████▌ | 11/22 [00:46<00:44, 4.00s/it]
Generated 28 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 20/20 [01:32<00:00, 4.64s/it]
Optimising conformer: 64%|█████████████▎ | 21/33 [00:59<00:26, 2.18s/it]
Generated 31 conformers.
Removed 23 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/27 [00:00<?, ?it/s]
Generated 30 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 39/39 [01:39<00:00, 2.55s/it]
Optimising conformer: 100%|█████████████████████| 25/25 [00:58<00:00, 2.36s/it]
Optimising conformer: 100%|█████████████████████| 22/22 [01:25<00:00, 3.87s/it]
Optimising conformer: 100%|█████████████████████| 33/33 [01:31<00:00, 2.76s/it]
Optimising conformer: 100%|███████████████████████| 8/8 [00:44<00:00, 5.56s/it]
Optimising conformer: 100%|█████████████████████| 15/15 [01:04<00:00, 4.28s/it]
Optimising conformer: 100%|███████████████████████| 8/8 [00:46<00:00, 5.83s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [00:56<00:00, 3.16s/it]
Optimising conformer: 100%|█████████████████████| 27/27 [00:50<00:00, 1.86s/it]
Generated 47 conformers.
Removed 31 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [00:33<00:00, 2.11s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 19 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 8%|█▋ | 1/13 [00:03<00:42, 3.52s/it]
Generated 25 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/14 [00:00<?, ?it/s]
Generated 20 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 18 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 5%|█▏ | 1/19 [00:07<02:21, 7.88s/it]
Generated 47 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 54%|███████████▊ | 7/13 [00:16<00:15, 2.59s/it]
Generated 32 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:15<00:00, 3.79s/it]
Optimising conformer: 0%| | 0/27 [00:00<?, ?it/s]
Generated 40 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/6 [00:00<?, ?it/s] Optimising conformer: 92%|███████████████████▍ | 12/13 [00:27<00:02, 2.34s/it]
Generated 15 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 13/13 [00:31<00:00, 2.43s/it]
Optimising conformer: 10%|██▏ | 3/30 [00:15<02:22, 5.27s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/13 [00:00<?, ?it/s]
Generated 27 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 71%|███████████████ | 10/14 [00:31<00:13, 3.36s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 15%|███▍ | 2/13 [00:08<00:44, 4.07s/it]
Generated 22 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 14/14 [00:41<00:00, 2.99s/it]
Optimising conformer: 100%|███████████████████████| 6/6 [00:25<00:00, 4.17s/it]
Optimising conformer: 100%|█████████████████████| 19/19 [00:50<00:00, 2.66s/it]
Optimising conformer: 62%|█████████████▌ | 8/13 [00:25<00:12, 2.47s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 40%|████████▍ | 12/30 [00:44<00:51, 2.87s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 39%|████████▎ | 15/38 [00:49<01:18, 3.39s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/6 [00:00<?, ?it/s]
Generated 6 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 13/13 [00:40<00:00, 3.08s/it]
Optimising conformer: 63%|█████████████▎ | 24/38 [01:09<00:31, 2.25s/it]
Generated 25 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 8/8 [00:38<00:00, 4.81s/it]
Optimising conformer: 66%|█████████████▊ | 25/38 [01:13<00:35, 2.72s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 6/6 [00:21<00:00, 3.50s/it]
Optimising conformer: 73%|███████████████▍ | 22/30 [01:16<00:20, 2.57s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/4 [00:00<?, ?it/s]
Generated 4 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 81%|█████████████████ | 22/27 [01:17<00:16, 3.21s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 4/4 [00:15<00:00, 3.81s/it]
Optimising conformer: 100%|█████████████████████| 27/27 [01:27<00:00, 3.26s/it]
Optimising conformer: 100%|█████████████████████| 30/30 [01:40<00:00, 3.34s/it]
Optimising conformer: 100%|█████████████████████| 38/38 [01:46<00:00, 2.82s/it]
Optimising conformer: 50%|███████████ | 8/16 [00:40<00:34, 4.28s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 56%|████████████▍ | 9/16 [00:47<00:35, 5.04s/it]
Generated 4 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 69%|██████████████▍ | 11/16 [00:58<00:27, 5.53s/it]
Generated 29 conformers.
