Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/epam/Indigo

Universal cheminformatics toolkit, utilities and database search tools
https://github.com/epam/Indigo

bingo cheminformatics chemistry dotnet inchi indigo java microsoft-sql-server molfile oracle postgresql python smarts smiles webassembly

Last synced: about 2 months ago
JSON representation

Universal cheminformatics toolkit, utilities and database search tools

Lists

README 

        
![Build Status](https://github.com/epam/indigo/workflows/CI/badge.svg)

[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)



# EPAM Indigo projects #



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



Licensed under the [Apache License version 2.0](LICENSE)



## 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](/bingo/bingo-elastic/java/README.md)

  - Python API. Full README is available [here](/bingo/bingo-elastic/python/README.md)

* 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 



Changelog could be found in [CHANGELOG.md](/CHANGELOG.md).



## Download ##



### Bindings in public repositories:

* .NET: 

* Java: 

* Python: 



## 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'

3) 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

```