diff --git a/.dvc/.gitignore b/.dvc/.gitignore deleted file mode 100644 index 528f30c..0000000 --- a/.dvc/.gitignore +++ /dev/null @@ -1,3 +0,0 @@ -/config.local -/tmp -/cache diff --git a/.dvc/config b/.dvc/config deleted file mode 100644 index e69de29..0000000 diff --git a/.dvc/plots/confusion.json b/.dvc/plots/confusion.json deleted file mode 100644 index af1b48d..0000000 --- a/.dvc/plots/confusion.json +++ /dev/null @@ -1,107 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "facet": { - "field": "rev", - "type": "nominal" - }, - "spec": { - "transform": [ - { - "aggregate": [ - { - "op": "count", - "as": "xy_count" - } - ], - "groupby": [ - "", - "" - ] - }, - { - "impute": "xy_count", - "groupby": [ - "rev", - "" - ], - "key": "", - "value": 0 - }, - { - "impute": "xy_count", - "groupby": [ - "rev", - "" - ], - "key": "", - "value": 0 - }, - { - "joinaggregate": [ - { - "op": "max", - "field": "xy_count", - "as": "max_count" - } - ], - "groupby": [] - }, - { - "calculate": "datum.xy_count / datum.max_count", - "as": "percent_of_max" - } - ], - "encoding": { - "x": { - "field": "", - "type": "nominal", - "sort": "ascending", - "title": "" - }, - "y": { - "field": "", - "type": "nominal", - "sort": "ascending", - "title": "" - } - }, - "layer": [ - { - "mark": "rect", - "width": 300, - "height": 300, - "encoding": { - "color": { - "field": "xy_count", - "type": "quantitative", - "title": "", - "scale": { - "domainMin": 0, - "nice": true - } - } - } - }, - { - "mark": "text", - "encoding": { - "text": { - "field": "xy_count", - "type": "quantitative" - }, - "color": { - "condition": { - "test": "datum.percent_of_max > 0.5", - "value": "white" - }, - "value": "black" - } - } - } - ] - } -} diff --git a/.dvc/plots/confusion_normalized.json b/.dvc/plots/confusion_normalized.json deleted file mode 100644 index 1d38849..0000000 --- a/.dvc/plots/confusion_normalized.json +++ /dev/null @@ -1,112 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "facet": { - "field": "rev", - "type": "nominal" - }, - "spec": { - "transform": [ - { - "aggregate": [ - { - "op": "count", - "as": "xy_count" - } - ], - "groupby": [ - "", - "" - ] - }, - { - "impute": "xy_count", - "groupby": [ - "rev", - "" - ], - "key": "", - "value": 0 - }, - { - "impute": "xy_count", - "groupby": [ - "rev", - "" - ], - "key": "", - "value": 0 - }, - { - "joinaggregate": [ - { - "op": "sum", - "field": "xy_count", - "as": "sum_y" - } - ], - "groupby": [ - "" - ] - }, - { - "calculate": "datum.xy_count / datum.sum_y", - "as": "percent_of_y" - } - ], - "encoding": { - "x": { - "field": "", - "type": "nominal", - "sort": "ascending", - "title": "" - }, - "y": { - "field": "", - "type": "nominal", - "sort": "ascending", - "title": "" - } - }, - "layer": [ - { - "mark": "rect", - "width": 300, - "height": 300, - "encoding": { - "color": { - "field": "percent_of_y", - "type": "quantitative", - "title": "", - "scale": { - "domain": [ - 0, - 1 - ] - } - } - } - }, - { - "mark": "text", - "encoding": { - "text": { - "field": "percent_of_y", - "type": "quantitative", - "format": ".2f" - }, - "color": { - "condition": { - "test": "datum.percent_of_y > 0.5", - "value": "white" - }, - "value": "black" - } - } - } - ] - } -} diff --git a/.dvc/plots/default.json b/.dvc/plots/default.json deleted file mode 100644 index 9cf71ce..0000000 --- a/.dvc/plots/default.json +++ /dev/null @@ -1,31 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "width": 300, - "height": 300, - "mark": { - "type": "line" - }, - "encoding": { - "x": { - "field": "", - "type": "quantitative", - "title": "" - }, - "y": { - "field": "", - "type": "quantitative", - "title": "", - "scale": { - "zero": false - } - }, - "color": { - "field": "rev", - "type": "nominal" - } - } -} diff --git a/.dvc/plots/linear.json b/.dvc/plots/linear.json