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License: MIT License
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Some question
Hello，I want to ask a question，can l get the source data named /home/aht/paper_code/shaungjia/chembl_webresource_client/scaffold_hopping_320target.csv？
Issue about translate
Hi, after training, I run the translate.py to generate SMILES with followed instruction, However I met some bug. Can you give me some solutions?
python translate.py -condition_dim 768 -use_graph_embedding -arch after_encoding -with_3d_confomer -model /data/u1/projects/mget_3d/experiments/data40_tue/3d_gcn/models/model_step_9500.pt -gpu 0 -src data40_tue_3d/src-test.txt -cond data40_tue_3d/cond-test.txt -output /data/u1/projects/mget_3d/summary_tue/data40/after/9500/pred.txt -beam_size 10 -n_best 10 -batch_size 16 -replace_unk -max_length 200 -fast -use_protein40
Traceback (most recent call last):
File "translate.py", line 100, in
main(opt)
File "translate.py", line 72, in main
opt = opt)
File "/home/data/aidd/deepHops/deephop/onmt/translate/translator.py", line 257, in translate
batch_data = self.translate_batch(batch, data, fast=self.fast)
File "/home/data/aidd/deepHops/deephop/onmt/translate/translator.py", line 441, in translate_batch
return_attention=self.replace_unk)
File "/home/data/aidd/deepHops/deephop/onmt/translate/translator.py", line 581, in _fast_translate_batch
[alive_seq.index_select(0, select_indices),
RuntimeError: expected scalar type Long but found Float
[INFO/MainProcess] process shutting down
[DEBUG/MainProcess] running all "atexit" finalizers with priority >= 0
[DEBUG/MainProcess] running the remaining "atexit" finalizers
data source
Hello，I want to ask a question，can l get the source data named /home/aht/paper_code/shaungjia/chembl_webresource_client/scaffold_hopping_320target.csv？
about the file ReadoutFunction
Hi,
I'm glad you can share the code. The ReadoutFunction module imported in MPNNs is not found. Where could I find the file? Thank you very much.
Installation
Hello!
I tried to install envs according to guide from README but I faced with problem:
conda create env -f=score/env.yaml
usage: conda create [-h] [--clone ENV] [-n ENVIRONMENT | -p PATH] [-c CHANNEL]
[--use-local] [--override-channels]
[--repodata-fn REPODATA_FNS] [--strict-channel-priority]
[--no-channel-priority] [--no-deps | --only-deps]
[--no-pin] [--copy] [-C] [-k] [--offline] [-d] [--json]
[-q] [-v] [-y] [--download-only] [--show-channel-urls]
[--file FILE] [--no-default-packages]
[--experimental-solver {classic,libmamba,libmamba-draft}]
[--dev]
[package_spec ...]
conda create: error: argument -f/--force: ignored explicit argument 'score/env.yaml'
Then I fixed it to more relevant one:
cd score
conda env create -f env.yaml
But it didn't work:
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- cudnn==7.6.5=cuda10.1_0
- tensorflow==2.1.0=gpu_py36h2e5cdaa_0
- fontconfig==2.13.1=he4413a7_1000
- cudatoolkit==10.1.243=h6bb024c_0
- c-ares==1.15.0=h7b6447c_1001
- matplotlib-base==3.1.1=py36hfd891ef_0
- xz==5.2.5=h7b6447c_0
- icu==58.2=hf484d3e_1000
- lzo==2.10=h14c3975_1000
- xorg-libxrender==0.9.10=h516909a_1002
- libprotobuf==3.11.4=hd408876_0
- wrapt==1.12.1=py36h7b6447c_1
- readline==8.0=h7b6447c_0
- libxcb==1.13=h14c3975_1002
- rdkit==2020.03.2.0=py36hc20afe1_1
- py-boost==1.67.0=py36h04863e7_4
- tk==8.6.10=hed695b0_0
- xorg-libxext==1.3.4=h516909a_0
- pthread-stubs==0.4=h14c3975_1001
- xorg-xproto==7.0.31=h14c3975_1007
- tornado==6.0.4=py36h8c4c3a4_1
- zlib==1.2.11=h516909a_1006
- grpcio==1.27.2=py36hf8bcb03_0
- pyqt==4.11.4=py36_3
- libuuid==2.32.1=h14c3975_1000
- jpeg==9c=h14c3975_1001
- tensorflow-gpu==2.1.0=h0d30ee6_0
- cupti==10.1.168=0
- hdf5==1.10.4=hb1b8bf9_0
- brotlipy==0.7.0=py36h8c4c3a4_1000
- libstdcxx-ng==9.1.0=hdf63c60_0
- tensorflow-base==2.1.0=gpu_py36h6c5654b_0
- xorg-libxdmcp==1.1.3=h516909a_0
- numexpr==2.7.1=py36h830a2c2_1
- pixman==0.34.0=h14c3975_1003
- cython==0.29.17=py36h831f99a_0
- xorg-libsm==1.2.3=h84519dc_1000
- h5py==2.10.0=py36h7918eee_0
- lz4-c==1.9.2=he1b5a44_1
- libiconv==1.15=h516909a_1006
- bzip2==1.0.8=h516909a_2
- numpy==1.18.4=py36h7314795_0
- libopenblas==0.3.7=h5ec1e0e_6
- xorg-libice==1.0.10=h516909a_0
- libgcc-ng==9.1.0=hdf63c60_0
- libtiff==4.1.0=hc7e4089_6
- scipy==1.4.1=py36h2d22cac_3
- sqlite==3.31.1=h62c20be_1
- libxml2==2.9.9=h13577e0_2
- freetype==2.10.2=he06d7ca_0
- pcre==8.44=he1b5a44_0
- ld_impl_linux-64==2.33.1=h53a641e_7
- zstd==1.4.4=h6597ccf_3
- openssl==1.1.1g=h516909a_0
- xorg-xextproto==7.3.0=h14c3975_1002
- kiwisolver==1.2.0=py36hdb11119_0
- gettext==0.19.8.1=h5e8e0c9_1
- protobuf==3.11.4=py36he6710b0_0
- ncurses==6.2=he6710b0_1
- libffi==3.3=he6710b0_1
- libxgboost==1.0.2=he1b5a44_1
- _tflow_select==2.1.0=gpu
- cryptography==2.9.2=py36h45558ae_0
- biopython==1.76=py36h516909a_0
- libedit==3.1.20181209=hc058e9b_0
- xorg-kbproto==1.0.7=h14c3975_1002
- pillow==7.1.2=py36h8328e55_0
- scikit-learn==0.23.0=py36h0e1014b_0
- pytables==3.6.1=py36h71ec239_0
- libboost==1.67.0=h46d08c1_4
- xorg-renderproto==0.11.1=h14c3975_1002
- xorg-libx11==1.6.9=h516909a_0
- libgfortran-ng==7.3.0=hdf63c60_5
- libwebp-base==1.1.0=h516909a_3
- python==3.6.10=h7579374_2
- pandas==1.0.3=py36h830a2c2_1
- xorg-libxau==1.0.9=h14c3975_0
- libpng==1.6.37=hed695b0_1
- blosc==1.18.1=he1b5a44_0
I used macOS Monterey 12.1
Is there a way to fix installation? Or maybe update a guide?
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