EPAM Indigo projects

Copyright (c) 2009-2022 EPAM Systems, Inc.

Licensed under the Apache License version 2.0

Introduction

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
  • Java API. Full README is available here
  • Python API. Full README is available here
• 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.

Download

https://lifescience.opensource.epam.com/download/indigo/index.html

Bindings in public repositories:

• .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/

Source code organization

Main directory structure layout:

• api: Indigo API sources
• bingo: Bingo sources
• core: Core algorithms and data structures sources
• third_party: sources for third-party libraries
• utils: 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.

Preinstalled build tools

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

Build instruction

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.

Run tests

Befo run any test you have to build and install indigo-python

1. 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'
2. 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:

1. Install epam-indigo
2. Install waitress python pip install waitress
3. 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

4. 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.

How to build Indigo-WASM

Build tools prerequisites

• 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.

Get Indigo sources

Clone (or checkout) Indigo repository

>git clone https://github.com/epam/Indigo.git

Build Indigo

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