Copyright (c) 2009-2022 EPAM Systems, Inc.
Licensed under the Apache License version 2.0
This repository includes:
- Bingo: Chemistry search engine for Oracle, Microsoft SQL Server and PostgreSQL databases
- Bingo-Elastic: Set of APIs for efficient chemistry search in Elasticsearch
- Indigo: Universal cheminformatics library with bindings to .NET, Java, Python, R and WebAssembly, and the following tools:
- Legio: GUI application for combinatorial chemistry
- ChemDiff: Visual comparison of two SDF or SMILES files
- indigo-depict: Molecule and reaction rendering utility
- indigo-cano: Canonical SMILES generator
- indigo-deco: R-Group deconvolution utility
Detailed documentation is available at http://lifescience.opensource.epam.com
Changelog could be found in CHANGELOG.md.
https://lifescience.opensource.epam.com/download/indigo/index.html
- .NET: https://www.nuget.org/packages/Indigo.Net
- Java: https://search.maven.org/search?q=g:com.epam.indigo
- Python: https://pypi.org/project/epam.indigo/
Main directory structure layout:
api
: Indigo API sourcesbingo
: Bingo sourcescore
: Core algorithms and data structures sourcesthird_party
: sources for third-party librariesutils
: utilities sources
Each project is placed in the corresponding directory with CMakeList.txt configuration file, that does not include other projects. In order to build the whole project with the correct references you need to use CMake configurations from the build_scripts directory.
To build the project from the sources, the following tools should be installed:
- GIT 1.8.2+
- C/C++ compilers with C++14 support (GCC, Clang and MSVC are officially supported)
- CMake 3.4+
- Python 3.6+
- JDK 1.8+
- .NET Standard 2.0+
- Emscripten SDK
- Ninja
Create build folder and use cmake with desired options. For instance:
Indigo/build>cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=ON -DBUILD_INDIGO_UTILS=ON
To build Indigo from console:
Indigo/build>cmake --build . --config Release --target all
or any of the following targets could be specified: --target { indigo-dotnet | indigo-java | indigo-python } Build results could be collected from Indigo/dist folder.
Befo run any test you have to build and install indigo-python
- Build indigo-python using '--target all' or '--target indigo=python'. Package should be in 'build' directory, it will be named like 'epam.indigo-version-arch.whl'
- Install package using pip
python -m pip uninstall epam.indigo -y ; python -m pip install dist/epam.indigo-version-arch.whl
Run integration test using python api/tests/integration/test.py -t 1
for all test, or python api/tests/integration/test.py -t 1 -p test_name
to run tests by mask test_name
.
To run backend API test:
- Install epam-indigo
- Install waitress
python pip install waitress
- Run backend service :
cd utils/indigo-service/backend/service
cp v2/common/config.py .
waitress-serve --listen="127.0.0.1:5000 [::1]:5000" app:app
you may use any port instead of 5000
- Run backend API test:
- set environment variable
export INDIGO_SERVICE_URL=http://localhost:5000/v2
(in powershell$env:INDIGO_SERVICE_URL="http://localhost:5000/v2"
) - run test
python utils/indigo-service/backend/service/tests/api/indigo_test.py
use-k test_name
to run test by pattern.
- Git
Make sure git is running from path:
>git --version
git version 2.26.2.windows.1
- Python (https://www.python.org/downloads/)
Make sure python is running from path:
>python --version
Python 3.9.0
- cmake (https://cmake.org/download/)
Make sure cmake is running from path:
>cmake --version
cmake version 3.18.4
- Install ninja (https://github.com/ninja-build/ninja/releases)
Download corresponding ninja-xxx.zip and unpack to folder on path. Make sure it's running from path:
>ninja --version
1.10.2
- Install emscripten sdk (https://github.com/emscripten-core/emsdk)
>git clone https://github.com/emscripten-core/emsdk.git
>cd emsdk
>./emsdk install latest
>./emsdk activate latest
>source ./emsdk_env.sh
Note: On Windows, run emsdk
instead of ./emsdk
, and emsdk_env.bat
instead of source ./emsdk_env.sh
, use cmd
instead of powershell
.
Clone (or checkout) Indigo repository
>git clone https://github.com/epam/Indigo.git
For each new session, set environment anew:
>cd emsdk
>./emsdk activate latest
If fresh build:
>mkdir build
>cd build
Now build:
>emcmake cmake .. -DCMAKE_BUILD_TYPE=Debug -G Ninja
>ninja indigo-ketcher-js-test