deleted file mode 100644 index 65549f9..0000000 --- a/.dvc/plots/linear.json +++ /dev/null @@ -1,116 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "width": 300, - "height": 300, - "layer": [ - { - "encoding": { - "x": { - "field": "", - "type": "quantitative", - "title": "" - }, - "y": { - "field": "", - "type": "quantitative", - "title": "", - "scale": { - "zero": false - } - }, - "color": { - "field": "rev", - "type": "nominal" - } - }, - "layer": [ - { - "mark": "line" - }, - { - "selection": { - "label": { - "type": "single", - "nearest": true, - "on": "mouseover", - "encodings": [ - "x" - ], - "empty": "none", - "clear": "mouseout" - } - }, - "mark": "point", - "encoding": { - "opacity": { - "condition": { - "selection": "label", - "value": 1 - }, - "value": 0 - } - } - } - ] - }, - { - "transform": [ - { - "filter": { - "selection": "label" - } - } - ], - "layer": [ - { - "mark": { - "type": "rule", - "color": "gray" - }, - "encoding": { - "x": { - "field": "", - "type": "quantitative" - } - } - }, - { - "encoding": { - "text": { - "type": "quantitative", - "field": "" - }, - "x": { - "field": "", - "type": "quantitative" - }, - "y": { - "field": "", - "type": "quantitative" - } - }, - "layer": [ - { - "mark": { - "type": "text", - "align": "left", - "dx": 5, - "dy": -5 - }, - "encoding": { - "color": { - "type": "nominal", - "field": "rev" - } - } - } - ] - } - ] - } - ] -} diff --git a/.dvc/plots/scatter.json b/.dvc/plots/scatter.json deleted file mode 100644 index 9af9304..0000000 --- a/.dvc/plots/scatter.json +++ /dev/null @@ -1,104 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "width": 300, - "height": 300, - "layer": [ - { - "encoding": { - "x": { - "field": "", - "type": "quantitative", - "title": "" - }, - "y": { - "field": "", - "type": "quantitative", - "title": "", - "scale": { - "zero": false - } - }, - "color": { - "field": "rev", - "type": "nominal" - } - }, - "layer": [ - { - "mark": "point" - }, - { - "selection": { - "label": { - "type": "single", - "nearest": true, - "on": "mouseover", - "encodings": [ - "x" - ], - "empty": "none", - "clear": "mouseout" - } - }, - "mark": "point", - "encoding": { - "opacity": { - "condition": { - "selection": "label", - "value": 1 - }, - "value": 0 - } - } - } - ] - }, - { - "transform": [ - { - "filter": { - "selection": "label" - } - } - ], - "layer": [ - { - "encoding": { - "text": { - "type": "quantitative", - "field": "" - }, - "x": { - "field": "", - "type": "quantitative" - }, - "y": { - "field": "", - "type": "quantitative" - } - }, - "layer": [ - { - "mark": { - "type": "text", - "align": "left", - "dx": 5, - "dy": -5 - }, - "encoding": { - "color": { - "type": "nominal", - "field": "rev" - } - } - } - ] - } - ] - } - ] -} diff --git a/.dvc/plots/smooth.json b/.dvc/plots/smooth.json deleted file mode 100644 index d497ce7..0000000 --- a/.dvc/plots/smooth.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "mark": { - "type": "line" - }, - "encoding": { - "x": { - "field": "", - "type": "quantitative", - "title": "" - }, - "y": { - "field": "", - "type": "quantitative", - "title": "", - "scale": { - "zero": false - } - }, - "color": { - "field": "rev", - "type": "nominal" - } - }, - "transform": [ - { - "loess": "", - "on": "", - "groupby": [ - "rev" - ], - "bandwidth": 0.3 - } - ] -} diff --git a/.dvcignore b/.dvcignore deleted file mode 100644 index 5197305..0000000 --- a/.dvcignore +++ /dev/null @@ -1,3 +0,0 @@ -# Add patterns of files dvc should ignore, which could improve -# the performance. Learn more at -# https://dvc.org/doc/user-guide/dvcignore diff --git a/.gitattributes b/.gitattributes index b62c1b7..d20a169 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,6 +1,3 @@ -*.csv filter=lfs diff=lfs merge=lfs -text -*.h5 filter=lfs diff=lfs merge=lfs -text -*.joblib