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pulimeng / DeepDrug3D

A convolutional neural network for classifying binding pockets based on spatial and chemical information extracted from the pockets.
GNU General Public License v3.0
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ValueError: could not convert string to float: #13

Open VaticanCameos99 opened 3 years ago

VaticanCameos99 commented 3 years ago

Thanks for making your code public. Had a doubt:

I am using Ubuntu 20.04

While running the voxelization.py file, I got a permission denied error for ./dligand-linux. I changed the permissions and next I see is this:

Calculating of the binding site potential energy ./dligand-linux: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "voxelization.py", line 83, in <module> Vox3DBuilder().voxelization(opt.f, opt.a, opt.r, opt.n, opt.o, opt.shape) File "voxelization.py", line 63, in voxelization pocket_grid = Grid3DBuilder.build(pdb_path, aux_input_path, r, N, output_folder, shape) File "/home/name/Downloads/Work/Name/DeepDrug3D/DataGeneration/build_grid.py", line 283, in build total_potE = potEnergy(new_site, 'dummy_mol2.mol2', output_trans_mol2_path) File "/home/name/Downloads/Work/Name/DeepDrug3D/DataGeneration/build_grid.py", line 221, in potEnergy potEs = np.array([single_potEnergy(loc1, ld_type_list, mol2_in_string, protein_file) for loc1 in binding_site]) File "/home/name/Downloads/Work/Name/DeepDrug3D/DataGeneration/build_grid.py", line 221, in <listcomp> potEs = np.array([single_potEnergy(loc1, ld_type_list, mol2_in_string, protein_file) for loc1 in binding_site]) File "/home/name/Downloads/Work/Name/DeepDrug3D/DataGeneration/build_grid.py", line 205, in single_potEnergy b = float(a) ValueError: could not convert string to float:

Note: the value of a is derived from the out variable which turns out to be an empty string.

How do I resolve this error?

VaticanCameos99 commented 3 years ago

This gives the same error. ./dligand-linux: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory

pulimeng commented 3 years ago

I'm not sure what is the problem exactly. Did you try install the corresponding lib?

VaticanCameos99 commented 3 years ago

I tried following the directions given here: https://community.progress.com/s/article/000055534 . But the corresponding library seems to be no longer existent.

VaticanCameos99 commented 3 years ago

I tried this on my local machine as well as on Colab. Same pattern of errors in both.