Custom evaluation failure
protbiochem opened this issue · comments
I've been using DeeplyTough for a while now, and recently our lab changed computers. I've been having issues with getting DeeplyTough to work on the new computer. I've been using the command
python $DEEPLYTOUGH/deeplytough/scripts/custom_evaluation.py --dataset_subdir 'custom' --output_dir $DEEPLYTOUGH/results --device 'cpu' --nworkers 4 --net $DEEPLYTOUGH/networks/deeplytough_toughm1_test.pth.tar
to initiate the comparison, and I've been using the sample dataset provided, but I can't seem to get it to work.
This is the output I've been getting
HTMD: Logging setup failed
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
but OpenBabel found ' ' (atom 1)
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
but OpenBabel found ' ' (atom 2)
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
but OpenBabel found ' ' (atom 3)
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
but OpenBabel found ' ' (atom 4)
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
but OpenBabel found ' ' (atom 5)
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
but OpenBabel found ' ' (atom 6)
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 77-78 should contain the element symbol of an atom.
Hey @protbiochem, nice to hear you've been using DeeplyTough for a while. This output is actually a warning and doesn't indicate failure – its actually openbabel complaining about the PDB format. Is there an error message?
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a9t/1a9t_clean.pdb)
1 molecule converted
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:No module named 'mdtraj'
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 158, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 145, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
ModuleNotFoundError: No module named 'mdtraj'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 167, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 145, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
ModuleNotFoundError: No module named 'mdtraj'
Total number of parameters: 390512
VoxelNetwork(
(0): GatedBlock(
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(8, 0)] -> [(16, 0), (16, 1), (16, 2), (16, 3), (48, 0)], size=7), eps=1e-05, momentum=0.1)
)
(1): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(16, 0), (16, 1), (16, 2), (16, 3)] -> [(32, 0), (32, 1), (32, 2), (32, 3), (96, 0)], size=3), eps=1e-05, momentum=0.1)
)
(2): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(32, 0), (32, 1), (32, 2), (32, 3)] -> [(48, 0), (48, 1), (48, 2), (48, 3), (144, 0)], size=3), eps=1e-05, momentum=0.1)
)
(3): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(48, 0), (48, 1), (48, 2), (48, 3)] -> [(64, 0), (64, 1), (64, 2), (64, 3), (192, 0)], size=3), eps=1e-05, momentum=0.1)
)
(4): GatedBlock(
(conv): SE3BNConvolution (SE3Kernel ([(64, 0), (64, 1), (64, 2), (64, 3)] -> [(256, 0)], size=3), eps=1e-05, momentum=0.1)
)
(5): ReLU(inplace)
(6): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
(7): Conv3d(256, 128, kernel_size=(1, 1, 1), stride=(1, 1, 1))
)
8it [00:00, 165.17it/s]
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a9t/1a9t_clean.npz,corresponding pdb likely could not be parsed
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 69, in
main()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 41, in main
entries = matcher.precompute_descriptors(entries)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/matchers/deeply_tough.py", line 46, in precompute_descriptors
feats = load_and_precompute_point_feats(self.model, self.args, pdb_list, point_list, self.device, self.nworkers, self.batch_size)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/predictor.py", line 37, in load_and_precompute_point_feats
dataset = PointOfInterestVoxelizedDataset(pdb_list, point_list, box_size=args.patch_size)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/datasets.py", line 220, in init
super().init(pdb_list, box_size=box_size, augm_rot=False, augm_mirror_prob=0)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/datasets.py", line 46, in init
assert len(self.pdb_list) > 0, f'No HTMD could be found but {len(pdb_list)}'
AssertionError: No HTMD could be found but 8PDB files were given, please call preprocess_once() on the dataset
Hey @protbiochem, yep this is a common error so might be worth looking at other issues (#1 #4). This error indicates that the HTMD output files could not be found/generated, have you added --db_preprocessing 1 to the command line input as per the README?
You could also check whether .npz files are created in the file directory (if you delete existing ones, they should be recreated).
To me it seems like the issue has to do with openbabel not working, hence all the errors in the beginning. It seems to me that it can't read the PDB file.
I've installed Deeplytough exactly as you indicated, with the only exception being I used conda to install openbabel instead of apt-get. Do you think this could have caused the problem?