filter=lfs diff=lfs merge=lfs -text -*.pkl filter=lfs diff=lfs merge=lfs -text + *.pt filter=lfs diff=lfs merge=lfs -text -*.tsv filter=lfs diff=lfs merge=lfs -text + diff --git a/Dockerfile b/Dockerfile index c8ca1e8..fa489b9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ FROM bentoml/model-server:0.11.0-py37 MAINTAINER ersilia -RUN conda install -c conda-forge rdkit=2021.03.4 +RUN pip install rdkit==2022.3.3 RUN pip install git+https://github.com/bp-kelley/descriptastorus.git@d552f934757378a61dd1799cdb589a864032cd1b RUN pip install tqdm==4.62.2 RUN pip install torch==1.9.0 @@ -9,4 +9,4 @@ RUN pip install scipy==1.7.1 RUN pip install scikit-learn==0.24.2 WORKDIR /repo -COPY ./repo +COPY . /repo diff --git a/data.h5 b/data.h5 deleted file mode 100644 index 0dabc80..0000000 --- a/data.h5 +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:26c4d449632ea072317c16e9d4857e419b67e1b7751f81a89a87c8e75fe9484e -size 800 diff --git a/data.h5.dvc b/data.h5.dvc deleted file mode 100644 index 7ab7106..0000000 --- a/data.h5.dvc +++ /dev/null @@ -1,4 +0,0 @@ -outs: -- md5: 6781e0baec8d65b9a95a3e879a5098d1 - size: 800 - path: data.h5 diff --git a/model/framework/finetune/clintox/fold_0/model_0/model.pt b/model/checkpoints/finetune/clintox/fold_0/model_0/model.pt similarity index 100% rename from model/framework/finetune/clintox/fold_0/model_0/model.pt rename to model/checkpoints/finetune/clintox/fold_0/model_0/model.pt diff --git a/model/framework/finetune/clintox/fold_1/model_0/model.pt b/model/checkpoints/finetune/clintox/fold_1/model_0/model.pt similarity index 100% rename from model/framework/finetune/clintox/fold_1/model_0/model.pt rename to model/checkpoints/finetune/clintox/fold_1/model_0/model.pt diff --git a/model/framework/finetune/clintox/fold_2/model_0/model.pt b/model/checkpoints/finetune/clintox/fold_2/model_0/model.pt similarity index 100% rename from model/framework/finetune/clintox/fold_2/model_0/model.pt rename to model/checkpoints/finetune/clintox/fold_2/model_0/model.pt diff --git a/model/framework/grover/Dockerfile b/model/framework/code/Dockerfile similarity index 100% rename from model/framework/grover/Dockerfile rename to model/framework/code/Dockerfile diff --git a/model/framework/grover/LICENSE b/model/framework/code/LICENSE similarity index 100% rename from model/framework/grover/LICENSE rename to model/framework/code/LICENSE diff --git a/model/framework/grover/README.md b/model/framework/code/README.md similarity index 100% rename from model/framework/grover/README.md rename to model/framework/code/README.md diff --git a/model/framework/grover/exampledata/finetune/bace.csv b/model/framework/code/exampledata/finetune/bace.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/bace.csv rename to model/framework/code/exampledata/finetune/bace.csv diff --git a/model/framework/grover/exampledata/finetune/bbbp.csv b/model/framework/code/exampledata/finetune/bbbp.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/bbbp.csv rename to model/framework/code/exampledata/finetune/bbbp.csv diff --git a/model/framework/grover/exampledata/finetune/clintox.csv b/model/framework/code/exampledata/finetune/clintox.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/clintox.csv rename to model/framework/code/exampledata/finetune/clintox.csv diff --git a/model/framework/grover/exampledata/finetune/esol.csv b/model/framework/code/exampledata/finetune/esol.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/esol.csv rename to model/framework/code/exampledata/finetune/esol.csv diff --git a/model/framework/grover/exampledata/finetune/freesolv.csv b/model/framework/code/exampledata/finetune/freesolv.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/freesolv.csv rename to model/framework/code/exampledata/finetune/freesolv.csv diff --git a/model/framework/grover/exampledata/finetune/lipo.csv b/model/framework/code/exampledata/finetune/lipo.