Removed 17 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 3/3 [00:12<00:00, 4.06s/it]
Optimising conformer: 75%|███████████████▊ | 12/16 [01:08<00:27, 6.86s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 81%|█████████████████ | 13/16 [01:11<00:16, 5.61s/it]
Generated 45 conformers.
Removed 28 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 25%|█████▌ | 3/12 [00:12<00:35, 3.99s/it]
Generated 4 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [01:23<00:00, 5.24s/it]
Optimising conformer: 75%|█████████████████▎ | 3/4 [00:10<00:03, 3.14s/it]
Generated 43 conformers.
Removed 31 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 58%|████████████▊ | 7/12 [00:27<00:16, 3.35s/it]
Generated 15 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:14<00:00, 3.61s/it]
Optimising conformer: 75%|████████████████▌ | 9/12 [00:31<00:08, 2.74s/it]
Generated 16 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/10 [00:00<?, ?it/s]
Generated 24 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/22 [00:00<?, ?it/s]
Generated 31 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 18%|████ | 2/11 [00:10<00:44, 4.96s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 12/12 [00:41<00:00, 3.45s/it]
Optimising conformer: 36%|████████ | 4/11 [00:17<00:29, 4.23s/it]
Generated 37 conformers.
Removed 25 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 18%|████ | 4/22 [00:15<01:16, 4.26s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [00:32<00:00, 3.27s/it]
Optimising conformer: 100%|█████████████████████| 10/10 [00:36<00:00, 3.70s/it]
Optimising conformer: 42%|█████████▏ | 5/12 [00:27<00:35, 5.00s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 55%|███████████▍ | 12/22 [00:41<00:35, 3.58s/it]
Generated 20 conformers.
Removed 15 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 50%|███████████ | 6/12 [00:31<00:27, 4.62s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 11/11 [00:51<00:00, 4.72s/it]
Optimising conformer: 0%| | 0/17 [00:00<?, ?it/s]
Generated 24 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 68%|██████████████▎ | 15/22 [00:53<00:26, 3.72s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 38 conformers.
Removed 22 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 86%|██████████████████▏ | 19/22 [01:09<00:11, 3.87s/it]
Generated 8 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 83%|█████████████████▌ | 10/12 [01:01<00:13, 6.69s/it]
Generated 23 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 5/5 [00:38<00:00, 7.62s/it]
Optimising conformer: 100%|█████████████████████| 22/22 [01:22<00:00, 3.76s/it]
Optimising conformer: 100%|█████████████████████| 12/12 [01:14<00:00, 6.19s/it]
Optimising conformer: 88%|████████████████████▏ | 7/8 [00:18<00:02, 2.18s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 8/8 [00:21<00:00, 2.71s/it]
Generated 16 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/3 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/11 [00:00<?, ?it/s]
Generated 22 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 31%|██████▉ | 5/16 [00:37<01:17, 7.00s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 3/3 [00:10<00:00, 3.63s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 45%|██████████ | 5/11 [00:15<00:16, 2.80s/it]
Generated 17 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 55%|████████████ | 6/11 [00:17<00:13, 2.63s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 11/11 [00:43<00:00, 3.94s/it]
Optimising conformer: 100%|█████████████████████| 11/11 [00:29<00:00, 2.69s/it]
Optimising conformer: 88%|██████████████████▌ | 15/17 [02:32<00:12, 6.15s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 94%|███████████████████▊ | 16/17 [01:26<00:05, 5.58s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 17/17 [01:29<00:00, 5.28s/it]
Optimising conformer: 100%|█████████████████████| 17/17 [02:42<00:00, 9.55s/it]
Optimising conformer: 81%|█████████████████ | 13/16 [01:24<00:16, 5.37s/it]
Generated 24 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 77%|████████████████▏ | 10/13 [00:34<00:07, 2.60s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 10%|██▏ | 1/10 [00:04<00:39, 4.41s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 85%|█████████████████▊ | 11/13 [00:40<00:07, 3.77s/it]
