# Introduction
This package contains the scoring functions for REINVENT.
# Installation
To install in REINVENT's environment either install from repo or use `pip install reinvent-scoring` for the latest
official release.
# Developing
## Setup environment
You can use Conda to create an environment with all the necessary packages installed.
```
$ conda env create -f reinvent_scoring
[...]
$ conda activate reinvent_scoring
```
## Run tests
The tests use the `unittest` package testing framework. Before you can run the tests make sure that you have created a
`config.json`file in the `reinvent_scoring/configs` directory. There is an example config in the same directory, which
you can base your own config off of. Make sure that you set `MAIN_TEST_PATH` to a non-existent directory; it is where
temporary files will be written during the tests; if it is set to an existing directory, that directory will be removed
once the tests have finished.
Some tests require a proprietary OpenEye license; you have to set up a few things to make the tests read your
license. The simple way is to just set the `OE_LICENSE` environment variable to the path of the file containing the
license. If you just want to set the license in the `reinvent_scoring` Conda environment, it is a bit more complicated,
but you only have to do it once.
```
(reinvent-scoring) $ cd $CONDA_PREFIX
$ mkdir -p etc/conda/activate.d
$ mkdir -p etc/conda/deactivate.d
```
Put the following in `etc/conda/activate.d/env_vars.sh`.
```
#!/bin/sh
export OE_LICENSE='</path/to/your/oe_license/file>'
```
And put the following in `etc/conda/deactivate.d/env_vars.sh`.
```
#!/bin/sh
unset OE_LICENSE
```
Once you have created the files, deactivate and re-activate the environment, and `echo $OE_LICENSE` should output the
path to the license file.
Once you have created a config file and configured your environment, you can run the tests, located in the
`unittest_reinvent` directory, by running
```
$ python main_test.py
```
# Building
- Building: `python setup.py sdist bdist_wheel`
- Upload build to test: `python -m twine upload --repository testpypi dist/*`
- Upload build: `python -m twine upload dist/*`
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PyPI 官网下载 | reinvent_scoring-0.0.50.tar.gz
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PyPI 官网下载 | reinvent_scoring-0.0.50.tar.gz (113个子文件)
setup.cfg 38B
fpscores.pkl.gz 3.67MB
README.md 2KB
PKG-INFO 3KB
PKG-INFO 3KB
component_specific_parameters_enum.py 9KB
parallel_rocs_similarity.py 8KB
selectivity_component.py 8KB
base_scoring_function.py 6KB
azgard.py 6KB
score_transformations.py 6KB
rocs_similarity.py 6KB
base_pip_model_batching_component.py 5KB
sascorer.py 5KB
rocs_specific_parameters_enum.py 5KB
base_clab_component.py 4KB
oehelper.py 4KB
scaffold_similarity.py 4KB
sas_component.py 4KB
base_pip_model_component.py 3KB
score_component_factory.py 3KB
predictive_property_component.py 3KB
dockstream.py 3KB
azdock.py 3KB
base_rest_component.py 3KB
diversity_filter_memory.py 3KB
diversity_filter_memory.py 3KB
base_structural_component.py 2KB
base_diversity_filter.py 2KB
transformation_type_enum.py 2KB
base_diversity_filter.py 2KB
scoring_function_component_enum.py 2KB
base_score_component.py 2KB
scikit_model_container.py 2KB
identical_topological_scaffold.py 2KB
identical_murcko_scaffold.py 2KB
jaccard_distance.py 2KB
tanimoto_similarity.py 2KB
base_physchem_component.py 1KB
base_console_invoked_component.py 1KB
matching_substructure.py 1KB
model_container.py 1KB
custom_product.py 1KB
oefuncs.py 1KB
no_filter_with_penalty.py 1KB
base_rocs_component.py 1KB
scoring_function_factory.py 1KB
custom_sum.py 1KB
score_summary.py 1KB
no_filter.py 1KB
custom_alerts_component.py 1KB
no_scaffold_filter.py 1KB
__init__.py 1KB
qed_score.py 1014B
descriptor_types_enum.py 970B
diversity_filter.py 962B
optuna_container.py 962B
rocs_similarity_measures_enum.py 943B
top_20.py 939B
setup.py 835B
__init__.py 768B
__init__.py 720B
__init__.py 711B
diversity_filter.py 707B
rocs_input_file_types_enum.py 668B
__init__.py 610B
__init__.py 595B
solubilityDD.py 585B
azlogd74.py 583B
container_type_enum.py 580B
hlm_clint.py 577B
hh_clint.py 575B
rh_clint.py 575B
caco2_intr.py 574B
caco2_efflux.py 573B
herg.py 563B
ratpk_pip.py 554B
diversity_filter_enum.py 473B
number_of_stereo_centers.py 469B
__init__.py 465B
rot_bonds.py 463B
graph_length.py 455B
hba.py 448B
hbd.py 448B
num_rings.py 447B
mol_weight.py 443B
pip_log_prediction_component.py 443B
pip_prediction_component.py 436B
slogp.py 435B
tpsa.py 431B
default_values.py 420B
utils.py 372B
scoring_function_enum.py 350B
logging_mode_enum.py 306B
component_parameters.py 294B
base_model_container.py 264B
__init__.py 199B
__init__.py 196B
diversity_filter_parameters.py 186B
diversity_filter_parameters.py 186B
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