Hey @protbiochem, that could be the case but it shouldn't be a problem to install conda vs apt-get. Usually the openbabel warnings are non-critical. Please try running with the db_preprocessing flag:
python $DEEPLYTOUGH/deeplytough/scripts/custom_evaluation.py --dataset_subdir 'custom' --output_dir $DEEPLYTOUGH/results --device 'cpu' --nworkers 4 --net $DEEPLYTOUGH/networks/deeplytough_toughm1_test.pth.tar --db_preprocessing 1Even when I try that input, I get a very similar output as before
setting PYTHONHOME environment
adding gasteiger charges to peptide
Some components of HTMD are now deactivated.
Update with 'conda update htmd -c acellera'
Visit https://software.acellera.com for more information
ERROR:misc.utils:Could not parse selection "protein". Is the selection a valid V MD atom selection?
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learnin g_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 1 58, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learnin g_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 1 46, in compute_channels
mol.filter('protein') # take only on-chain atoms
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/ python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 66 4, in filter
s = self.atomselect(sel)
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/ python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 63 0, in atomselect
occupancy=self.occupancy, bonds=self._getBonds(fileBonds, guessBonds))
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/ python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/vmdparser.py", line 1 60, in vmdselection
raise NameError('Could not parse selection "' + selection + '". Is the selec tion a valid VMD atom selection?')
NameError: Could not parse selection "protein". Is the selection a valid VMD ato m selection?
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learnin g_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 1 67, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learnin g_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 1 46, in compute_channels
mol.filter('protein') # take only on-chain atoms
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/ python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 66 4, in filter
s = self.atomselect(sel)
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/ python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 63 0, in atomselect
occupancy=self.occupancy, bonds=self._getBonds(fileBonds, guessBonds))
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/ python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/vmdparser.py", line 1 60, in vmdselection
raise NameError('Could not parse selection "' + selection + '". Is the selec tion a valid VMD atom selection?')
NameError: Could not parse selection "protein". Is the selection a valid VMD ato m selection?
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/ Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/cu stom/1a9t/1a9t_clean.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
Some components of HTMD are now deactivated.
Update with 'conda update htmd -c acellera'
Visit https://software.acellera.com for more information
1 molecule converted
setting PYTHONHOME environment
adding gasteiger charges to peptide
Some components of HTMD are now deactivated.
Update with 'conda update htmd -c acellera'
Visit https://software.acellera.com for more information
ERROR:misc.utils:Could not parse selection "protein". Is the selection a valid VMD atom selection?
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 158, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 146, in compute_channels
mol.filter('protein') # take only on-chain atoms
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 664, in filter
s = self.atomselect(sel)
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 630, in atomselect
occupancy=self.occupancy, bonds=self._getBonds(fileBonds, guessBonds))
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/vmdparser.py", line 160, in vmdselection
raise NameError('Could not parse selection "' + selection + '". Is the selection a valid VMD atom selection?')
NameError: Could not parse selection "protein". Is the selection a valid VMD atom selection?
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 167, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 146, in compute_channels
mol.filter('protein') # take only on-chain atoms
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 664, in filter
s = self.atomselect(sel)
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/molecule.py", line 630, in atomselect
occupancy=self.occupancy, bonds=self._getBonds(fileBonds, guessBonds))
File "/uufs/chpc.utah.edu/common/home/u1261874/anaconda3/envs/deeplytough/lib/python3.6/site-packages/htmd-0.0.0-py3.6.egg/htmd/molecule/vmdparser.py", line 160, in vmdselection
raise NameError('Could not parse selection "' + selection + '". Is the selection a valid VMD atom selection?')
NameError: Could not parse selection "protein". Is the selection a valid VMD atom selection?