Generated 25 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 94%|███████████████████▋ | 15/16 [01:32<00:04, 4.67s/it]
Generated 42 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [01:38<00:00, 6.14s/it]
Optimising conformer: 100%|█████████████████████| 13/13 [00:50<00:00, 3.89s/it]
Optimising conformer: 80%|█████████████████▌ | 8/10 [00:24<00:06, 3.04s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 20%|████▍ | 6/30 [00:17<01:10, 2.93s/it]
Generated 25 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/15 [00:00<?, ?it/s]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [00:34<00:00, 3.43s/it]
Generated 39 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/4 [00:00<?, ?it/s]
Generated 18 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 37%|███████▋ | 11/30 [00:32<00:59, 3.15s/it]
Generated 4 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 53%|███████████▋ | 9/17 [00:36<00:30, 3.77s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 20 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:16<00:00, 4.15s/it]
Optimising conformer: 100%|███████████████████████| 3/3 [00:15<00:00, 5.06s/it]
Optimising conformer: 63%|█████████████▎ | 19/30 [00:54<00:29, 2.65s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 70%|██████████████▋ | 21/30 [00:59<00:22, 2.47s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 56%|████████████▍ | 9/16 [00:28<00:19, 2.80s/it]
Generated 46 conformers.
Removed 26 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 40%|████████▍ | 12/30 [00:40<00:58, 3.25s/it]
Generated 30 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 17/17 [01:18<00:00, 4.60s/it]
Optimising conformer: 100%|█████████████████████| 15/15 [01:03<00:00, 4.25s/it]
Optimising conformer: 100%|█████████████████████| 30/30 [01:27<00:00, 2.91s/it]
Optimising conformer: 25%|█████▌ | 4/16 [00:18<00:50, 4.24s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 16/16 [00:50<00:00, 3.13s/it]
Optimising conformer: 67%|██████████████ | 20/30 [01:02<00:22, 2.25s/it]
Generated 28 conformers.
Removed 22 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 70%|██████████████▋ | 21/30 [01:04<00:19, 2.21s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 50%|██████████▌ | 10/20 [00:29<00:31, 3.15s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 80%|████████████████▊ | 24/30 [01:12<00:14, 2.37s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 30/30 [01:26<00:00, 2.89s/it]
Optimising conformer: 100%|█████████████████████| 20/20 [00:55<00:00, 2.80s/it]
Optimising conformer: 100%|███████████████████████| 6/6 [00:33<00:00, 5.53s/it]
Optimising conformer: 100%|█████████████████████| 16/16 [00:56<00:00, 3.53s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 58%|████████████▊ | 7/12 [04:55<01:21, 16.28s/it]
Generated 23 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 30 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 18%|████ | 2/11 [00:05<00:22, 2.49s/it] Optimising conformer: 0%| | 0/13 [00:00<?, ?it/s]
Generated 33 conformers.
Removed 20 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/12 [00:00<?, ?it/s]
Generated 18 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 11/11 [00:26<00:00, 2.44s/it]
Optimising conformer: 0%| | 0/11 [00:00<?, ?it/s]
Generated 22 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 29 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/20 [00:00<?, ?it/s]
Generated 46 conformers.
Removed 26 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 13/13 [00:28<00:00, 2.20s/it]
Optimising conformer: 100%|█████████████████████| 12/12 [05:34<00:00, 27.90s/it]
Optimising conformer: 100%|█████████████████████| 11/11 [00:20<00:00, 1.82s/it]
Optimising conformer: 50%|███████████ | 6/12 [00:30<00:28, 4.77s/it]
Generated 45 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [00:51<00:00, 3.24s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [00:41<00:00, 2.30s/it]
Optimising conformer: 100%|█████████████████████| 12/12 [00:49<00:00, 4.13s/it]
Optimising conformer: 100%|█████████████████████| 20/20 [00:41<00:00, 2.07s/it]
Optimising conformer: 100%|█████████████████████| 27/27 [00:56<00:00, 2.09s/it]
The chemical space has been updated with the scores of the built molecules. Also shown are the latest predicted scores given by the regression model.
