libmolgrid
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gnina
Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows
I'm now trying to reproduce 3D-cnn result with keras/tensorflow using cross dock dataset can I regard the example code in https://gnina.github.io/libmolgrid/tutorials/train_basic_CNN_with_Tensorflow.html as def2017 model generation? If it's true, to make...
Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.13.7 to 1.14.3. Release notes Sourced from nokogiri's releases. 1.14.3 / 2023-04-11 Security [CRuby] Vendored libxml2 is updated to address CVE-2023-29469, CVE-2023-28484, and one other security-related issue....
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I'm trying to install libmolgrid in fresh environment after typing cmake when I type make, I got following error [ 60%] Building CXX object python/CMakeFiles/molgrid.dir/bindings_grids.cpp.o In file included from /lwork01/miniconda3/envs/py39/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,...
Hi, I'm converting a _pdb_ file to a _gninatype_ file. I have a process similar to the _gninatype_ function in the [link](https://github.com/devalab/DeepPocket/blob/main/types_and_gninatyper.py) ``` def gninatype(file): # creates gninatype file for...
I have a gninatypes file. The path of this file is `gninatype_dir` I have a sample.types file containing a single line. The contents of the file are as follows. `12.531857...
Hi authors, I have an issue using the `stratify` functions in `ExampleProvider`. I tried two ways : 1. `train_samples = molgrid.ExampleProvider(ligmolcache=args.trligte, recmolcache=args.trrecte, shuffle=True, default_batch_size=args.batch_size, iteration_scheme=molgrid.IterationScheme.SmallEpoch, balanced=True, stratify_pos=3, stratify_step=1, stratify_max=6, stratify_min=0)`...
I got error about libmolgrid, when I ran make. Could you please help me to solve this issue? 
Hello we had to add `86` to `CMakeLists.txt` inn `CMAKE_CUDA_ARCHITECTURES` to allow libmolgrod to run on A100 cards NB we build libmolgrid and gnina to run on all cuda devices...
Hi, when I installed the molgrid, I run the pytest .. as you said in https://github.com/mattragoza/conda-molgrid. there are errors as follows: ```python pytest .. ..... ============================== *** Open Babel Warning...
/tmp/libmolgrid/src/grid_maker.cu:279: invalid argument --------------------------------------------------------------------------- CLI error 2022-01-27 12:32:12.810627: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1159] Device interconnect StreamExecutor with strength 1 edge matrix: 2022-01-27 12:32:12.810659: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1165] 0 1 2 3 4 5 6 7...