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/lipo.csv rename to model/framework/code/exampledata/finetune/lipo.csv diff --git a/model/framework/grover/exampledata/finetune/qm7.csv b/model/framework/code/exampledata/finetune/qm7.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/qm7.csv rename to model/framework/code/exampledata/finetune/qm7.csv diff --git a/model/framework/grover/exampledata/finetune/qm8.csv b/model/framework/code/exampledata/finetune/qm8.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/qm8.csv rename to model/framework/code/exampledata/finetune/qm8.csv diff --git a/model/framework/grover/exampledata/finetune/sider.csv b/model/framework/code/exampledata/finetune/sider.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/sider.csv rename to model/framework/code/exampledata/finetune/sider.csv diff --git a/model/framework/grover/exampledata/finetune/tox21.csv b/model/framework/code/exampledata/finetune/tox21.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/tox21.csv rename to model/framework/code/exampledata/finetune/tox21.csv diff --git a/model/framework/grover/exampledata/finetune/toxcast.csv b/model/framework/code/exampledata/finetune/toxcast.csv similarity index 100% rename from model/framework/grover/exampledata/finetune/toxcast.csv rename to model/framework/code/exampledata/finetune/toxcast.csv diff --git a/model/framework/grover/exampledata/pretrain/tryout.csv b/model/framework/code/exampledata/pretrain/tryout.csv similarity index 100% rename from model/framework/grover/exampledata/pretrain/tryout.csv rename to model/framework/code/exampledata/pretrain/tryout.csv diff --git a/model/framework/grover/grover/data/__init__.py b/model/framework/code/grover/data/__init__.py similarity index 100% rename from model/framework/grover/grover/data/__init__.py rename to model/framework/code/grover/data/__init__.py diff --git a/model/framework/grover/grover/data/dist_sampler.py b/model/framework/code/grover/data/dist_sampler.py similarity index 100% rename from model/framework/grover/grover/data/dist_sampler.py rename to model/framework/code/grover/data/dist_sampler.py diff --git a/model/framework/grover/grover/data/groverdataset.py b/model/framework/code/grover/data/groverdataset.py similarity index 100% rename from model/framework/grover/grover/data/groverdataset.py rename to model/framework/code/grover/data/groverdataset.py diff --git a/model/framework/grover/grover/data/moldataset.py b/model/framework/code/grover/data/moldataset.py similarity index 100% rename from model/framework/grover/grover/data/moldataset.py rename to model/framework/code/grover/data/moldataset.py diff --git a/model/framework/grover/grover/data/molfeaturegenerator.py b/model/framework/code/grover/data/molfeaturegenerator.py similarity index 100% rename from model/framework/grover/grover/data/molfeaturegenerator.py rename to model/framework/code/grover/data/molfeaturegenerator.py diff --git a/model/framework/grover/grover/data/molgraph.py b/model/framework/code/grover/data/molgraph.py similarity index 100% rename from model/framework/grover/grover/data/molgraph.py rename to model/framework/code/grover/data/molgraph.py diff --git a/model/framework/grover/grover/data/scaler.py b/model/framework/code/grover/data/scaler.py similarity index 100% rename from model/framework/grover/grover/data/scaler.py rename to model/framework/code/grover/data/scaler.py diff --git a/model/framework/grover/grover/data/task_labels.py b/model/framework/code/grover/data/task_labels.py similarity index 100% rename from model/framework/grover/grover/data/task_labels.py rename to model/framework/code/grover/data/task_labels.py diff --git a/model/framework/grover/grover/data/torchvocab.py