Comments (5)
You can use the command python3 generate.py config/generate.config
to generate molecules for each of the selected test targets that were used for evaluations in our Chemical Science article.
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Thank you very much for your kind reply!
May I ask how to count the evaluation metrics like validity, novelty, and uniqueness?
Thank you again.
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Excuse me, when I use the command python3 generate.py config/generate.config
. It appears a problem as follows:
Traceback (most recent call last):
File "generate.py", line 48, in
main(sys.argv[1:])
File "generate.py", line 41, in main
debug=args.debug,
File "/da1/home/changhaoyu/liGAN/liGAN/generating.py", line 98, in init
**output_kws,
File "/da1/home/changhaoyu/liGAN/liGAN/generating.py", line 671, in init
self.metrics = pd.DataFrame(columns=columns).set_index(columns)
File "/home/changhaoyu/anaconda3/envs/py37/lib/python3.7/site-packages/pandas/core/frame.py", line 392, in init
mgr = init_dict(data, index, columns, dtype=dtype)
File "/home/changhaoyu/anaconda3/envs/py37/lib/python3.7/site-packages/pandas/core/internals/construction.py", line 196, in init_dict
nan_dtype)
File "/home/changhaoyu/anaconda3/envs/py37/lib/python3.7/site-packages/pandas/core/dtypes/cast.py", line 1175, in construct_1d_arraylike_from_scalar
dtype = dtype.dtype
AttributeError: type object 'object' has no attribute 'dtype'
How can I solve it?
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@Layne-Huang I just added a script scripts/valid_novel_unique.py
which can be used as follows:
(LiGAN) [mtragoza@dv002 LiGAN]$ python scripts/valid_novel_unique.py -h
usage: valid_novel_unique.py [-h] [--groupby GROUPBY] [-o OUT_FILE] data_root train_file metrics_file
positional arguments:
data_root
train_file
metrics_file
optional arguments:
-h, --help show this help message and exit
--groupby GROUPBY
-o OUT_FILE, --out_file OUT_FILE
(LiGAN) [mtragoza@dv002 LiGAN]$ python scripts/valid_novel_unique.py data/crossdock2020/ data/it2_tt_0_lowrmsd_valid_mols_test0_1000.types DEMO.gen_metrics
Loading train set molecules
Loading generated molecules
% valid % novel % unique
all
all 100.0 100.0 100.0
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@Matheo-Chang I moved this to a separate issue #48.
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Related Issues (20)
- AttributeError: type object 'object' has no attribute 'dtype' HOT 9
- where is the output for generated molecules and matrix? HOT 4
- gnina minmize problem HOT 2
- Can not access to https://bits.csb.pitt.edu/files/ to download those files HOT 2
- Segmentation Fault when running tests HOT 1
- tests ValueError: File does not exist: data/test_pockets/xxx HOT 3
- change configuration file for prior (no lig) sampling HOT 1
- Error when run cmake of libmogrid HOT 4
- Errors when run pytest tests HOT 12
- how I can export embeddings HOT 3
- Get Stuck when runing generate.py HOT 2
- Train_file and test_file are missing HOT 1
- CUDNN Error (out of memory?): CUDNN_STATUS_EXECUTION_FAILED HOT 2
- Get killed when running generate.py HOT 5
- Cannot use model with `fit_atoms: True` HOT 8
- Changing parameters while testing the model HOT 6
- KeyError: 'minimizedAffinity' in tests HOT 6
- Environment.yml isnt complete and libmolgrid git command fails HOT 3
- Changes required to train the CGAN model
- Data link failure
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