Total number of parameters: 390512
VoxelNetwork(
(0): GatedBlock(
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(8, 0)] -> [(16, 0), (16, 1), (16, 2), (16, 3), (48, 0)], size=7), eps=1e-05, momentum=0.1)
)
(1): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(16, 0), (16, 1), (16, 2), (16, 3)] -> [(32, 0), (32, 1), (32, 2), (32, 3), (96, 0)], size=3), eps=1e-05, momentum=0.1)
)
(2): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(32, 0), (32, 1), (32, 2), (32, 3)] -> [(48, 0), (48, 1), (48, 2), (48, 3), (144, 0)], size=3), eps=1e-05, momentum=0.1)
)
(3): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(48, 0), (48, 1), (48, 2), (48, 3)] -> [(64, 0), (64, 1), (64, 2), (64, 3), (192, 0)], size=3), eps=1e-05, momentum=0.1)
)
(4): GatedBlock(
(conv): SE3BNConvolution (SE3Kernel ([(64, 0), (64, 1), (64, 2), (64, 3)] -> [(256, 0)], size=3), eps=1e-05, momentum=0.1)
)
(5): ReLU(inplace)
(6): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
(7): Conv3d(256, 128, kernel_size=(1, 1, 1), stride=(1, 1, 1))
)
2it [00:00, 41.03it/s]
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a9t/1a9t_clean.npz,corresponding pdb likely could not be parsed
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 69, in
main()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 41, in main
entries = matcher.precompute_descriptors(entries)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/matchers/deeply_tough.py", line 46, in precompute_descriptors
feats = load_and_precompute_point_feats(self.model, self.args, pdb_list, point_list, self.device, self.nworkers, self.batch_size)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/predictor.py", line 37, in load_and_precompute_point_feats
dataset = PointOfInterestVoxelizedDataset(pdb_list, point_list, box_size=args.patch_size)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/datasets.py", line 220, in init
super().init(pdb_list, box_size=box_size, augm_rot=False, augm_mirror_prob=0)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/datasets.py", line 46, in init
assert len(self.pdb_list) > 0, f'No HTMD could be found but {len(pdb_list)}'
AssertionError: No HTMD could be found but 2PDB files were given, please call preprocess_once() on the dataset
Hey @protbiochem, thanks for the extended stack trace and apologies for the delay. This is much more clarifying.
- There is indeed a bug in the current setup. I believe the issue is something around VMD which htmd uses under the hood (this is after the openbabel stage). The main error is here:
"NameError: Could not parse selection "protein". Is the selection a valid VMD atom selection?". - There are also some more minor issues that can be solved by installing mdtraj, natlib and periodictable using pip.
I am still working on a good solution, but to confirm the above you could:
- Confirm that
pdbqtfiles are created and can be loaded into pymol (this proves that openbabel is doing its job) - In the short term, you can comment out
line 146indeeplytough/misc/utils.py:
mol.filter('protein') # take only on-chain atom
This will be safe if there are no waters/metals/ligands in your input file.
Cheers, J.
Hey @protbiochem, I have opened a PR with fixes for your bug thanks for reporting: #14
If you want to try and run the code in the fork (https://github.com/JoshuaMeyers/DeeplyTough), I have updated misc/utils.py with changes that should solve your issue along with the installation of the additional requirements in requirements.txt via pip.
I will merge on Sunday if I don't hear back. Thanks again
After reinstalling everything, it seemed to go much better, but still ended in an error, granted it was a different error
here is the output from running the example dataset from the custom evaluation
HTMD: Logging setup failed
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 30, in
from .formats.registry import FormatRegistry
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a9t/1a9t_clean.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
INFO:misc.utils:Pre-processing /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/custom/1a05B/1a05B.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
ERROR:misc.utils:numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 200, in htmd_featurizer
compute_channels()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/misc/utils.py", line 164, in compute_channels
mol = htmdmol.Molecule(pdbqt_path)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 237, in init
self.read(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/molecule.py", line 896, in read
from htmd.simlist import Sim, Frame
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/simlist.py", line 403, in
from htmd.molecule.readers import _TOPOLOGY_READERS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/htmd-0.0.0-py3.7.egg/htmd/molecule/readers.py", line 1464, in
from mdtraj.core.trajectory import _TOPOLOGY_EXTS as _MDTRAJ_TOPOLOGY_EXTS
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/init.py", line 31, in
from .formats.xtc import load_xtc
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in
from .dcd import DCDTrajectoryFile
File "mdtraj/formats/dcd/dcd.pyx", line 1, in init mdtraj.formats.dcd
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
compute 0.pkl.gz... save 0.pkl.gz... done
compute 0.pkl.gz... save 0.pkl.gz... done
compute 1.pkl.gz... save 1.pkl.gz... done
compute 1.pkl.gz... save 1.pkl.gz... done
compute 2.pkl.gz... save 2.pkl.gz... done
compute 2.pkl.gz... save 2.pkl.gz... done
compute 3.pkl.gz... save 3.pkl.gz... done
compute 3.pkl.gz... save 3.pkl.gz... done
compute 4.pkl.gz... save 4.pkl.gz... done
compute 5.pkl.gz... save 5.pkl.gz... done
compute 4.pkl.gz... save 4.pkl.gz... done
compute 6.pkl.gz... save 6.pkl.gz... done
compute 5.pkl.gz... save 5.pkl.gz... done
compute 7.pkl.gz... save 7.pkl.gz... done
compute 6.pkl.gz... save 6.pkl.gz... done
compute 7.pkl.gz... save 7.pkl.gz... done
compute 8.pkl.gz... save 8.pkl.gz... done
compute 9.pkl.gz... save 9.pkl.gz... done
compute 10.pkl.gz... save 10.pkl.gz... done
compute 11.pkl.gz... save 11.pkl.gz... done
compute 12.pkl.gz... save 12.pkl.gz... done
compute 13.pkl.gz... save 13.pkl.gz... done
compute 14.pkl.gz... save 14.pkl.gz... done
compute 8.pkl.gz... save 8.pkl.gz... done
compute 15.pkl.gz... save 15.pkl.gz... done
compute 16.pkl.gz... save 16.pkl.gz... done
compute 17.pkl.gz... save 17.pkl.gz... done
compute 18.pkl.gz... save 18.pkl.gz... done
compute 19.pkl.gz... save 19.pkl.gz... done
compute 20.pkl.gz... save 20.pkl.gz... done
compute 21.pkl.gz... save 21.pkl.gz... done
compute 22.pkl.gz... save 22.pkl.gz... done
compute 23.pkl.gz... save 23.pkl.gz... done
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compute 25.pkl.gz... save 25.pkl.gz... done
compute 26.pkl.gz... save 26.pkl.gz... done
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compute 9.pkl.gz... save 9.pkl.gz... done
compute 28.pkl.gz... save 28.pkl.gz... done
compute 29.pkl.gz... save 29.pkl.gz... done
compute 30.pkl.gz... save 30.pkl.gz... done
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compute 42.pkl.gz... save 42.pkl.gz... done
compute 10.pkl.gz... save 10.pkl.gz... done
compute 43.pkl.gz... save 43.pkl.gz... done
Total number of parameters: 390512
VoxelNetwork(
(0): GatedBlock(
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(8, 0)] -> [(16, 0), (16, 1), (16, 2), (16, 3), (48, 0)], size=7), eps=1e-05, momentum=0.1)
)
(1): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(16, 0), (16, 1), (16, 2), (16, 3)] -> [(32, 0), (32, 1), (32, 2), (32, 3), (96, 0)], size=3), eps=1e-05, momentum=0.1)
)
(2): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(32, 0), (32, 1), (32, 2), (32, 3)] -> [(48, 0), (48, 1), (48, 2), (48, 3), (144, 0)], size=3), eps=1e-05, momentum=0.1)
)
(3): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(48, 0), (48, 1), (48, 2), (48, 3)] -> [(64, 0), (64, 1), (64, 2), (64, 3), (192, 0)], size=3), eps=1e-05, momentum=0.1)
)
(4): GatedBlock(
(conv): SE3BNConvolution (SE3Kernel ([(64, 0), (64, 1), (64, 2), (64, 3)] -> [(256, 0)], size=3), eps=1e-05, momentum=0.1)
)
(5): ReLU(inplace)
(6): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
(7): Conv3d(256, 128, kernel_size=(1, 1, 1), stride=(1, 1, 1))
)
8it [00:00, 111.09it/s]
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a9t/1a9t_clean.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: /uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/datasets/processed/htmd/custom/1a05B/1a05B.npz,corresponding pdb likely could not be parsed
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 69, in
main()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 41, in main
entries = matcher.precompute_descriptors(entries)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/matchers/deeply_tough.py", line 46, in precompute_descriptors
feats = load_and_precompute_point_feats(self.model, self.args, pdb_list, point_list, self.device, self.nworkers, self.batch_size)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/predictor.py", line 37, in load_and_precompute_point_feats
dataset = PointOfInterestVoxelizedDataset(pdb_list, point_list, box_size=args.patch_size)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/datasets.py", line 220, in init
super().init(pdb_list, box_size=box_size, augm_rot=False, augm_mirror_prob=0)
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/engine/datasets.py", line 46, in init
assert len(self.pdb_list) > 0, f'No HTMD could be found but {len(pdb_list)}'
AssertionError: No HTMD could be found but 8PDB files were given, please call preprocess_once() on the dataset
Segmentation fault
Hey @protbiochem, glad to see a different issue. Could you try reinstalling numpy as per https://stackoverflow.com/questions/66060487/valueerror-numpy-ndarray-size-changed-may-indicate-binary-incompatibility-exp
pip uninstall numpy
pip install numpy==1.19.2
Thank you for helping me. A different issue has arisen
python $DEEPLYTOUGH/deeplytough/scripts/custom_evaluation.py --dataset_subdir 'custom' --output_dir $DEEPLYTOUGH/results --device 'cpu' --nworkers 4 --db_preprocessing 1 --net $DEEPLYTOUGH/networks/deeplytough_toughm1_test.pth.tar
HTMD: Logging setup failed
Total number of parameters: 390512
VoxelNetwork(
(0): GatedBlock(
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(8, 0)] -> [(16, 0), (16, 1), (16, 2), (16, 3), (48, 0)], size=7), eps=1e-05, momentum=0.1)
)
(1): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(16, 0), (16, 1), (16, 2), (16, 3)] -> [(32, 0), (32, 1), (32, 2), (32, 3), (96, 0)], size=3), eps=1e-05, momentum=0.1)
)
(2): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(32, 0), (32, 1), (32, 2), (32, 3)] -> [(48, 0), (48, 1), (48, 2), (48, 3), (144, 0)], size=3), eps=1e-05, momentum=0.1)
)
(3): GatedBlock(
(scalar_act): ScalarActivation()
(gate_act): ScalarActivation()
(conv): SE3BNConvolution (SE3Kernel ([(48, 0), (48, 1), (48, 2), (48, 3)] -> [(64, 0), (64, 1), (64, 2), (64, 3), (192, 0)], size=3), eps=1e-05, momentum=0.1)
)
(4): GatedBlock(
(conv): SE3BNConvolution (SE3Kernel ([(64, 0), (64, 1), (64, 2), (64, 3)] -> [(256, 0)], size=3), eps=1e-05, momentum=0.1)
)
(5): ReLU(inplace)
(6): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
(7): Conv3d(256, 128, kernel_size=(1, 1, 1), stride=(1, 1, 1))
)
2it [00:00, 90.72it/s]
INFO:engine.datasets:Dataset size: 2
0%| | 0/1 [00:00<?, ?it/s]/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/torch/utils/checkpoint.py:21: UserWarning: None of the inputs have requires_grad=True. Gradients will be None
warnings.warn("None of the inputs have requires_grad=True. Gradients will be None")
/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/envs/deeplytough/lib/python3.6/site-packages/torch/nn/functional.py:1332: UserWarning: nn.functional.sigmoid is deprecated. Use torch.sigmoid instead.
warnings.warn("nn.functional.sigmoid is deprecated. Use torch.sigmoid instead.")
100%|████████████████████████████████████████████████| 1/1 [00:13<00:00, 13.24s/it]
1it [00:00, 2015.52it/s]
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 69, in
main()
File "/uufs/chpc.utah.edu/common/home/u1261874/storage/Nathan/research/learning_programs/DeeplyTough_new/DeeplyTough-master/deeplytough/scripts/custom_evaluation.py", line 61, in main
for p, s in zip(results['pairs'], results['scores']):
TypeError: zip argument #2 must support iteration
Hey @byustudent, thanks for the message. This error is due to a known bug if you only have one pair in your input csv (the np.squeeze() function removes too many dimensions from the 'scores'). I will try to get a fix for this but in the meantime the quick fix is to make sure you are at least comparing two pairs (it can be the same pair twice).