b/model/framework/code/grover/data/torchvocab.py similarity index 100% rename from model/framework/grover/grover/data/torchvocab.py rename to model/framework/code/grover/data/torchvocab.py diff --git a/model/framework/grover/grover/model/layers.py b/model/framework/code/grover/model/layers.py similarity index 100% rename from model/framework/grover/grover/model/layers.py rename to model/framework/code/grover/model/layers.py diff --git a/model/framework/grover/grover/model/models.py b/model/framework/code/grover/model/models.py similarity index 100% rename from model/framework/grover/grover/model/models.py rename to model/framework/code/grover/model/models.py diff --git a/model/framework/grover/grover/util/metrics.py b/model/framework/code/grover/util/metrics.py similarity index 100% rename from model/framework/grover/grover/util/metrics.py rename to model/framework/code/grover/util/metrics.py diff --git a/model/framework/grover/grover/util/multi_gpu_wrapper.py b/model/framework/code/grover/util/multi_gpu_wrapper.py similarity index 100% rename from model/framework/grover/grover/util/multi_gpu_wrapper.py rename to model/framework/code/grover/util/multi_gpu_wrapper.py diff --git a/model/framework/grover/grover/util/nn_utils.py b/model/framework/code/grover/util/nn_utils.py similarity index 100% rename from model/framework/grover/grover/util/nn_utils.py rename to model/framework/code/grover/util/nn_utils.py diff --git a/model/framework/grover/grover/util/parsing.py b/model/framework/code/grover/util/parsing.py similarity index 100% rename from model/framework/grover/grover/util/parsing.py rename to model/framework/code/grover/util/parsing.py diff --git a/model/framework/grover/grover/util/scheduler.py b/model/framework/code/grover/util/scheduler.py similarity index 100% rename from model/framework/grover/grover/util/scheduler.py rename to model/framework/code/grover/util/scheduler.py diff --git a/model/framework/grover/grover/util/utils.py b/model/framework/code/grover/util/utils.py similarity index 100% rename from model/framework/grover/grover/util/utils.py rename to model/framework/code/grover/util/utils.py diff --git a/model/framework/grover/main.py b/model/framework/code/main.py similarity index 81% rename from model/framework/grover/main.py rename to model/framework/code/main.py index e707e5e..baa8b41 100644 --- a/model/framework/grover/main.py +++ b/model/framework/code/main.py @@ -69,7 +69,7 @@ def smiles_to_dataframe(txt_file_path): p = Path(s) model_path = str(p.parent.parent.absolute()) - args = Namespace(batch_size=32, checkpoint_dir=model_path+'/framework/finetune/clintox', checkpoint_path=None, checkpoint_paths=[model_path+'/framework/finetune/clintox/fold_0/model_0/model.pt', model_path+'/framework/finetune/clintox/fold_2/model_0/model.pt', model_path+'/framework/finetune/clintox/fold_1/model_0/model.pt'], cuda=False, data_path=csv_path, ensemble_size=3, features_generator=None, features_path=[features_path], fingerprint=False, gpu=0, no_cache=True, no_features_scaling=True, output_path=output_path, parser_name='predict') + args = Namespace(batch_size=32, checkpoint_dir=model_path+'/checkpoints/finetune/clintox', checkpoint_path=None, checkpoint_paths=[model_path+'/checkpoints/finetune/clintox/fold_0/model_0/model.pt', model_path+'/checkpoints/finetune/clintox/fold_2/model_0/model.pt', model_path+'/checkpoints/finetune/clintox/fold_1/model_0/model.pt'], cuda=False, data_path=csv_path, ensemble_size=3, features_generator=None, features_path=[features_path], fingerprint=False, gpu=0, no_cache=True, no_features_scaling=True, output_path=output_path, parser_name='predict') sf.save_features_main(csv_path, features_path) diff --git a/model/framework/grover/requirements.txt b/model/framework/code/requirements.txt similarity index 100% rename from model/framework/grover/requirements.txt