# show chemical space
cs
| Smiles | score | h | Training | Success | enamine_searched | enamine_id | regression | 2D | |
|---|---|---|---|---|---|---|---|---|---|
| 0 | [H]OC([H])([H])c1c([H])nc([H])c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN | 3.040 | |
| 1 | [H]c1nc([H])c(C([H])([H])OC([H])([H])[H])c([H]... | <NA> | 6 | False | NaN | False | NaN | 3.850 | |
| 2 | [H]c1nc([H])c(C([H])([H])N([H])[H])c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN | 3.426 | |
| 3 | [H]c1nc([H])c(C([H])([H])Cl)c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN | 3.378 | |
| 4 | [H]c1nc([H])c(C([H])([H])F)c([H])c1[H] | <NA> | 6 | False | NaN | False | NaN | 3.723 | |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 2495 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2N2C... | <NA> | 6 | False | NaN | False | NaN | 3.153 | |
| 2496 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2N2C... | <NA> | 6 | False | NaN | False | NaN | 3.176 | |
| 2497 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2-c2... | <NA> | 6 | False | NaN | False | NaN | 3.135 | |
| 2498 | [H]Oc1c([H])c([H])c([H])c(-c2c([H])c([H])c([H]... | <NA> | 6 | False | NaN | False | NaN | 1.976 | |
| 2499 | [H]c1nc([H])c(-c2c([H])c([H])c([H])c([H])c2C([... | <NA> | 6 | False | NaN | False | NaN | 3.096 | |
2500 rows × 9 columns
If we like, we can finish with a greedy selection (ie picking the best binders as predicted by the regression model):
cs.model = Model.gaussian_process()
cs.query = Query.Greedy()
picks = cs.active_learning(50)
picks_results = cs.evaluate(
picks, num_conf=50, gnina_gpu=True, penalty=0.0, al_ignore_penalty=False
)
# save the new results
picks_results.to_csv("notebook_greedy_results.csv")
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Generated 18 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 6%|█▏ | 1/18 [00:03<01:07, 3.96s/it]
Generated 23 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 22%|████▉ | 4/18 [00:11<00:40, 2.87s/it]
Generated 15 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 50%|███████████▌ | 2/4 [00:08<00:08, 4.04s/it]
Generated 28 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 44%|█████████▊ | 8/18 [00:22<00:27, 2.80s/it]
Generated 29 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 19%|████▏ | 3/16 [00:19<01:20, 6.22s/it]
Generated 41 conformers.
Removed 22 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 22 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:14<00:00, 3.72s/it]
Optimising conformer: 25%|█████▌ | 4/16 [00:29<01:31, 7.62s/it]
Generated 33 conformers.
Removed 20 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 16%|███▍ | 3/19 [00:11<00:58, 3.65s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 15%|███▍ | 2/13 [00:13<01:15, 6.90s/it]
Generated 40 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|███████████████████████| 4/4 [00:23<00:00, 5.81s/it]
Optimising conformer: 100%|█████████████████████| 18/18 [00:51<00:00, 2.86s/it]
Optimising conformer: 63%|█████████████▎ | 12/19 [00:36<00:22, 3.18s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 53%|███████████ | 10/19 [00:37<00:31, 3.46s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 50%|███████████ | 8/16 [01:02<01:03, 7.92s/it]
Generated 48 conformers.
Removed 39 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [01:01<00:00, 3.82s/it]
Optimising conformer: 100%|█████████████████████| 19/19 [01:00<00:00, 3.17s/it]
Optimising conformer: 85%|█████████████████▊ | 11/13 [00:51<00:07, 3.77s/it]
Generated 42 conformers.
