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View Code? Open in Web Editor NEWZero-Shot 3D Drug Design by Sketching and Generating (NeurIPS 2022)
Zero-Shot 3D Drug Design by Sketching and Generating (NeurIPS 2022)
Hi longlongman,
I've tried using your encoder-decoder on CASP-ligands but wasn't successful in fully decoding(recovering) the ligands after encoding (molecule cut off, some atoms missing)
I'm suspecting whether if it's because the patch size for the shapepretrainingencoder is too small? or maybe due to maxlen_coef being too small?
any ideas on getting the full molecule?
thanks
I want to reproduce the results of this paper for my research work but I am not able to download datasets from ZINC20 or ZINC15 for the data preprocessing, the links I am using are: https://zinc20.docking.org/substances/, https://zinc15.docking.org/substances/
the downloads are not happening like after sometimes it says failed, Is there any google drive/one drive link where the data is already available to use or any other references will also help. Please help me out to sort this issue.
Thanks in advance.
Dear Longlongman,
is the vocab file provided, a partial vocab file?? If it isn't could you provide the full vocab file? some fragments aren't being properly decoded compared to the original. Maybe this is the reason why?
thanks
after get_fragment_vocab i get 2 pkl files
at get_training_data i put in
BRICS_RING_R.vocab.pkl path..
there's an error
Traceback (most recent call last):
frag_idx = vocab[frag_smi][2]
TypeError: 'Mol' object is not subscriptable
hi, my gpu keeps busting up when i'm trying to generate.
horovodrun -np 8 bycha-run
--config configs/generating.yaml
--lib shape_pretraining
--task.mode evaluate
--task.data.train.path data
--task.data.valid.path.samples /home/kiwoong/DESERT/data/sample_shapes.pkl
--task.data.test.path.samples /home/kiwoong/DESERT/data/sample_shapes.pkl
--task.dataloader.train.max_samples 1
--task.dataloader.valid.sampler.max_samples 1
--task.dataloader.test.sampler.max_samples 1
--task.model.path /home/kiwoong/DESERT/trainer/save_model_dir/1WW_30W_5048064.pt
--task.evaluator.save_hypo_dir /home/kiwoong/DESERT/trainer/save_hypo_di
this is the bash file I'm running right now.
How do you reduce the batch size?? In the config file for generation it seems that the only option is max_sample, which i set to 1 but increases steadily. thanks.
Hello longlongman,
I'm new to deep learning. Please bear with me for some dump questions.
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
tensorflow 2.4.0 requires typing-extensions~=3.7.4, but you have typing-extensions 4.7.1 which is incompatible.
File "get_training_data.py", line 31, in <module>
with open(vocab_path, 'rb') as fr:
IsADirectoryError: [Errno 21] Is a directory: '/home/ubuntu/user_space/DESERT/preparation/vocab'
The vocab directory contains two files produced by
'get_fragment_vocab.py' : 'BRICS_RING_R.vocab.pkl' and 'BRICS_RING_R.494789.pkl'
class: ShapePretrainingDatasetShard
path: ---TRAINING DATA PATH---
vocab_path: ---VOCAB PATH---
sample_each_shard: 500000
shuffle: True
valid:
class: ShapePretrainingDataset
path:
samples: ---VALID DATA PATH---
vocab: ---VOCAB PATH---
test:
class: ShapePretrainingDataset
path:
samples: ---TEST DATA PATH---
vocab: ---VOCAB PATH---
The ---TRAINING DATA PATH--- is simply the path to get 0.pkl and 1.pkl
But what about valid data path and test data path? ( I just put it same as training data path)
When executing train.sh another error occured
pkg_resources.DistributionNotFound: The 'typing-extensions~=3.7.4' distribution was not found and is required by tensorflow
And I believe it is related with the first error during installing.
4. For the sketching process, where to fill in the path for input ligand sdf in sketch.py?
When sketching the pocket by sketch.py , the following error occurred:
File "sketching.py", line 2, in <module>
from shape_utils import get_atom_stamp
File "/home/ubuntu/user_space/DESERT/sketch/shape_utils.py", line 3, in <module>
from common import ATOM_RADIUS, ATOMIC_NUMBER, ATOMIC_NUMBER_REVERSE
ImportError: cannot import name 'ATOM_RADIUS' from 'common' (/home/ubuntu/miniconda3/envs/DESERT/lib/python3.7/site-packages/common/__init__.py)
bycha-run \
--config configs/generating.yaml \
--lib shape_pretraining \
--task.mode evaluate \
--task.data.train.path data \
--task.data.valid.path.samples ❗❗❗FILL_THIS(MOLECULE SHAPES SAMPLED FROM CAVITY)❗❗❗ \
--task.data.test.path.samples ❗❗❗FILL_THIS❗❗❗ \
--task.dataloader.train.max_samples 1 \
--task.dataloader.valid.sampler.max_samples 1 \
--task.dataloader.test.sampler.max_samples 1 \
--task.model.path ❗❗❗FILL_THIS❗❗❗ \
--task.evaluator.save_hypo_dir ❗❗❗FILL_THIS❗❗❗
What should the path for task.data.test.path.samples ?
Is task.model.path the path to 1WW_30W_5048064.pt ?
Sorry for bothering
Hi !
thanks for sharing your excellent work!
I am unable to do the final step of generate after modifying part of your code to successfully train and get pockets, could you please upload the latest and correct full code?
Thanks!
Hello, I have a question, when running the file get_fragment_vocab.py, the vocab of the fragment can be saved, why does the fragment need to be re-acquired in the file get_training_data.py, and align it with the previously saved fragment, and finally get the rotation matrix ? why do that? thank you very much.
Hi!
Thank u for sharing your excellent work!
when I try to run this on my mac book pro(m1 pro),it just doesn't work
so could u please share a dock file or something can work on mac?
thanks!
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