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
  • 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.

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

This is an alternative setup solution next to have it on your PC directly. It builds on having the tools in a docker container and VSCode acts as a client.

1. Docker Desktop (or docker engine if you prefer)
2. VSCode

1. Clone this repository
2. Open in VSCode
3. Follow recommendation to install the Dev Container Extension
4. Open in Dev Container

The first time takes some minutes but afterwards you can directly develop from VSCode.

Remark for Windows Users: Its a known limitation that on windows the overlay driver is super slow, so if you want to have a fast IDE, clone your container into a volume rather than natively on the client or in your WSL distribution.

To build the project from the sources, the following tools should be installed:

Required:

• GIT 1.8.2+
• C/C++ compilers with C++14 support (GCC, Clang and MSVC are officially supported)
• CMake 3.4+
• Python 3.6+

Required to build all targets:

• JDK 1.8+
• .NET Standard 2.0+

Required to build Indigo-WASM:

• Emscripten SDK
• Ninja

Python

• wheel package installed. Command: python -m pip install wheel
• setuptools version less than 72.0.0 package installed. Command: python -m pip install setuptools==68.0.0
• waitress package installed (to run backend API test). Command: python -m pip install waitress
• flasgger package installed (to run backend API test). Command: python -m pip install flasgger
• psycopg2 package installed (to run backend API test). Command: python -m pip install psycopg2
• sqlalchemy package installed (to run backend API test). Command: python -m pip install sqlalchemy
• numpy package installed (to run backend API test). Command: python -m pip install numpy
• celery package installed (to run backend API test). Command: python -m pip install celery
• marshmallow package installed (to run backend API test). Command: python -m pip install marshmallow
• redis package installed (to run backend API test). Command: python -m pip install redis
• flask_httpauth package installed (to run backend API test). Command: python -m pip install flask_httpauth
• pyparsing package installed (to run backend API test). Command: python -m pip install pyparsing
• requests package installed (to run backend API test). Command: python -m pip install requests
• pillow package installed (required for rendering tests). Command: python -m pip install pillow

On Linux use python3 insted of python. Using virtual environment might be required as well.

On Windows use cmd to run the commands.

1. Create build folder

   mkdir build
   

2. Move to build folder

   cd build
   

3. Run CMake to configure the project with desired options. For instance:

   cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=ON -DBUILD_INDIGO_UTILS=ON
   

4. Build Indigo from console:

   cmake --build . --config Release --target <target name>
   

Replace <target name> with any of the following targets you need:

• ALL_BUILD (on Windows)
• all (on Linux)
• indigo-dotnet
• indigo-java
• indigo-python

Build results could be collected from Indigo/dist folder.

'indigo-python' target is commonly used.

Befor running any test you have to build and install indigo-python

1. Build indigo-python using --target indigo-python or --target ALL_BUILD(on Windows) or --target all(on Linux). See Build instruction above.

   • On Windows the package should be in 'Indigo/api/python/dist' folder
   • On Linux it is located in 'Indigo\dist' folder

Package will be named like 'epam.indigo-<version-arch>.whl'. For instance: epam.indigo-1.29.0.dev2-py3-none-win_amd64.whl

2. Install package using pip

   • If Indigo package has been already installed, uninstall it with the following command: python -m pip uninstall <path-to-.whl-file> -y

   python -m pip install <path-to-.whl-file>
   

   Replace <path-to-.whl-file> with the right path to .whl package. For instance: python -m pip install ../api/python/dist/epam.indigo-1.29.0.dev2-py3-none-win_amd64.whl

3. Run integration test

   to run all test

   python api/tests/integration/test.py -t 1
   

   to run tests by mask use test_name

   python api/tests/integration/test.py -t 1 -p test_name
   

   to update all tests "ref/" using -u flag

   python api/tests/integration/test.py -u
   

   to update all tests "ref/" without -u flag

   export INDIGO_UPDATE_TESTS="True"
   python api/tests/integration/test.py
   

   to update a single test's "ref/" by mask use test_name and -u flag

   python api/tests/integration/test.py -t 1 -p test_name -u
   

1. Build and install indigo-python

2. Set environment variable by running this command:

   for Linux

   export INDIGO_SERVICE_URL=http://localhost:5000/v2
   

   for Windows in PowerShell

   $env:INDIGO_SERVICE_URL="http://localhost:5000/v2"
   

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:

   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

Prepare conda build environment as described at https://docs.conda.io/projects/conda-build/en/stable/install-conda-build.html Change directory to ```recipe-conda``, set INDIGO_VERSION to existing Indigo version(already published at PyPi), run conda build: Linux/Mac:

>cd conda-recipe
>INDIGO_VERSION=1.29.0 conda build .

Windows(using cmd):

>cd conda-recipe
>set INDIGO_VERSION=1.29.0
>conda build .

To upload packages: install anaconda-client, login, and upload packet using command provided by conda-build in output

>conda install anaconda-client
>anaconda login
Enter username:
Enter password:
>anaconda upload /conda-build-dir/packet-name