Removed 21 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 55%|███████████▍ | 12/22 [00:43<00:41, 4.20s/it]
Generated 24 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 92%|███████████████████▍ | 12/13 [00:58<00:04, 4.70s/it]
Generated 38 conformers.
Removed 29 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 19/19 [01:08<00:00, 3.59s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 59%|████████████▍ | 13/22 [00:46<00:34, 3.79s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 13/13 [01:02<00:00, 4.77s/it]
Optimising conformer: 89%|████████████████████▍ | 8/9 [00:36<00:03, 3.97s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|███████████████████████| 9/9 [00:40<00:00, 4.54s/it]
Optimising conformer: 19%|████▏ | 4/21 [00:27<01:40, 5.93s/it]
Generated 19 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 44%|██████████▏ | 4/9 [00:23<00:25, 5.15s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 22/22 [01:17<00:00, 3.54s/it]
Optimising conformer: 100%|█████████████████████| 16/16 [02:00<00:00, 7.56s/it]
Optimising conformer: 100%|█████████████████████| 10/10 [00:34<00:00, 3.44s/it]
Optimising conformer: 100%|███████████████████████| 9/9 [00:39<00:00, 4.44s/it]
Generated 45 conformers.
Removed 28 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 52%|███████████ | 11/21 [00:48<00:36, 3.69s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 57%|████████████ | 12/21 [00:50<00:30, 3.37s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 62%|█████████████ | 13/21 [00:53<00:24, 3.07s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 54%|███████████▊ | 7/13 [00:28<00:21, 3.58s/it]
Generated 26 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 18%|███▉ | 3/17 [00:10<00:45, 3.22s/it]
Generated 16 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 62%|█████████████▌ | 8/13 [00:32<00:18, 3.67s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 18 conformers.
Removed 2 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 13/13 [00:49<00:00, 3.83s/it]
Optimising conformer: 53%|███████████▋ | 9/17 [00:34<00:27, 3.46s/it]
Generated 19 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 21/21 [01:26<00:00, 4.13s/it]
Optimising conformer: 100%|█████████████████████| 14/14 [00:34<00:00, 2.43s/it]
Optimising conformer: 55%|███████████▌ | 11/20 [00:36<00:28, 3.15s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 31%|██████▉ | 5/16 [00:15<00:33, 3.01s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/10 [00:00<?, ?it/s]
Generated 14 conformers.
Removed 4 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 75%|███████████████▊ | 15/20 [00:47<00:14, 2.81s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/16 [00:00<?, ?it/s]
Generated 24 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [00:50<00:00, 3.15s/it]
Optimising conformer: 75%|███████████████▊ | 12/16 [00:34<00:12, 3.12s/it]
Generated 34 conformers.
Removed 22 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 17/17 [01:10<00:00, 4.17s/it]
Optimising conformer: 81%|█████████████████ | 13/16 [00:37<00:09, 3.17s/it]
Generated 43 conformers.
Removed 29 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 20/20 [01:06<00:00, 3.30s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 94%|███████████████████▋ | 15/16 [00:46<00:03, 3.82s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 7%|█▌ | 1/14 [00:11<02:25, 11.18s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 16/16 [00:50<00:00, 3.13s/it]
Optimising conformer: 56%|████████████▍ | 9/16 [00:39<00:26, 3.83s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 69%|██████████████▍ | 11/16 [00:44<00:16, 3.32s/it]
Generated 18 conformers.
Removed 12 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 81%|█████████████████ | 13/16 [00:53<00:11, 3.87s/it]
Generated 29 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 50%|███████████▌ | 3/6 [00:12<00:12, 4.00s/it]
Generated 22 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [01:03<00:00, 3.98s/it]
Optimising conformer: 0%| | 0/22 [00:00<?, ?it/s]
Generated 29 conformers.
Removed 7 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 71%|███████████████ | 10/14 [00:51<00:19, 4.92s/it]
Generated 48 conformers.