rename to model/framework/code/requirements.txt diff --git a/model/framework/grover/scripts/__init__.py b/model/framework/code/scripts/__init__.py similarity index 100% rename from model/framework/grover/scripts/__init__.py rename to model/framework/code/scripts/__init__.py diff --git a/model/framework/grover/scripts/build_vocab.py b/model/framework/code/scripts/build_vocab.py similarity index 100% rename from model/framework/grover/scripts/build_vocab.py rename to model/framework/code/scripts/build_vocab.py diff --git a/model/framework/grover/scripts/save_features.py b/model/framework/code/scripts/save_features.py similarity index 100% rename from model/framework/grover/scripts/save_features.py rename to model/framework/code/scripts/save_features.py diff --git a/model/framework/grover/scripts/split_data.py b/model/framework/code/scripts/split_data.py similarity index 100% rename from model/framework/grover/scripts/split_data.py rename to model/framework/code/scripts/split_data.py diff --git a/model/framework/grover/task/__init__.py b/model/framework/code/task/__init__.py similarity index 100% rename from model/framework/grover/task/__init__.py rename to model/framework/code/task/__init__.py diff --git a/model/framework/grover/task/cross_validate.py b/model/framework/code/task/cross_validate.py similarity index 100% rename from model/framework/grover/task/cross_validate.py rename to model/framework/code/task/cross_validate.py diff --git a/model/framework/grover/task/fingerprint.py b/model/framework/code/task/fingerprint.py similarity index 100% rename from model/framework/grover/task/fingerprint.py rename to model/framework/code/task/fingerprint.py diff --git a/model/framework/grover/task/grovertrainer.py b/model/framework/code/task/grovertrainer.py similarity index 100% rename from model/framework/grover/task/grovertrainer.py rename to model/framework/code/task/grovertrainer.py diff --git a/model/framework/grover/task/predict.py b/model/framework/code/task/predict.py similarity index 100% rename from model/framework/grover/task/predict.py rename to model/framework/code/task/predict.py diff --git a/model/framework/grover/task/pretrain.py b/model/framework/code/task/pretrain.py similarity index 100% rename from model/framework/grover/task/pretrain.py rename to model/framework/code/task/pretrain.py diff --git a/model/framework/grover/task/run_evaluation.py b/model/framework/code/task/run_evaluation.py similarity index 100% rename from model/framework/grover/task/run_evaluation.py rename to model/framework/code/task/run_evaluation.py diff --git a/model/framework/grover/task/train.py b/model/framework/code/task/train.py similarity index 100% rename from model/framework/grover/task/train.py rename to model/framework/code/task/train.py diff --git a/model/framework/run.sh b/model/framework/run.sh new file mode 100644 index 0000000..b591c58 --- /dev/null +++ b/model/framework/run.sh @@ -0,0 +1 @@ +python $1/code/main.py $2 $3 \ No newline at end of file diff --git a/src/service.py b/src/service.py index d12d85e..5c44de8 100644 --- a/src/service.py +++ b/src/service.py @@ -30,7 +30,7 @@ class Model(object): def __init__(self): self.DATA_FILE = "_data.csv" self.PRED_FILE = "_pred.csv" - self.RUN_FILE = "_run.sh" + self.RUN_FILE = "run.sh" self.LOG_FILE = "_run.log" def load(self, framework_dir, checkpoints_dir): @@ -53,7 +53,7 @@ def predict(self, smiles_list): f.write(smiles + os.linesep) run_file = os.path.join(tmp_folder, self.RUN_FILE) with open(run_file, "w") as f: - lines = ["python {0}/grover/main.py {1} {2}".format(self.framework_dir, data_file, pred_file)] + lines = ["bash {0}/run.sh {0} {1} {2}".format(self.framework_dir, data_file, pred_file)] f.write(os.linesep.join(lines)) cmd = "bash {0}".format(run_file) with open(log_file, "w") as fp: