protbiochem commented 2 years ago

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.

JoshuaMeyers commented 2 years ago

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?

protbiochem commented 2 years ago

*** 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

JoshuaMeyers commented 2 years ago

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).

protbiochem commented 2 years ago

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?

JoshuaMeyers commented 2 years ago

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 1

protbiochem commented 2 years ago

Even 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

JoshuaMeyers commented 2 years ago

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 pdbqt files 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 146 in deeplytough/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.

JoshuaMeyers commented 2 years ago

Hey @protbiochem, I have opened a PR with fixes for your bug thanks for reporting: https://github.com/BenevolentAI/DeeplyTough/pull/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

byustudent commented 2 years ago

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 compute 24.pkl.gz... save 24.pkl.gz... done compute 25.pkl.gz... save 25.pkl.gz... done compute 26.pkl.gz... save 26.pkl.gz... done compute 27.pkl.gz... save 27.pkl.gz... done 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 compute 31.pkl.gz... save 31.pkl.gz... done compute 32.pkl.gz... save 32.pkl.gz... done compute 33.pkl.gz... save 33.pkl.gz... done compute 34.pkl.gz... save 34.pkl.gz... done compute 35.pkl.gz... save 35.pkl.gz... done compute 36.pkl.gz... save 36.pkl.gz... done compute 37.pkl.gz... save 37.pkl.gz... done compute 38.pkl.gz... save 38.pkl.gz... done compute 39.pkl.gz... save 39.pkl.gz... done compute 40.pkl.gz... save 40.pkl.gz... done compute 41.pkl.gz... save 41.pkl.gz... done 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

JoshuaMeyers commented 2 years ago

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

byustudent commented 2 years ago

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

JoshuaMeyers commented 2 years ago

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).

BenevolentAI / DeeplyTough

Custom evaluation failure #12

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)