Removed 27 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 12/12 [00:55<00:00, 4.59s/it]
Optimising conformer: 100%|███████████████████████| 6/6 [00:24<00:00, 4.10s/it]
Optimising conformer: 5%|█ | 1/22 [00:04<01:38, 4.67s/it]
Generated 19 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 90%|███████████████████▊ | 9/10 [01:16<00:07, 7.63s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [01:20<00:00, 8.08s/it]
Optimising conformer: 100%|█████████████████████| 14/14 [01:04<00:00, 4.59s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 19%|████▏ | 4/21 [00:21<01:23, 4.94s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 91%|███████████████████ | 10/11 [00:37<00:03, 3.88s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 11/11 [00:42<00:00, 3.88s/it]
Optimising conformer: 50%|██████████▌ | 11/22 [00:30<00:31, 2.84s/it]
Generated 19 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 11/11 [00:40<00:00, 3.71s/it]
Optimising conformer: 11%|██▌ | 1/9 [00:07<01:00, 7.53s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 38%|████████▍ | 8/21 [00:39<00:59, 4.55s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 10/10 [00:41<00:00, 4.10s/it]
Optimising conformer: 62%|█████████████ | 13/21 [00:52<00:23, 2.90s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/19 [00:00<?, ?it/s]
Generated 29 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/4 [00:00<?, ?it/s]
Generated 13 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 11%|██▎ | 2/19 [00:06<00:48, 2.87s/it]
Generated 23 conformers.
Removed 5 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 89%|████████████████████▍ | 8/9 [00:37<00:03, 3.98s/it]
Generated 17 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 22/22 [01:13<00:00, 3.34s/it]
Optimising conformer: 100%|███████████████████████| 9/9 [00:42<00:00, 4.74s/it]
Optimising conformer: 100%|███████████████████████| 4/4 [00:14<00:00, 3.74s/it]
Optimising conformer: 100%|█████████████████████| 21/21 [01:18<00:00, 3.74s/it]
Optimising conformer: 24%|█████▏ | 4/17 [00:14<00:42, 3.31s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 63%|█████████████▎ | 12/19 [00:33<00:19, 2.84s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 41%|█████████ | 7/17 [00:23<00:30, 3.08s/it]
Generated 39 conformers.
Removed 15 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/24 [00:00<?, ?it/s]
Generated 31 conformers.
Removed 9 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 47%|██████████▎ | 8/17 [00:26<00:27, 3.11s/it]
Generated 16 conformers.
Removed 0 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 8%|█▊ | 2/24 [00:10<02:00, 5.47s/it]
Generated 21 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 19/19 [00:51<00:00, 2.70s/it]
Optimising conformer: 27%|██████ | 6/22 [00:23<00:58, 3.67s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 25%|█████▌ | 6/24 [00:30<01:22, 4.60s/it]
Generated 27 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/21 [00:00<?, ?it/s]
Generated 33 conformers.
Removed 13 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Generated 27 conformers.
Removed 6 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 17/17 [01:04<00:00, 3.77s/it]
Optimising conformer: 50%|██████████▌ | 11/22 [00:40<00:44, 4.06s/it]
Generated 23 conformers.
Removed 8 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 16/16 [00:52<00:00, 3.27s/it]
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/43 [00:00<?, ?it/s]
Generated 44 conformers.
Removed 1 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 82%|█████████████████▏ | 18/22 [01:11<00:19, 4.99s/it]
Generated 34 conformers.
Removed 14 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 15/15 [01:06<00:00, 4.46s/it]
Optimising conformer: 100%|█████████████████████| 22/22 [01:26<00:00, 3.91s/it]
Optimising conformer: 20%|████▍ | 4/20 [00:15<01:00, 3.75s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 25%|█████▌ | 5/20 [00:24<01:24, 5.62s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 0%| | 0/24 [00:00<?, ?it/s]
Generated 27 conformers.
Removed 3 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 24/24 [01:53<00:00, 4.74s/it]
Optimising conformer: 90%|███████████████████ | 19/21 [01:18<00:06, 3.17s/it]
Generated 44 conformers.
Removed 33 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 21/21 [01:26<00:00, 4.11s/it]
Optimising conformer: 78%|████████████████▎ | 14/18 [02:36<00:42, 10.54s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 15/15 [01:26<00:00, 5.79s/it]
Optimising conformer: 8%|█▊ | 2/24 [00:21<03:39, 9.99s/it]/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/parmed/structure.py:1799: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
coords = np.asanyarray(value, dtype=np.float64)
Optimising conformer: 100%|█████████████████████| 20/20 [01:40<00:00, 5.01s/it]
Optimising conformer: 83%|█████████████████▌ | 20/24 [01:56<00:09, 2.26s/it]
Generated 34 conformers.
Removed 18 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 18/18 [03:00<00:00, 10.01s/it]
Optimising conformer: 100%|█████████████████████| 20/20 [01:17<00:00, 3.89s/it]
Optimising conformer: 100%|█████████████████████| 24/24 [02:03<00:00, 5.14s/it]
Optimising conformer: 100%|█████████████████████| 11/11 [00:44<00:00, 4.02s/it]
Optimising conformer: 0%| | 0/22 [00:00<?, ?it/s]
Generated 32 conformers.
Removed 10 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 0%| | 0/23 [00:00<?, ?it/s]
Generated 40 conformers.
Removed 17 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 5%|█ | 1/22 [00:03<01:06, 3.19s/it]
Generated 34 conformers.
Removed 11 conformers.
using ani2x
/home/dresio/software/mambaforge/envs/fegrow/lib/python3.11/site-packages/torchani/resources/
failed to equip `nnpops` with error: No module named 'NNPOps'
Optimising conformer: 100%|█████████████████████| 43/43 [01:52<00:00, 2.61s/it]
Optimising conformer: 100%|█████████████████████| 24/24 [01:14<00:00, 3.12s/it]
Optimising conformer: 100%|█████████████████████| 16/16 [00:41<00:00, 2.58s/it]
Optimising conformer: 100%|█████████████████████| 23/23 [00:36<00:00, 1.60s/it]
Optimising conformer: 100%|█████████████████████| 22/22 [00:46<00:00, 2.09s/it]
Optimising conformer: 100%|█████████████████████| 23/23 [00:48<00:00, 2.12s/it]
Write out the chemical space and top scoring structures:
# save the chemical space of built molecules:
failed = False
unbuilt = False
with Chem.SDWriter("notebook_chemspace.sdf") as SD:
columns = cs.df.columns.to_list()
columns.remove("Mol")
for i, row in cs.df.iterrows():
# ignore this molecule because it failed during the build
if failed is False and row.Success is False:
continue
# ignore this molecule because it was not built yet
if unbuilt is False and not row.Success:
continue
mol = row.Mol
mol.SetIntProp("index", i)
for column in columns:
value = getattr(row, column)
mol.SetProp(column, str(value))
mol.ClearProp("attachement_point")
SD.write(mol)
# save the structures of the top 10 molecules in ranked order as a sdf file:
molecules = []
input_sdf = "notebook_chemspace.sdf"
best_n = 10
with Chem.SDMolSupplier(input_sdf) as SDF:
# for each mol
for mol in SDF:
if mol is None:
continue
if mol.GetPropsAsDict()["Success"] == "True":
molecules.append(mol)
# sort by the key
sorted_molecules = sorted(
molecules, key=lambda m: m.GetPropsAsDict()["score"], reverse=True
)
with Chem.SDWriter(f"top_{best_n:d}_{input_sdf}") as SDF_OUT:
for i, mol in enumerate(sorted_molecules):
if i == best_n:
break
SDF_OUT.write(mol)
print("Done")
Done
Note that the options in this tutorial are set to give a fast run time. For full scale simulations, the number of active learning cycles, the size of the chemical space and number of compounds picked per cycle can all be increased.